Contacts of the helix formed by residues 101 - 113 (chain A) in PDB entry 3TKL
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 ASN 101 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ASP* 2.7 40.2 + - - +
97A GLU* 2.9 26.9 + - - +
98A SER 3.8 2.7 - - - +
99A PHE 3.1 0.4 - - - -
100A ASN* 1.3 77.3 - - - +
102A VAL* 1.3 63.7 + - - +
103A LYS 3.0 2.9 - - - -
104A GLN* 2.9 30.1 + - + +
105A TRP* 3.0 17.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A VAL* 4.1 13.9 - - + -
90A VAL 5.2 1.1 - - - +
91A TYR* 4.0 17.7 - - + -
98A SER 3.5 11.3 + - - +
99A PHE* 3.1 23.4 + - + +
101A ASN* 1.3 76.3 - - - +
103A LYS* 1.3 56.2 + - - +
105A TRP* 3.7 9.6 - - + +
106A LEU* 2.9 36.5 + - + +
121A LEU* 3.9 30.7 - - + -
142A PHE* 3.6 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A PHE 4.5 0.4 + - - -
100A ASN 3.7 7.0 + - - +
101A ASN 3.0 0.6 - - - -
102A VAL* 1.3 80.7 - - - +
104A GLN* 1.3 75.2 + - - +
106A LEU* 3.4 6.7 + - - +
107A GLN* 3.1 43.8 + - - +
142A PHE* 4.7 18.3 - - + -
286B HIS* 5.7 1.1 - - - -
289B ASP* 2.8 32.0 + - - -
291B LYS* 6.3 0.4 - - - +
292B THR* 3.7 5.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ASN 3.3 21.1 - - - +
101A ASN* 2.9 20.8 + - + +
103A LYS* 1.3 99.2 - - - +
105A TRP* 1.3 60.9 + - + +
107A GLN* 3.2 20.1 + - - +
108A GLU* 2.9 26.3 + - - +
292B THR* 4.4 5.9 - - - +
295B SER* 6.1 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ILE* 3.9 13.6 - - + +
18A GLY* 3.4 40.8 - - - -
19A ASP* 2.7 32.0 + - - +
69A GLY* 4.2 11.0 - - - -
74A ARG* 3.4 52.3 - - - -
89A VAL* 3.9 18.8 - - + -
90A VAL 5.5 0.7 - - - -
98A SER 5.0 2.2 - - - -
101A ASN* 3.0 30.4 + - + +
102A VAL* 3.7 9.9 - - + +
104A GLN* 1.3 78.2 - - + +
106A LEU* 1.3 61.2 + - - +
108A GLU* 3.1 31.5 + - + +
109A ILE* 3.1 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A VAL* 4.3 17.9 - - + -
102A VAL* 2.9 24.1 + - + +
103A LYS* 3.6 5.6 - - - +
105A TRP* 1.3 75.0 - - - +
107A GLN* 1.3 59.2 + - + +
109A ILE* 3.2 9.5 + - + +
110A ASP* 3.0 32.0 + - - +
119A LYS* 3.8 33.4 + - + +
121A LEU* 6.5 0.2 - - + -
142A PHE* 3.7 22.7 - - + -
146A LEU* 3.7 30.1 - - + -
148A ILE* 3.9 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LYS* 3.1 35.4 + - + +
104A GLN* 3.2 17.6 + - - +
106A LEU* 1.3 74.3 - - + +
108A GLU* 1.3 65.3 + - - +
110A ASP* 3.5 11.0 + - - +
111A ARG* 3.0 23.2 + - - +
282B LEU* 5.4 3.7 - - + +
286B HIS* 3.9 30.3 - - + +
292B THR* 3.2 42.1 - - - +
295B SER* 4.9 4.3 + - - -
296B LEU* 5.1 14.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ILE* 4.1 0.7 - - - +
74A ARG* 2.6 45.1 + - - -
77A THR* 4.0 4.8 + - - +
81A TYR* 2.6 27.6 + - - +
104A GLN 2.9 13.0 + - - +
105A TRP* 3.1 27.2 + - + +
107A GLN* 1.3 73.7 - - - +
109A ILE* 1.3 64.0 + - - +
111A ARG* 3.2 7.0 + - - +
112A TYR* 3.0 41.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ILE* 3.1 23.3 - - + -
81A TYR* 2.7 40.6 - - + +
87A ILE* 3.6 16.8 - - + -
89A VAL* 4.7 2.2 - - + -
105A TRP 3.1 8.9 + - - +
106A LEU* 3.2 16.4 + - + +
108A GLU* 1.3 75.5 - - - +
110A ASP* 1.3 64.8 - - - +
111A ARG 3.1 0.2 + - - -
113A ALA* 2.8 33.5 + - + +
117A VAL* 3.6 22.7 - - + -
119A LYS* 3.6 31.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LEU* 3.0 11.6 + - - +
107A GLN* 3.5 16.8 - - + +
108A GLU 3.4 0.2 - - - -
109A ILE* 1.3 80.1 - - - +
111A ARG* 1.3 62.0 + - - +
113A ALA 4.5 6.9 - - - +
119A LYS* 3.0 24.0 + - - -
278B LYS* 3.3 23.1 + - - +
282B LEU* 4.0 17.5 - - + -
285B LYS* 3.8 24.2 + - - -
286B HIS* 4.5 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A GLN 3.0 17.7 + - - +
108A GLU* 3.6 6.7 - - - +
109A ILE 3.1 0.4 - - - -
110A ASP* 1.3 80.5 - - - +
112A TYR* 1.3 96.5 + - + +
113A ALA 5.1 0.5 - - - +
275B ASP* 2.6 42.7 + - - +
278B LYS* 3.6 25.2 - - + +
279B LEU* 3.7 24.6 - - + +
282B LEU* 4.2 8.1 - - + -
296B LEU* 5.9 2.5 - - + -
299B GLU* 3.4 39.0 + - - +
303B ILE* 3.9 16.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A THR* 3.3 26.9 - - + +
78A SER* 3.5 33.9 - - - +
81A TYR* 3.6 32.0 - + + +
82A ARG* 5.9 1.0 - - - -
108A GLU* 3.0 40.5 + - + +
111A ARG* 1.3 128.1 + - + +
113A ALA* 1.3 64.9 + - - +
275B ASP* 4.2 10.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A TYR* 3.6 25.1 - - + +
84A ALA* 5.8 0.9 - - + +
87A ILE* 5.1 0.2 - - + -
109A ILE* 2.8 27.8 + - + +
110A ASP 4.5 5.9 - - - +
111A ARG 5.1 0.5 - - - +
112A TYR* 1.3 77.5 - - - +
114A SER* 1.3 66.9 + - - +
115A GLU* 3.6 1.6 + - - -
117A VAL* 3.7 31.0 - - + -
----------------------------------------------------------
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