Contacts of the helix formed by residues 101 - 124 (chain T) in PDB entry 5GJQ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 101 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96T GLU 3.9 5.8 + - - +
99T LYS* 3.4 10.9 + - + +
100T GLY* 1.3 77.9 - - - +
102T TRP* 1.3 57.3 + - - +
103T ASN* 3.8 9.9 - - + +
104T ARG* 3.3 30.1 - - + +
105T LYS* 2.8 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 102 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100T GLY 4.0 8.0 + - - -
101T GLU* 1.3 72.6 - - - +
103T ASN* 1.3 55.8 + - - +
104T ARG 3.4 0.2 - - - -
105T LYS* 3.5 12.7 - - + +
106T SER* 2.7 30.0 + - - -
153T GLN* 5.5 2.9 - - + -
154T TRP* 4.3 20.6 - - - +
157T LEU* 5.1 18.6 - - + -
158T ARG* 6.0 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 103 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101T GLU* 3.4 9.9 - - + +
102T TRP* 1.3 76.1 - - - +
104T ARG* 1.3 59.5 + - - +
106T SER* 3.3 7.2 - - - -
107T PRO* 2.8 34.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 104 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96T GLU* 5.2 2.0 - - - -
99T LYS* 4.6 13.7 - - + -
101T GLU* 3.3 28.6 + - + +
103T ASN* 1.3 75.4 - - - +
105T LYS* 1.3 52.9 + - - +
107T PRO* 4.6 1.7 - - - +
108T ASN* 2.6 41.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 105 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96T GLU* 4.0 28.0 - - + +
97T GLN* 5.3 1.3 - - - +
101T GLU 2.8 20.1 + - - +
102T TRP* 3.5 15.7 - - + +
104T ARG* 1.3 73.1 - - - +
106T SER* 1.3 66.4 + - - +
108T ASN* 3.2 2.4 + - - +
109T LEU* 2.9 20.4 + - - +
150T ILE* 5.5 5.2 - - + +
154T TRP* 4.2 15.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 106 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102T TRP 2.7 23.0 + - - -
103T ASN* 3.1 10.9 + - - -
105T LYS* 1.3 72.5 - - - +
107T PRO* 1.4 59.7 - - - +
109T LEU* 2.9 29.1 + - - +
110T SER* 4.0 4.3 + - - -
154T TRP* 4.7 9.0 - - - -
158T ARG* 4.6 19.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 107 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103T ASN 2.8 17.0 - - - +
104T ARG* 4.6 1.3 - - - +
106T SER* 1.4 74.7 - - - +
108T ASN* 1.3 60.4 + - - +
109T LEU 3.2 0.4 + - - -
110T SER* 4.0 13.5 + - - +
111T LYS* 3.8 10.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 108 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92T THR* 4.8 13.7 - - - -
96T GLU* 4.7 15.3 - - + -
104T ARG 2.6 26.1 + - - +
105T LYS* 3.5 6.5 - - - +
107T PRO* 1.3 75.8 - - - +
109T LEU* 1.3 58.6 + - - +
111T LYS* 3.0 24.2 - - - +
112T CYS* 3.1 24.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 109 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105T LYS 2.9 8.4 + - - +
106T SER* 2.9 16.1 + - - +
108T ASN* 1.3 75.6 - - - +
110T SER* 1.3 58.0 + - - +
112T CYS* 2.7 32.8 + - + +
113T GLY* 2.9 12.4 + - - +
116T LEU* 4.4 21.8 - - + -
147T ILE* 5.5 6.3 - - + +
151T GLY* 4.6 17.9 - - - +
154T TRP* 6.3 3.8 - - + -
155T SER* 5.4 0.9 - - - +
167T TYR* 3.4 35.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 110 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16N GLU* 5.6 3.8 - - - +
106T SER 4.1 6.2 + - - -
107T PRO* 4.0 12.5 + - - +
108T ASN 3.6 0.4 - - - -
109T LEU* 1.3 78.6 - - - +
111T LYS* 1.3 62.5 + - - +
113T GLY* 3.0 16.8 + - - +
114T GLU* 4.0 8.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 111 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107T PRO 3.8 8.1 - - - +
108T ASN* 3.0 34.5 - - - +
110T SER* 1.3 74.0 - - - +
112T CYS* 1.3 61.6 + - - +
114T GLU* 3.9 16.5 + - - +
115T GLU* 4.6 2.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 112 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89T GLN* 5.6 6.3 - - + +
92T THR* 3.7 26.7 - - - -
93T GLY* 5.6 1.1 - - - -
108T ASN* 3.1 24.9 - - - -
109T LEU* 2.7 19.6 + - + +
111T LYS* 1.3 73.0 - - - +
113T GLY* 1.3 62.5 + - - +
114T GLU 2.9 4.0 + - - -
115T GLU* 3.1 10.2 + - + +
116T LEU* 2.9 35.5 + - + +
