Contacts of the helix formed by residues 83 - 99 (chain A) in PDB entry 2VZE
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 PHE 83 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LEU* 3.9 21.1 - - + +
54A TRP* 3.6 22.7 - + + -
55A ALA* 3.5 18.4 - - - +
58A GLU* 3.3 18.2 + - - +
63A ARG* 3.5 14.1 - - - -
66A SER* 3.4 17.0 + - - -
67A PRO 3.6 15.5 - - - -
68A ALA* 3.7 16.8 - - + -
82A ASN* 1.3 76.5 - - - +
84A ARG* 1.3 57.9 + - - +
86A LEU* 3.8 3.0 - - - +
87A SER* 2.9 28.2 + - - -
277A TRP* 3.8 16.8 - + - -
280A GLY* 3.3 41.3 - - - -
281A ALA 3.5 11.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ALA* 3.9 12.7 - - - +
58A GLU* 3.1 26.4 + - + +
59A LYS* 3.8 49.1 + - + +
82A ASN* 3.5 5.8 - - - +
83A PHE* 1.3 75.1 - - - +
85A GLU* 1.3 57.3 + - - +
87A SER* 3.1 1.9 + - - -
88A GLU* 2.8 67.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A MET* 3.9 8.7 - - - +
81A TRP* 3.6 18.2 - - + -
82A ASN* 2.8 57.0 + - - +
84A ARG* 1.3 77.8 - - + +
86A LEU* 1.3 57.8 + - - +
88A GLU* 3.4 14.6 + - - +
89A ASN* 2.8 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LEU* 3.4 31.4 - - + -
68A ALA* 3.9 11.7 - - + -
69A LEU* 4.5 17.9 - - + -
81A TRP* 3.9 14.1 - - + -
82A ASN 2.8 16.5 + - - +
83A PHE* 3.8 5.2 - - + +
85A GLU* 1.3 76.3 - - - +
87A SER* 1.3 59.2 + - - +
89A ASN* 4.7 0.2 - - - -
90A SER* 2.8 31.1 + - - -
120A TRP* 5.5 1.1 - - + -
121A LEU* 4.3 15.5 - - + -
124A LEU* 4.0 13.5 - - + -
277A TRP* 3.5 40.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LEU* 4.6 4.0 - - - +
52A ASP* 3.0 20.0 + - - -
55A ALA* 3.6 18.8 - - - +
59A LYS* 5.1 4.9 + - - -
83A PHE 2.9 18.9 + - - -
84A ARG* 3.4 4.5 - - - -
86A LEU* 1.3 77.1 - - - +
88A GLU* 1.3 62.7 + - - +
90A SER* 2.7 21.8 + - - -
91A GLN* 2.9 35.3 + - - +
128A ARG* 3.7 3.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A LYS* 5.2 9.4 - - - +
84A ARG* 2.8 57.6 + - + +
85A GLU* 3.8 13.6 - - - +
87A SER* 1.3 74.4 - - - +
89A ASN* 1.3 61.9 + - - +
91A GLN* 3.2 8.3 + - - +
92A GLN* 3.0 26.8 + - - +
203A THR* 3.9 35.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A TRP* 3.0 31.9 + - + +
85A GLU 2.8 21.3 + - - +
86A LEU 4.2 0.2 - - - +
88A GLU* 1.3 73.6 - - - +
90A SER* 1.3 57.2 + - - +
92A GLN* 2.5 36.7 + - - +
93A ALA* 3.1 20.4 + - - +
121A LEU* 3.6 25.4 - - + +
198A LEU* 3.6 20.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU 2.8 14.9 + - - -
87A SER* 2.7 20.3 + - - -
89A ASN* 1.3 75.6 - - - +
91A GLN* 1.3 57.6 - - - +
93A ALA* 3.3 10.3 + - - +
94A ALA* 3.0 21.5 + - - +
121A LEU* 4.0 8.9 - - - +
124A LEU* 3.9 29.2 - - - +
125A GLY* 3.9 2.8 - - - -
128A ARG* 3.1 33.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ASP* 4.7 2.8 + - - -
59A LYS* 5.1 8.9 - - - +
87A SER* 2.9 39.0 + - - +
88A GLU* 3.2 5.9 + - - +
90A SER* 1.3 73.8 - - - +
92A GLN* 1.3 66.6 + - - +
94A ALA* 3.3 3.1 + - - +
