Contacts of the helix formed by residues 97 - 110 (chain B) in PDB entry 2V3D
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 SER 97 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B ALA* 3.5 17.3 - - - +
96B LEU* 1.3 74.0 - - - +
98B PRO* 1.3 77.4 - - - +
99B PRO* 3.6 6.6 - - - +
100B ALA 3.0 5.4 + - - -
101B GLN* 2.9 19.5 + - - +
409B ASP* 2.7 35.6 + - - -
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Residues in contact with PRO 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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96B LEU 3.8 1.3 - - - +
97B SER* 1.3 83.8 - - - +
99B PRO* 1.3 71.2 - - + +
101B GLN* 3.2 23.9 - - - +
102B ASN* 3.0 33.1 + - - +
163B ARG* 5.4 1.8 - - - +
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Residues in contact with PRO 99 (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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20B ALA* 3.4 27.1 - - + +
97B SER* 3.5 11.7 - - - +
98B PRO* 1.3 98.1 - - + +
100B ALA* 1.3 59.4 + - - +
102B ASN* 3.5 10.4 + - + +
103B LEU* 3.1 26.3 + - - +
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Residues in contact with ALA 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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19B ASN 3.7 30.3 - - - +
20B ALA* 3.8 2.3 - - - +
96B LEU* 3.9 17.3 - - + -
97B SER* 3.0 19.5 + - - +
99B PRO* 1.3 76.0 - - - +
101B GLN* 1.3 60.0 + - - +
103B LEU* 3.2 1.7 + - - +
104B LEU* 2.8 26.3 + - - +
409B ASP* 3.9 12.8 - - - +
411B PHE* 3.3 11.6 - - + -
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Residues in contact with GLN 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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93B ILE* 3.2 27.9 - - + +
94B LEU* 3.4 26.4 + - - +
96B LEU* 2.8 28.4 + - + +
97B SER 2.9 11.7 + - - +
98B PRO* 3.2 27.7 - - - +
100B ALA* 1.3 75.7 - - - +
102B ASN* 1.3 57.6 + - - +
104B LEU* 3.3 4.0 + - - +
105B LEU* 2.9 33.6 + - - +
163B ARG* 2.8 39.9 + - - +
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Residues in contact with ASN 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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98B PRO* 3.0 27.1 + - - +
99B PRO* 3.8 8.1 - - + +
100B ALA 3.2 0.2 - - - -
101B GLN* 1.3 73.1 - - - +
103B LEU* 1.3 62.7 + - + +
105B LEU* 3.9 6.3 - - - +
106B LYS* 2.8 40.8 + - + +
163B ARG* 2.6 31.5 + - - +
167B LEU* 4.3 10.1 - - + +
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Residues in contact with LEU 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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19B ASN 3.2 23.8 - - - +
20B ALA 3.8 14.8 - - - +
21B THR 4.2 2.9 - - - -
22B TYR 3.9 22.7 - - - +
23B CYS* 4.0 13.7 - - + +
99B PRO 3.1 10.8 + - - +
100B ALA 3.2 6.9 + - - +
102B ASN* 1.3 75.8 - - + +
104B LEU* 1.3 65.6 + - - +
106B LYS* 3.8 16.5 - - + +
107B SER* 2.9 27.4 + - - -
411B PHE* 3.6 11.4 - - + -
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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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93B ILE* 3.8 38.6 - - + -
96B LEU* 3.8 22.0 - - + -
100B ALA 2.8 13.5 + - - +
101B GLN* 3.6 8.1 - - - +
103B LEU* 1.3 76.6 - - - +
105B LEU* 1.3 69.2 + - + +
107B SER* 3.2 13.0 + - - -
108B TYR* 3.4 31.6 + - + -
384B ALA* 4.5 2.2 - - + -
402B ILE* 3.8 32.1 - - + -
404B VAL* 4.1 7.9 - - + -
411B PHE* 3.3 18.5 - - + -
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Residues in contact with LEU 105 (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 MET* 4.8 3.8 - - + -
93B ILE* 4.2 27.1 - - + -
101B GLN 2.9 22.6 + - - +
102B ASN* 4.0 1.1 - - - +
104B LEU* 1.3 78.5 - - + +
106B LYS* 1.3 52.6 + - - +
108B TYR* 3.3 1.4 + - - -
109B PHE* 2.8 63.3 + - + +
160B LEU* 4.0 21.5 - - + +
163B ARG* 3.9 46.7 - - + +
164B ALA* 4.6 4.0 - - + +
167B LEU* 3.6 20.2 - - + -
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Residues in contact with LYS 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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102B ASN* 2.8 30.2 + - + +
103B LEU* 3.8 17.4 - - + +
105B LEU* 1.3 70.2 - - - +
107B SER* 1.3 66.8 + - - +
110B SER* 3.0 46.3 + - - +
112B GLU* 2.9 37.5 + - + -
113B GLY* 3.5 4.8 - - - -
167B LEU* 3.8 28.0 - - + -
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Residues in contact with SER 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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23B CYS* 3.5 12.3 - - - -
24B ASP 4.7 1.3 + - - -
103B LEU 2.9 17.9 + - - -
104B LEU* 3.4 11.9 - - - -
106B LYS* 1.3 74.7 - - - +
108B TYR* 1.3 57.7 + - - +
113B GLY* 3.2 7.5 - - - -
114B ILE* 2.9 24.9 + - - +
402B ILE* 4.7 4.3 - - - -
411B PHE* 4.1 0.9 - - - -
413B LYS* 3.2 34.5 + - - +
417B PHE* 3.3 22.1 - - - -
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Residues in contact with TYR 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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104B LEU* 3.4 21.8 + - + -
105B LEU* 3.3 3.1 + - + +
106B LYS 3.2 0.4 - - - -
107B SER* 1.3 80.5 - - - +
109B PHE* 1.3 83.1 + + + +
110B SER 3.6 0.4 - - - -
114B ILE* 3.7 2.0 - - - +
115B GLY 3.2 8.0 + - - -
116B TYR* 2.9 66.5 + + + +
380B ASP* 4.6 0.7 + - - -
383B LEU* 2.7 54.6 + - + +
401B PRO* 3.6 23.3 - - + +
402B ILE* 3.5 21.3 - - + +
417B PHE* 3.6 25.8 - + - -
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Residues in contact with PHE 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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85B MET* 5.1 1.3 - - + -
105B LEU* 2.8 36.9 + - + +
108B TYR* 1.3 89.1 - + + +
110B SER* 1.3 63.1 + - - +
111B GLU* 5.7 0.2 - - - +
115B GLY* 4.5 6.1 - - - -
116B TYR* 3.6 45.6 - + + +
118B ILE 4.4 2.0 - - - -
119B ILE* 3.6 37.5 - - + -
164B ALA* 3.6 41.5 - - + +
167B LEU* 4.2 3.8 - - + -
168B ALA* 3.2 25.0 - - + +
169B GLN 4.7 0.2 + - - -
172B VAL* 4.8 6.7 - - + -
383B LEU* 4.3 18.6 - - + -
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Residues in contact with SER 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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105B LEU 4.1 0.2 + - - -
106B LYS* 3.0 43.8 + - - +
109B PHE* 1.3 80.8 - - - +
111B GLU* 1.3 60.1 + - - +
112B GLU* 3.1 23.0 + - - +
113B GLY 3.0 15.4 + - - -
115B GLY* 3.2 19.6 + - - -
167B LEU* 3.4 20.2 - - - -
168B ALA* 4.7 0.2 - - - +
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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
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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