147T ILE* 6.1 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 113 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11N LEU* 5.7 2.3 - - - +
16N GLU* 6.4 0.4 - - - -
19N LEU* 5.5 7.8 - - - +
109T LEU* 2.9 14.0 + - - -
110T SER* 3.0 10.3 + - - -
112T CYS* 1.3 76.7 - - - +
114T GLU* 1.3 55.8 + - - +
116T LEU* 3.3 15.9 - - - +
117T GLY* 2.8 22.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 114 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16N GLU* 4.8 18.8 - - + -
19N LEU* 6.3 2.2 - - - -
110T SER 4.2 8.1 - - - +
111T LYS* 4.1 13.7 - - - +
112T CYS 2.9 1.8 + - - -
113T GLY* 1.3 72.5 - - - +
115T GLU* 1.3 57.4 + - - +
116T LEU 3.0 1.1 - - - -
117T GLY* 2.5 23.7 + - - -
118T ARG* 3.0 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 115 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89T GLN* 2.1 52.3 - - + +
111T LYS 4.6 1.9 + - - +
112T CYS* 3.1 10.5 + - - +
114T GLU* 1.3 77.5 - - - +
116T LEU* 1.3 59.0 + - + +
117T GLY 3.2 0.2 - - - -
118T ARG* 4.5 7.6 - - + +
119T LEU* 2.8 52.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 116 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11N LEU* 5.1 4.7 - - + +
109T LEU* 4.4 11.0 - - + -
112T CYS* 2.9 31.6 + - + +
113T GLY* 3.3 16.6 - - - +
115T GLU* 1.3 79.2 - - + +
117T GLY* 1.3 51.3 + - - +
119T LEU* 4.8 8.7 - - + -
120T LYS* 2.4 39.4 + - - +
144T ALA* 6.3 0.9 - - + -
147T ILE* 3.7 43.5 - - + -
148T LEU* 5.7 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 117 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11N LEU* 5.5 2.7 - - - -
19N LEU* 5.5 12.6 - - - -
22N PHE* 5.4 8.0 - - - +
113T GLY 2.8 9.6 + - - -
114T GLU* 2.5 17.8 + - - -
116T LEU* 1.3 69.9 - - - +
118T ARG* 1.3 58.7 + - - -
120T LYS* 3.2 5.9 - - - +
121T LEU* 2.9 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 118 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114T GLU 3.0 8.6 + - - +
115T GLU* 4.1 9.2 - - + +
117T GLY* 1.3 72.2 - - - +
119T LEU* 1.3 62.1 + - + +
121T LEU* 2.6 42.1 + - + +
122T VAL* 3.0 15.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 119 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115T GLU* 2.8 47.7 + - + +
116T LEU* 4.3 10.3 - - + -
118T ARG* 1.3 76.2 - - + +
120T LYS* 1.3 53.0 + - - +
122T VAL* 2.7 14.3 + - + -
123T LEU* 2.5 47.1 + - + +
124T LEU 3.3 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 120 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11N LEU* 3.4 31.4 - - + -
26N LYS* 5.7 3.6 - - + -
116T LEU* 2.4 31.9 + - - +
117T GLY* 3.2 10.1 - - - +
118T ARG 3.0 0.2 - - - -
119T LEU* 1.3 76.5 - - - +
121T LEU* 1.3 56.6 + - - +
124T LEU* 1.8 81.5 + - + +
170T GLN* 6.1 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 121 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22N PHE* 4.6 19.1 - - + +
26N LYS* 2.4 43.5 - - + -
117T GLY 2.9 19.2 + - - +
118T ARG* 2.6 22.7 + - + +
120T LYS* 1.3 71.2 - - - +
122T VAL* 1.3 59.3 + - + +
124T LEU* 4.4 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 122 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118T ARG* 3.0 22.2 + - + +
119T LEU* 2.7 22.8 + - + +
120T LYS 3.0 0.2 - - - -
121T LEU* 1.3 76.9 - - + +
123T LEU* 1.3 69.4 + - + +
124T LEU 3.1 7.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 123 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119T LEU* 2.5 28.3 + - + +
122T VAL* 1.3 77.4 - - + +
124T LEU* 1.3 61.3 + - - +
126T LEU* 2.6 40.6 - - + +
140T GLN* 3.6 40.6 - - + +
141T LEU 5.3 0.2 - - - +
144T ALA* 4.8 13.9 - - + -
174T TYR* 5.1 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 124 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7N GLY* 5.9 5.8 - - - -
8N ILE* 5.7 6.7 - - + -
11N LEU* 4.9 2.0 - - + -
26N LYS* 6.5 0.7 - - + -
119T LEU 3.3 2.4 + - - -
120T LYS* 1.8 69.0 + - + +
121T LEU* 4.4 0.6 - - - -
122T VAL 3.1 7.5 - - - +
123T LEU* 1.3 82.4 - - - +
125T GLU* 1.3 62.8 + - + +
126T LEU* 2.7 16.4 + - - -
174T TYR* 5.2 3.4 - - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il