Contacts of the helix formed by residues 101 - 114 (chain B) in PDB entry 4Q96
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 LYS 101 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ALA* 3.6 30.1 - - + +
96A ALA* 3.9 15.9 - - + -
97A ASP* 2.7 31.9 + - - +
97B ASP 4.9 11.1 + - - -
98B GLU 4.4 3.5 + - - +
100B CYS* 1.3 79.6 - - + +
102B LYS* 1.3 66.0 + - - +
103B PRO* 3.3 2.9 - - - -
104B LEU* 3.1 17.1 + - + +
105B GLU* 3.1 23.1 + - - +
129B MET* 3.4 31.1 - - + +
130B GLU* 6.1 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B GLU* 2.8 46.7 + - - +
99B GLY 3.3 10.9 + - - +
101B LYS* 1.3 76.0 - - - +
103B PRO* 1.4 71.5 - - + +
105B GLU* 3.1 27.3 + - - +
106B ARG* 3.0 57.5 + - + +
202B SO4 3.2 33.4 - - - +
1614F SER* 3.5 15.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LEU* 3.5 36.1 - - + -
61A TYR* 4.1 9.9 + - - +
99B GLY 3.6 9.6 - - - +
100B CYS 3.9 7.6 - - - +
101B LYS 3.5 2.9 - - - -
102B LYS* 1.4 94.6 - - + +
104B LEU* 1.3 58.7 + - + +
106B ARG* 3.3 12.4 + - + +
107B LEU* 3.0 28.7 + - - +
1614F SER* 5.3 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LEU* 3.8 18.8 - - + -
60A LEU* 3.6 30.5 - - + -
89A PHE* 4.3 8.1 - - + +
92A VAL* 3.9 22.9 - - + -
93A ALA* 4.0 21.5 - - + +
96A ALA* 4.8 3.1 - - + -
100B CYS 5.4 0.9 - - - +
101B LYS* 3.1 23.0 + - + +
103B PRO* 1.3 76.9 - - + +
105B GLU* 1.3 62.5 + - - +
107B LEU* 3.3 7.9 + - + +
108B LEU* 3.1 27.4 + - - +
129B MET* 3.4 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B GLU 5.1 1.0 - - - +
101B LYS 3.1 11.3 + - - +
102B LYS* 3.5 40.8 + - - +
104B LEU* 1.3 77.1 - - - +
106B ARG* 1.3 57.9 + - - +
108B LEU* 3.5 4.4 + - - +
109B ASN* 3.1 46.5 + - - +
129B MET* 4.0 18.1 - - + +
202B SO4 4.7 5.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B LYS* 3.0 45.4 + - + +
103B PRO* 3.7 9.7 - - + +
105B GLU* 1.3 73.4 - - + +
107B LEU* 1.3 61.9 + - - +
109B ASN* 3.2 12.7 + - - +
110B ILE* 2.9 35.3 + - + +
202B SO4 2.4 42.6 + - - +
1611F BTN 4.0 42.2 - - - +
1612F SER* 2.9 35.8 + - - +
1614F SER* 4.4 2.8 + - - -
1701F UNX 3.4 15.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LEU* 5.1 2.5 - - + -
60A LEU* 4.0 36.6 - - + +
61A TYR* 4.3 15.0 - - + -
64A ASN* 3.7 31.4 - - + +
89A PHE* 4.0 19.1 - - + -
103B PRO 3.0 15.7 + - - +
104B LEU* 3.3 7.2 + - - +
106B ARG* 1.3 77.8 - - - +
108B LEU* 1.3 61.2 + - - +
110B ILE* 3.2 12.5 + - + +
111B TRP* 3.1 35.6 + - + +
1624C PRO* 4.0 16.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A PHE* 3.5 29.6 - - + -
104B LEU 3.1 15.1 + - - +
105B GLU* 3.7 7.0 - - - +
107B LEU* 1.3 77.1 - - - +
109B ASN* 1.3 57.4 + - - +
111B TRP* 3.2 11.7 + - + +
112B GLN* 2.8 29.0 + - - +
122B ILE* 4.2 9.7 - - + +
125B LEU* 3.8 29.6 - - + +
126B LYS* 3.7 40.6 - - + +
129B MET* 3.7 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B GLU* 3.1 39.1 + - - +
106B ARG* 3.2 15.3 + - - +
108B LEU* 1.3 73.9 - - - +
110B ILE* 1.3 61.4 + - + +
112B GLN* 3.8 16.4 - - - +
113B GLU* 2.9 43.2 + - - +
126B LYS* 4.9 8.5 - - - -
202B SO4 5.3 3.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ASN* 4.8 0.9 - - - +
68A GLN* 4.1 15.5 - - - +
106B ARG* 2.9 18.8 + - + +
107B LEU* 3.2 11.2 + - - +
109B ASN* 1.3 76.8 - - + +
111B TRP* 1.3 60.9 + - + +
113B GLU* 3.3 12.0 + - - +
114B ARG* 2.8 50.6 + - - +
1624C PRO* 3.6 29.6 - - + +
1625C THR* 3.6 18.6 - - + -
1611F BTN 3.3 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 4.8 2.5 - - + -
63A ALA* 5.3 0.9 - - + -
64A ASN* 2.8 47.7 + - + +
67A ILE* 4.5 8.7 - - + +
68A GLN* 5.0 0.2 - - - +
85A LEU* 3.8 30.5 - - + -
89A PHE* 3.6 34.8 - + - -
107B LEU* 3.1 31.9 + - + +
108B LEU* 3.5 15.5 - - + +
110B ILE* 1.3 79.6 - - + +
112B GLN* 1.3 62.8 + - - +
115B SER* 3.1 3.3 + - - -
116B VAL* 2.9 57.3 + - + +
117B TYR* 3.9 15.3 + + - +
122B ILE* 3.9 10.3 - - + -
125B LEU* 3.8 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B LEU 2.8 16.9 + - - +
109B ASN* 3.8 14.3 - - - +
111B TRP* 1.3 77.3 - - - +
113B GLU* 1.3 64.4 + - + +
115B SER* 3.1 17.4 + - - +
117B TYR 5.1 0.4 - - - +
119B GLY* 5.5 6.1 + - - -
122B ILE* 3.9 23.9 - - + +
126B LYS* 3.2 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ASN* 2.9 29.5 + - + +
110B ILE* 3.8 13.6 - - - +
112B GLN* 1.3 79.2 - - + +
114B ARG* 1.3 63.0 + - + +
115B SER* 3.5 3.8 + - - -
1630C SER 4.3 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLN* 2.8 42.0 + - - +
110B ILE* 2.8 29.6 + - + +
113B GLU* 1.3 77.8 - - + +
115B SER* 1.3 71.1 + - - +
116B VAL* 3.2 11.8 + - + -
1625C THR* 2.8 46.7 + - - +
1627C PRO* 2.9 22.4 + - - +
1629C TYR* 3.3 19.3 + - + +
1630C SER* 3.5 17.6 - - - +
1631C NH2 3.0 20.7 + - - +
----------------------------------------------------------
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