95A ASN* 3.0 27.4 + - - -
128A ARG* 3.4 26.2 - - - +
202A SER 4.0 2.2 - - - -
203A THR 3.4 23.9 + - - +
204A THR* 3.5 3.6 - - - +
205A HIS* 2.8 47.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLU* 3.0 13.0 + - - +
89A ASN* 2.5 40.6 + - - +
91A GLN* 1.3 78.1 - - - +
93A ALA* 1.3 60.0 + - - +
95A ASN 3.3 0.9 + - - -
96A VAL* 3.1 26.3 + - - +
198A LEU* 3.1 34.1 + - + +
199A ASN* 4.1 11.5 + - - +
201A ALA* 3.3 19.3 + - + +
202A SER 3.4 23.1 + - - +
203A THR* 3.9 16.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ASN 3.1 13.1 + - - +
90A SER 3.4 7.9 - - - +
91A GLN 3.2 0.6 - - - -
92A GLN* 1.3 75.1 - - - +
94A ALA* 1.3 62.1 + - - +
96A VAL* 3.2 6.8 + - - +
97A LEU* 3.1 30.2 + - + +
121A LEU* 3.3 33.2 - - + +
122A VAL* 4.6 2.7 - - - +
125A GLY* 4.1 2.7 - - - -
194A PHE* 4.4 9.4 - - + -
198A LEU* 3.5 13.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A SER 3.0 13.7 + - - +
91A GLN 3.6 3.8 - - - +
93A ALA* 1.3 75.2 - - - +
95A ASN* 1.3 54.2 + - - +
97A LEU* 3.8 2.2 - - - +
98A SER* 2.6 40.3 + - - -
125A GLY* 3.7 25.0 - - - +
128A ARG* 3.9 5.4 - - + -
129A ALA* 4.3 1.5 - - + +
205A HIS* 3.4 36.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A GLN 3.0 15.4 + - - +
92A GLN 3.7 4.9 - - - +
93A ALA 3.2 0.4 - - - -
94A ALA* 1.3 73.4 - - - +
96A VAL* 1.3 61.9 + - - +
98A SER* 4.1 3.3 + - - -
99A GLY* 2.8 30.6 + - - +
100A ALA* 3.2 3.5 + - - +
201A ALA* 3.9 10.8 - - + -
202A SER* 2.5 39.1 + - - +
204A THR 3.2 19.9 + - - +
205A HIS* 3.3 21.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A GLN 3.1 20.3 + - - +
93A ALA* 3.2 9.8 + - - +
95A ASN* 1.3 77.3 - - - +
97A LEU* 1.3 57.8 + - + +
100A ALA* 3.5 7.9 + - + +
101A CYS* 3.0 30.2 + - - -
181A LEU* 4.1 24.0 - - + -
194A PHE* 4.2 14.6 - - + -
197A LEU* 3.6 28.7 - - + +
198A LEU* 3.5 34.5 - - + +
201A ALA* 4.0 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ALA* 3.1 22.8 + - + +
94A ALA* 3.8 2.9 - - - +
96A VAL* 1.3 80.1 - - + +
98A SER* 1.3 57.6 + - - +
101A CYS* 3.3 15.7 - - - +
102A GLY 3.4 0.7 + - - -
103A LEU* 3.0 39.3 + - + +
109A VAL* 4.9 5.8 - - + -
122A VAL* 4.0 16.4 - - + +
125A GLY* 3.7 29.6 - - - -
126A CYS* 3.8 8.5 - - - +
129A ALA* 5.1 0.2 - - + -
131A LEU* 3.7 16.4 - - + -
158A VAL* 4.6 11.4 - - + -
181A LEU* 3.8 26.5 - - + -
194A PHE* 5.3 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ALA 2.6 23.8 + - - -
95A ASN* 4.1 1.6 + - - -
97A LEU* 1.3 75.5 - - - +
99A GLY* 1.3 60.1 + - - +
102A GLY* 3.4 16.6 - - - -
103A LEU 3.4 19.8 - - - +
104A GLN* 4.3 5.9 + - - -
129A ALA* 4.0 17.7 - - - -
205A HIS* 3.7 15.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ASN* 2.8 15.1 + - - -
98A SER* 1.3 79.3 + - - +
100A ALA* 1.3 66.6 + - - +
101A CYS 3.3 0.7 - - - -
102A GLY* 3.3 9.5 + - - -
----------------------------------------------------------
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