Contacts of the helix formed by residues 76 - 90 (chain A) in PDB entry 2W99
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 76 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A GLU* 3.8 28.0 - - + +
75A GLU* 1.3 83.3 - - - +
77A VAL* 1.3 64.0 + - - +
78A PHE 3.5 0.2 - - - -
79A PRO* 3.5 9.2 - - - +
80A LEU* 3.1 26.6 + - - +
114A LYS* 3.7 37.6 - - + +
156A THR* 3.8 18.2 + - - +
158A HIS* 4.3 16.7 - - + +
159A ASP* 4.3 9.0 - - - +
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Residues in contact with VAL 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A CYS* 4.4 12.3 - - - -
73A CYS* 4.3 10.5 - - + -
74A GLU* 2.8 30.2 + - + +
76A GLU* 1.3 77.3 - - - +
78A PHE* 1.3 60.0 + - - +
80A LEU* 3.4 3.7 + - - -
81A ALA* 3.0 24.3 + - - +
107A MET* 4.4 7.9 - - + +
110A ALA* 3.4 9.1 - - + +
111A SER* 3.8 28.9 - - - +
114A LYS* 4.0 13.0 - - + -
115A GLU* 3.8 31.9 - - + +
119A LEU* 5.0 0.9 - - + -
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Residues in contact with PHE 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ALA* 3.1 28.5 - - + -
64A MET* 3.8 21.1 - - + -
65A LEU* 3.7 30.5 - - + -
68A CYS* 3.8 22.1 - - + +
75A GLU 3.8 4.3 + - - +
77A VAL* 1.3 78.2 - - - +
79A PRO* 1.3 69.2 - - + +
81A ALA* 2.9 21.1 + - - +
82A MET* 3.0 32.4 + - + +
107A MET* 5.5 0.2 - - - -
187A ALA* 4.0 18.8 - - + -
190A ALA* 3.5 26.9 - - + -
191A THR* 3.7 16.4 - - + -
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Residues in contact with PRO 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A GLU 3.1 13.0 - - - +
76A GLU 3.5 9.0 - - - +
78A PHE* 1.3 102.6 - - + +
80A LEU* 1.3 60.3 + - - +
82A MET* 4.0 5.2 - - + -
83A ASN* 3.4 18.5 + - - +
156A THR* 4.0 5.6 - - + +
157A PRO* 4.0 20.6 - - + -
158A HIS* 3.3 29.8 - - + +
186A VAL* 4.5 7.2 - - + -
187A ALA* 6.5 0.2 - - - -
190A ALA* 4.8 2.9 - - + -
195A PHE* 3.6 22.4 - - + -
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Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A GLU 3.1 18.9 + - - +
77A VAL 3.6 4.7 - - - +
78A PHE 3.1 0.8 - - - -
79A PRO* 1.3 77.3 - - - +
81A ALA* 1.3 63.8 + - - +
83A ASN* 3.3 9.1 - - + +
84A TYR* 3.2 54.8 + - + +
110A ALA* 4.1 16.4 - - + +
113A MET* 4.3 4.0 - - + -
114A LYS* 3.7 40.4 - - + +
152A LEU 4.0 8.3 - - - +
154A ALA* 4.1 17.9 - - + +
155A MET 4.8 0.4 - - - +
156A THR* 3.7 14.1 - - + +
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Residues in contact with ALA 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A MET* 3.3 24.7 - - + -
77A VAL 3.0 12.5 + - - +
78A PHE 2.9 7.2 + - - +
80A LEU* 1.3 76.3 - - - +
82A MET* 1.3 57.1 + - - +
84A TYR* 3.2 3.2 + - - -
85A LEU* 2.8 26.0 + - - +
106A CYS* 3.2 41.7 - - - +
107A MET* 3.5 8.1 - - + +
110A ALA* 3.8 2.2 - - + +
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Residues in contact with MET 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ARG* 3.5 22.2 - - + +
61A ALA* 3.1 35.4 - - + +
64A MET* 3.6 26.2 - - - +
78A PHE* 3.0 32.4 + - + +
79A PRO* 4.0 1.8 - - + +
80A LEU 3.3 0.2 - - - -
81A ALA* 1.3 74.2 - - - +
83A ASN* 1.3 60.8 + - - +
85A LEU* 3.7 14.9 - - + +
86A ASP* 2.9 37.5 + - - +
190A ALA* 3.2 20.9 - - + +
195A PHE* 3.9 20.2 - - + -
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Residues in contact with ASN 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A CYS* 3.6 21.5 + - - +
40A PRO* 4.6 8.7 - - - +
79A PRO 3.4 12.7 + - - +
80A LEU* 3.3 13.5 - - + +
82A MET* 1.3 78.7 - - - +
84A TYR* 1.3 57.3 + - - +
86A ASP* 3.4 3.5 + - - +
87A ARG* 2.9 66.0 + - - +
154A ALA* 3.6 16.1 - - - +
155A MET 5.0 7.3 + - - +
