Contacts of the helix formed by residues 2 - 11 (chain D) in PDB entry 6H2V
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 LYS 2 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76C LEU* 3.8 22.2 - - + -
100C THR 3.1 27.7 + - - -
101C ASN* 5.0 0.2 - - - +
102C ILE 3.5 20.0 - - - -
103C ASP* 2.8 18.1 + - - +
1D MET* 1.3 78.1 - - - +
3D LEU* 1.3 59.9 + - - +
4D LEU* 3.2 2.2 - - + +
5D THR* 3.2 8.0 + - - +
6D HIS* 3.1 22.5 + - - +
33D CME 4.8 3.2 + - - +
35D VAL* 3.4 9.0 - - - +
88D LEU 3.4 11.9 - - - +
89D LEU* 2.7 40.5 + - + +
91D VAL 3.9 7.4 - - - -
92D GLU* 3.3 27.3 + - + +
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Residues in contact with LEU 3 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D MET* 4.9 2.5 - - + -
2D LYS* 1.3 72.0 - - - +
4D LEU* 1.4 62.9 + - - +
6D HIS* 3.8 9.6 + - + +
7D ASN* 3.1 22.7 + - - +
25D LEU* 3.7 31.2 - - + -
54D PHE* 4.1 24.3 - - + -
57D ALA* 3.8 10.8 - - + -
58D ALA* 4.4 10.8 - - - +
61D LEU* 4.1 12.8 - - + -
63D LEU* 4.0 26.2 - - + -
87D LEU 3.3 25.4 - - - +
88D LEU* 3.3 9.3 + - - +
91D VAL* 3.9 12.8 + - + +
93D VAL* 5.0 2.2 - - + -
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Residues in contact with LEU 4 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C VAL* 4.4 4.3 - - + -
76C LEU* 3.8 26.7 - - + -
2D LYS* 5.0 0.4 - - + -
3D LEU* 1.4 77.2 - - - +
5D THR* 1.4 57.5 + - - +
7D ASN* 3.1 10.5 + - + +
8D LEU* 2.9 43.3 + - + +
41D PHE* 3.8 31.2 - - + -
45D MET* 4.3 19.3 - - + -
49D VAL* 4.3 15.5 - - + -
88D LEU* 2.9 40.5 + - + +
89D LEU* 4.2 6.1 - - + -
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Residues in contact with THR 5 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C LEU* 3.7 12.3 - - - +
78C VAL* 4.3 10.9 - - + +
103C ASP* 2.6 39.9 + - - +
104C MET 5.4 0.2 - - - +
105C VAL* 4.1 26.0 - - + -
1D MET* 3.9 12.6 - - + -
2D LYS* 3.2 7.8 + - - +
4D LEU* 1.4 76.3 - - - +
6D HIS* 1.3 56.3 + - - +
8D LEU* 3.2 13.5 + - + +
9D LEU* 2.9 36.5 + - + +
114D PRO* 5.3 0.2 - - + -
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Residues in contact with HIS 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D MET* 3.8 26.1 - - + -
2D LYS 3.1 7.8 + - - +
3D LEU* 3.8 13.8 + - + +
5D THR* 1.3 74.3 - - - +
7D ASN* 1.3 65.1 + - - +
9D LEU* 3.4 5.9 + - - +
10D SER* 3.0 45.5 + - - -
22D PRO* 5.3 0.4 - - + -
23D LEU* 2.8 27.6 + - + -
25D LEU* 4.3 7.0 - - + +
53D ALA* 3.6 31.6 + - + -
54D PHE* 5.0 0.6 + - - -
57D ALA* 3.6 22.0 - - + +
98D LEU* 3.6 26.7 - - + -
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Residues in contact with ASN 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D LEU 3.1 14.5 + - - +
4D LEU* 3.1 18.2 + - + +
6D HIS* 1.3 78.7 + - - +
8D LEU* 1.4 57.3 + - + +
10D SER* 3.3 3.9 + - - -
11D SER* 2.9 34.4 + - - -
48D LYS 4.4 2.1 - - - +
49D VAL* 3.6 14.8 - - - +
50D GLU* 2.9 49.7 + - - +
53D ALA* 3.9 3.8 - - - +
54D PHE* 3.7 25.1 - - - +
88D LEU* 5.3 0.9 - - + +
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Residues in contact with LEU 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C VAL* 4.2 14.8 - - + -
76C LEU* 4.6 2.9 - - + -
78C VAL* 4.2 14.1 - - + -
115C ARG 3.0 10.0 - - - +
116C MET* 3.5 12.3 - - - +
119C SER* 3.3 34.0 + - - +
120C PHE* 3.8 33.0 - - + -
4D LEU* 2.9 33.3 + - + +
5D THR* 3.2 12.8 + - + +
7D ASN* 1.4 74.8 - - + +
9D LEU* 1.3 57.6 + - + +
11D SER* 2.9 23.4 + - - -
45D MET* 6.0 2.0 - - - -
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Residues in contact with LEU 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C PHE* 4.7 0.7 - - + -
105C VAL* 4.2 28.3 - - + -
115C ARG* 3.4 23.7 - - - +
116C MET* 3.9 27.0 - - + +
1D MET* 4.5 4.7 - - - -
5D THR* 2.9 25.5 + - + +
6D HIS* 3.7 6.1 - - - +
7D ASN 3.3 0.2 - - - -
8D LEU* 1.3 77.5 - - + +
10D SER* 1.4 54.6 + - - +
23D LEU* 4.0 18.2 - - + +
98D LEU* 3.8 26.5 - - + -
114D PRO* 4.3 16.6 - - + -
116D MET* 4.5 13.7 - - + +
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Residues in contact with SER 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C ARG* 3.4 16.7 - - - +
6D HIS* 3.0 29.6 + - - -
7D ASN 3.9 2.2 - - - -
9D LEU* 1.4 76.0 - - - +
11D SER* 1.4 64.1 + - - +
12D HIS* 3.6 3.8 + - - +
21D PHE 4.1 8.8 - - - +
22D PRO* 4.1 8.1 - - - -
23D LEU* 3.2 35.2 + - - +
50D GLU* 3.8 5.5 - - - +
53D ALA* 4.2 14.4 - - - -
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Residues in contact with SER 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C ASN 4.2 0.9 - - - +
115C ARG* 2.7 54.1 + - - +
116C MET* 4.3 0.3 - - - -
117C SER 4.8 3.8 + - - +
119C SER* 3.8 15.5 - - - -
7D ASN* 2.9 21.3 + - - -
8D LEU* 2.9 11.4 + - - -
10D SER* 1.4 72.0 - - - +
12D HIS* 1.4 56.5 + - - +
48D LYS 6.1 0.9 - - - -
50D GLU* 3.7 12.7 + - - -
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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