Contacts of the helix formed by residues 95 - 112 (chain B) in PDB entry 2YVC
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 GLN 95 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B GLY 3.4 22.2 + - - -
40B ARG* 2.9 53.6 + - - +
41B GLU* 2.6 35.0 + - + +
94B ILE* 1.3 74.5 - - + +
96B GLU* 1.3 66.6 + - - +
97B ILE* 2.9 19.0 + - + +
98B THR* 3.0 16.3 + - - +
99B GLN* 3.1 13.7 + - - +
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Residues in contact with GLU 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B ILE 3.5 4.5 + - - +
95B GLN* 1.3 70.6 - - - +
97B ILE* 1.3 64.6 + - - +
99B GLN* 3.5 16.6 - - - +
100B ARG* 3.2 25.2 + - - +
185B GLU* 3.2 44.1 - - + +
188B MET* 5.7 2.4 - - - +
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Residues in contact with ILE 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B VAL* 3.8 24.9 - - + +
38B GLY 3.5 20.9 - - - +
39B LEU* 4.5 8.5 - - + -
95B GLN* 2.9 25.4 + - + +
96B GLU* 1.3 75.2 - - - +
98B THR* 1.3 71.1 + - - +
100B ARG* 3.0 45.8 + - - +
101B LEU* 3.2 38.6 + - + +
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Residues in contact with THR 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU* 3.6 11.9 - - + +
41B GLU* 2.8 43.7 + - + +
44B PHE* 4.2 0.7 - - + -
45B PHE* 3.7 30.5 - - + -
93B LEU* 3.6 25.1 - - + -
95B GLN* 3.0 14.4 + - - +
97B ILE* 1.3 74.6 - - - +
99B GLN* 1.3 66.2 + - - +
101B LEU* 3.3 3.3 + - - +
102B PHE* 3.2 22.5 + - + -
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Residues in contact with GLN 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LEU* 2.8 47.0 + - + +
94B ILE 3.7 10.7 + - - -
95B GLN 3.1 16.8 - - - +
96B GLU* 3.5 16.6 - - - +
98B THR* 1.3 77.0 - - - +
100B ARG* 1.3 62.6 + - - +
102B PHE* 3.2 5.4 + - - +
103B PHE* 3.0 23.4 + - - +
185B GLU* 4.7 9.4 - - - +
188B MET* 5.6 8.1 - - + +
189B MET* 3.4 37.4 - - + +
192B LEU* 4.0 3.8 - - + +
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Residues in contact with ARG 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ASP* 2.8 34.4 + - - -
96B GLU* 3.2 9.6 + - - +
97B ILE* 3.0 44.1 + - - +
99B GLN* 1.3 78.7 - - - +
101B LEU* 1.3 59.8 + - - +
103B PHE* 3.3 6.0 + - - +
104B LEU* 2.8 44.7 + - + +
188B MET* 3.9 30.0 - - + +
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Residues in contact with LEU 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B THR* 3.8 31.0 - - + +
12B MET* 3.7 22.0 - - + +
13B ASP* 4.1 12.8 - - - +
37B VAL* 5.2 5.8 - - + -
39B LEU* 4.6 6.7 - - + -
45B PHE* 4.1 25.7 - - + -
80B PHE* 4.5 14.8 - - + +
97B ILE* 3.2 41.7 + - + +
98B THR 3.9 5.4 - - - +
100B ARG* 1.3 78.1 - - - +
102B PHE* 1.3 61.5 + - - +
104B LEU* 4.1 1.8 - - + -
105B GLN* 3.3 25.1 + - - +
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Residues in contact with PHE 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B PHE* 3.7 18.6 - + - -
45B PHE* 3.9 16.4 - + - -
82B ALA* 3.6 20.0 - - + -
84B PHE 3.6 19.3 - - - -
85B PHE* 3.6 35.2 - + - -
86B PRO* 3.8 16.6 - - + -
93B LEU* 3.6 35.0 - - + -
98B THR 3.2 19.9 + - - -
99B GLN 3.2 8.3 + - - +
101B LEU* 1.3 75.6 - - - +
103B PHE* 1.3 57.8 + - - +
105B GLN* 3.1 4.7 + - - +
106B VAL* 2.6 41.7 + - + +
192B LEU* 4.2 10.3 - - + -
201B TYR* 5.0 2.0 - - - -
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Residues in contact with PHE 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B GLN 3.0 13.6 + - - +
100B ARG 3.6 3.8 - - - +
102B PHE* 1.3 79.0 - - - +
104B LEU* 1.3 85.6 + - + +
107B LYS* 2.8 53.2 + - + +
129B ALA* 4.1 18.6 - - + -
132B ALA* 4.8 4.0 - - + -
187B SER 5.1 0.2 - - - -
188B MET* 3.7 49.4 - - + -
191B TYR* 3.6 46.1 - + + -
192B LEU* 3.8 18.3 - - + +