195A PHE* 3.9 10.3 - - + -
200A PRO* 5.6 8.3 - - - +
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Residues in contact with TYR 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A LEU* 3.2 32.3 + - + +
81A ALA* 3.2 8.4 + - - +
83A ASN* 1.3 79.1 - - - +
85A LEU* 1.3 57.5 + - - +
87A ARG* 3.4 19.0 + - - +
88A PHE* 3.0 30.8 + - - +
106A CYS* 3.7 31.0 - - - -
109A VAL* 3.5 24.5 - - + -
110A ALA* 3.7 14.6 - - - -
113A MET* 3.8 11.1 - - - +
144A LEU* 4.0 8.8 - - + +
148A LEU* 3.6 24.2 - - + +
152A LEU* 2.5 48.6 + - + +
154A ALA* 4.7 0.2 - - + -
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Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ARG* 4.0 19.5 - - + +
60A VAL* 4.8 9.2 - - + -
64A MET* 4.4 11.7 - - + -
81A ALA 2.8 19.5 + - - +
82A MET* 3.7 13.5 - - + +
83A ASN 3.2 0.2 - - - -
84A TYR* 1.3 74.2 - - - +
86A ASP* 1.3 81.4 + - - +
88A PHE* 3.2 4.1 + - - +
89A LEU* 2.9 48.6 + - + +
99A LEU* 4.7 11.2 - - + -
102A LEU* 4.4 9.6 - - + -
103A GLY* 4.2 27.4 - - - +
106A CYS* 3.5 11.8 - - + -
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Residues in contact with ASP 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A PRO* 3.7 20.3 - - + +
44A TYR* 2.9 29.4 + - + -
57A ARG* 2.9 35.2 + - - -
82A MET 2.9 21.2 + - - +
83A ASN* 3.9 3.5 - - - +
85A LEU* 1.3 73.9 - - - +
87A ARG* 1.3 56.9 + - - +
89A LEU 3.6 0.2 + - - -
90A SER* 2.5 38.1 + - - -
195A PHE* 3.8 12.1 - - - +
196A ILE* 3.7 14.9 - - - +
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Residues in contact with ARG 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A THR 4.7 1.8 + - - -
38A CYS* 2.8 53.8 + - - +
39A ALA 4.3 1.8 - - - +
40A PRO* 4.1 13.0 - - + -
83A ASN* 2.9 46.0 + - - +
84A TYR* 3.8 17.5 - - - +
86A ASP* 1.3 77.1 - - - +
88A PHE* 1.3 60.0 + - - +
90A SER* 3.5 9.0 - - - -
91A LEU* 3.2 30.5 + - + +
148A LEU* 3.8 32.6 + - + +
151A ASN* 2.8 39.8 + - - +
154A ALA* 4.0 1.4 - - - +
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Residues in contact with PHE 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A TYR 3.0 17.4 + - - +
85A LEU 3.7 3.8 - - - +
86A ASP 3.1 0.4 - - - -
87A ARG* 1.3 76.9 - - - +
89A LEU* 1.3 55.4 + - + +
90A SER 2.9 4.5 - - - -
91A LEU* 2.8 5.1 + - - +
92A GLU* 2.5 62.6 + - + -
94A VAL* 3.9 13.9 - - + -
102A LEU* 3.7 31.4 - - + -
140A MET* 4.9 6.7 - - + -
143A LEU* 3.8 21.1 - - + -
144A LEU* 3.8 31.9 - - + -
147A LYS* 3.1 38.8 - - + -
148A LEU* 4.6 2.7 - - + -
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Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A TYR* 3.3 45.4 - - + +
48A VAL* 3.6 6.8 - - - +
49A GLN* 2.9 37.0 + - + +
52A VAL* 4.8 8.1 - - + -
57A ARG* 5.4 3.1 - - + -
85A LEU* 2.9 43.2 + - + +
88A PHE* 1.3 76.5 - - - +
90A SER* 1.3 61.4 + - - +
91A LEU 3.4 0.2 + - - -
94A VAL* 4.0 15.9 - - + -
99A LEU* 4.3 15.3 - - + -
102A LEU* 3.2 28.0 - - + -
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Residues in contact with SER 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A PRO* 3.4 3.0 - - - +
41A SER* 2.9 37.9 + - - -
44A TYR* 3.3 16.7 - - - -
48A VAL* 3.3 20.0 - - - +
86A ASP 2.5 22.3 + - - -
87A ARG* 3.5 11.9 - - - -
88A PHE 2.9 0.8 - - - -
89A LEU* 1.3 79.3 - - - +
91A LEU* 1.3 61.2 + - - +
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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
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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) + - + + + + + -
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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