Contacts of the helix formed by residues 85 - 99 (chain B) in PDB entry 2V1T
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 ASP 85 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B LEU* 2.8 37.6 + - + +
81B LEU* 4.7 0.2 - - - -
83B GLN* 3.3 8.7 - - + +
84B GLY* 1.3 72.9 - - - +
86B TYR* 1.3 57.6 + - - +
87B GLU* 3.5 3.2 + - - +
88B LYS* 3.4 40.5 + - - +
89B GLY* 2.9 26.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B LEU* 3.8 34.3 + - + +
84B GLY* 3.1 35.2 + - - -
85B ASP* 1.3 72.6 - - - +
87B GLU* 1.3 67.2 - - - +
90B VAL* 2.9 29.7 + - + +
115B PRO* 5.9 2.7 - - + -
118B VAL* 3.8 25.8 - - + -
121B MSE 4.1 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ASP* 3.5 1.1 - - - +
86B TYR* 1.3 77.9 - - - +
88B LYS* 1.3 78.3 + - + +
90B VAL* 3.4 0.3 + - - +
91B ASP* 2.9 34.8 + - - +
121B MSE 4.2 6.2 - - - -
125B LYS* 3.1 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LYS* 6.3 0.7 - - - +
80B LEU* 3.9 16.8 - - + -
85B ASP* 3.4 35.7 + - - +
87B GLU* 1.3 94.6 - - + +
89B GLY* 1.3 61.3 + - - +
91B ASP* 3.2 11.5 + - - +
92B HIS* 3.0 40.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B GLY* 3.5 32.5 - - - -
80B LEU* 3.8 8.9 - - - +
81B LEU* 4.3 8.5 - - - -
85B ASP 2.9 18.5 + - - -
86B TYR 3.9 0.7 - - - -
88B LYS* 1.3 76.8 - - - +
90B VAL* 1.3 57.4 + - - +
92B HIS 3.3 1.6 + - - -
93B LEU* 3.0 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B LEU* 4.3 3.1 - - + +
86B TYR 2.9 21.0 + - - +
87B GLU 3.7 3.1 - - - +
89B GLY* 1.3 73.9 - - - +
91B ASP* 1.3 59.8 + - - +
93B LEU* 3.1 9.6 + - + +
94B THR* 2.8 30.4 + - + +
118B VAL* 3.8 32.5 - - + +
121B MSE 4.0 14.6 - - + -
122B LEU* 3.6 31.4 - - + +
125B LYS* 3.5 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LYS* 5.1 8.8 + - - -
87B GLU* 2.9 31.9 + - - +
88B LYS* 3.2 14.3 + - - +
90B VAL* 1.3 76.5 - - - +
92B HIS* 1.3 60.6 + - + +
94B THR* 3.0 10.0 + - - -
95B ASN* 2.9 37.0 + - - +
125B LYS* 3.2 30.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ASN* 5.3 4.7 - - - -
73B GLU* 2.6 57.7 + - - +
76B LEU* 3.6 24.6 - - + +
77B GLY* 3.8 4.9 - - - -
80B LEU* 3.5 24.6 - - + +
88B LYS* 3.0 32.0 + - - +
89B GLY 3.8 5.2 - - - +
90B VAL 3.2 0.2 - - - -
91B ASP* 1.3 79.5 - - + +
93B LEU* 1.3 61.9 + - - +
95B ASN* 3.2 11.2 + - - +
96B ALA* 3.2 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ILE* 3.8 33.9 - - + +
77B GLY* 3.9 11.7 - - - -
78B GLU* 4.2 5.2 - - - +
81B LEU* 3.7 30.1 - - + -
89B GLY 3.0 14.9 + - - +
90B VAL* 3.6 10.1 - - + +
92B HIS* 1.3 76.0 - - - +
94B THR* 1.3 57.8 + - - +
96B ALA* 3.3 7.3 + - - +
97B ILE* 3.0 31.0 + - - +
110B LEU* 4.4 17.7 - - + +
114B LEU* 4.5 19.3 - - + -
122B LEU* 4.3 11.9 - - + -
19D LEU* 4.5 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B VAL* 2.8 26.0 + - + +
91B ASP* 3.0 19.6 + - - -
93B LEU* 1.3 69.7 - - - +
95B ASN* 1.3 60.1 + - - +
97B ILE* 3.8 8.6 - - + +
98B ALA* 2.9 29.5 + - - +
122B LEU* 3.7 42.6 - - + +
125B LYS* 3.6 25.7 + - - +
126B LEU* 4.2 10.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A PHE* 3.7 25.3 - - + -
73A GLU* 4.7 3.1 - - - +
92A HIS* 5.7 2.3 - - - -
95A ASN* 3.6 23.1 + - - +
69B PHE* 3.9 14.9 - - + -
73B GLU* 2.9 24.8 + - + +
91B ASP* 2.9 24.0 + - - +
92B HIS* 3.2 15.4 + - - +
94B THR* 1.3 77.0 + - - +
96B ALA* 1.3 61.5 + - - +
98B ALA* 3.1 15.9 + - - +
99B VAL* 3.4 14.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B PHE* 3.4 27.0 - - + +
73B GLU* 4.0 12.7 - - + +
74B ILE* 3.7 30.5 - - + +
92B HIS 3.2 9.9 + - - +
93B LEU 3.3 9.6 + - - +
95B ASN* 1.3 79.4 - - - +
97B ILE* 1.3 62.5 + - - +
98B ALA 3.3 0.3 + - - -
99B VAL* 3.3 21.2 + - - +
100B CYS* 3.6 2.9 + - - +
106B LEU* 5.2 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LEU 3.0 19.3 + - - +
94B THR* 3.8 8.1 - - - +
96B ALA* 1.3 73.9 - - - +
98B ALA* 1.3 60.5 + - - +
100B CYS* 3.1 27.9 + - - +
103B PRO* 4.0 21.8 - - + +
106B LEU* 3.9 24.7 - - + -
107B LEU* 3.8 19.5 - - + -
110B LEU* 3.6 25.4 - - + -
122B LEU* 3.9 19.7 - - + -
126B LEU* 4.0 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ALA* 3.4 24.0 - - - +
69A PHE* 3.6 25.0 - - + +
72A GLU* 5.2 4.6 - - - +
94B THR 2.9 18.4 + - - +
95B ASN* 3.1 8.7 + - - +
97B ILE* 1.3 77.4 - - - +
99B VAL* 1.3 55.7 + - - +
100B CYS 3.4 0.9 - - - -
126B LEU* 5.3 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU* 3.4 21.9 - - + +
62A ASP 4.0 6.2 - - - +
65A ALA* 3.8 13.5 - - - +
66A VAL* 4.4 4.9 + - - -
69A PHE* 3.6 41.1 - - + -
99A VAL* 4.4 1.3 - - + -
66B VAL* 3.6 31.3 - - + +
69B PHE* 4.3 10.5 - - + -
70B PHE* 4.1 17.9 - - + -
95B ASN 3.4 9.2 + - - +
96B ALA* 3.4 16.2 - - - +
97B ILE 3.3 0.2 - - - -
98B ALA* 1.3 76.0 - - - +
100B CYS* 1.3 59.1 + - - +
101B GLY 3.8 1.4 + - - -
----------------------------------------------------------
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