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Residues in contact with LEU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B MET* 3.4 38.1 - - + +
13B ASP* 3.7 30.1 - - + +
100B ARG* 2.8 30.5 + - + +
101B LEU* 5.6 0.4 - - - -
103B PHE* 1.3 99.5 - - + +
105B GLN* 1.3 59.5 + - - +
107B LYS* 3.9 11.6 - - + +
108B GLU* 3.1 29.5 + - - +
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Residues in contact with GLN 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B MET* 3.6 20.7 - - - +
45B PHE* 5.4 0.3 - - - -
80B PHE 4.8 0.2 - - - +
81B ARG* 3.3 24.5 - - - +
82B ALA* 2.7 58.3 + - - +
85B PHE* 3.9 14.4 - - + -
101B LEU 3.3 19.0 + - - +
102B PHE* 3.1 3.5 + - - +
104B LEU* 1.3 74.9 - - - +
106B VAL* 1.3 69.2 + - + +
108B GLU* 3.1 11.4 + - - +
109B ALA* 3.0 22.7 + - + +
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Residues in contact with VAL 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B PHE* 4.0 18.6 - - + -
102B PHE* 2.6 27.0 + - + +
105B GLN* 1.3 72.2 - - + +
107B LYS* 1.3 66.8 + - - +
109B ALA* 3.1 10.2 + - - +
110B ILE* 3.0 25.5 + - + +
115B ILE* 4.8 6.3 - - + -
191B TYR* 4.4 1.6 - - + -
192B LEU* 3.9 18.4 - - + -
195B ALA* 3.6 31.0 - - + -
201B TYR* 3.8 28.9 - - + -
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Residues in contact with LYS 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B PHE* 2.8 49.1 + - + +
104B LEU* 3.9 10.3 - - + +
106B VAL* 1.3 73.0 - - - +
108B GLU* 1.3 59.5 + - + +
110B ILE* 2.9 21.4 + - - +
111B LEU* 2.9 34.7 + - + +
126B ALA* 5.6 1.8 - - - +
129B ALA* 3.5 23.2 - - + +
151B ARG 4.3 11.2 + - - -
152B LEU* 5.2 9.1 + - - +
191B TYR* 3.2 32.3 + - + +
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Residues in contact with GLU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ARG* 5.7 7.1 + - - +
12B MET* 3.5 17.7 - - + +
81B ARG* 3.9 18.0 + - - -
104B LEU 3.1 18.5 + - - +
105B GLN* 3.1 13.5 + - - +
107B LYS* 1.3 80.8 - - + +
109B ALA* 1.3 85.5 + - - +
111B LEU* 3.5 14.9 + - + +
112B ASN* 3.1 43.8 + - - +
114B GLU* 4.4 3.6 - - - +
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Residues in contact with ALA 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B GLN* 3.0 9.6 + - + +
106B VAL* 3.4 10.3 - - - +
108B GLU* 1.3 86.5 + - - +
110B ILE* 1.3 58.3 + - - +
112B ASN* 2.9 17.2 + - - -
114B GLU* 3.0 41.7 + - + +
115B ILE* 4.1 20.9 - - + -
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Residues in contact with ILE 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B VAL* 3.0 18.5 + - + +
107B LYS 2.9 9.9 + - - +
109B ALA* 1.3 76.1 - - - +
111B LEU* 1.3 62.1 + - + +
113B ASP 3.2 9.9 + - - -
115B ILE* 3.8 28.3 - - + +
117B CYS* 4.0 22.4 - - + -
122B ALA* 5.9 0.9 - - + -
125B LEU* 3.8 22.0 - - + -
154B PRO* 3.4 22.9 - - + +
156B ARG* 3.7 3.3 + - - -
191B TYR* 3.6 21.8 - - - +
195B ALA* 3.9 22.4 - - + -
198B LEU* 4.3 6.5 - - + -
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Residues in contact with LEU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ASN* 5.0 0.2 + - - -
107B LYS* 2.9 61.3 + - + +
108B GLU* 3.5 13.0 - - + +
109B ALA 3.3 0.2 - - - -
110B ILE* 1.3 78.9 - - + +
112B ASN* 1.3 59.4 + - - +
113B ASP* 3.3 5.5 + - - +
151B ARG* 3.1 51.3 + - + +
152B LEU 3.3 35.0 - - - +
153B LEU 3.6 13.9 - - - +
154B PRO* 3.6 13.5 - - + +
155B GLN* 4.0 0.7 + - - +
191B TYR* 5.0 1.6 - - - +
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Residues in contact with ASN 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ASN* 3.0 36.2 + - + +
75A PRO* 4.5 6.4 - - - +
108B GLU* 3.1 30.5 + - - +
109B ALA 2.9 5.0 + - - +
111B LEU* 1.3 74.0 - - - +
113B ASP* 1.3 73.7 + - - +
114B GLU* 3.1 34.2 + - + +
151B ARG* 2.2 36.5 + - - +
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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