Contacts of the helix formed by residues 6 - 17 (chain A) in PDB entry 2B7T
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 PRO 6 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A VAL 5.0 0.2 - - - +
5A LEU* 1.4 83.0 - - + -
7A LYS* 1.3 66.2 + - - +
8A ASN* 3.4 2.2 + - - -
9A ALA 3.7 2.4 + - - -
10A LEU* 3.0 32.9 + - + +
55A LYS* 3.8 35.0 - - + +
58A LYS* 5.2 4.5 - - + -
59A LEU* 3.6 27.8 - - + +
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Residues in contact with LYS 7 (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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3A PRO* 3.8 34.9 + - + +
5A LEU 3.0 10.0 + - - -
6A PRO* 1.3 68.4 - - - +
8A ASN* 1.3 72.5 + - - +
11A MET* 3.0 35.7 + - + +
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Residues in contact with ASN 8 (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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6A PRO 4.5 1.9 - - - +
7A LYS* 1.3 81.6 + - + +
9A ALA* 1.3 76.9 + - - +
11A MET* 3.5 13.7 - - + +
12A GLN* 3.0 26.8 + - - +
59A LEU* 4.7 6.9 - - - +
63A GLU* 6.3 0.2 - - - +
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Residues in contact with ALA 9 (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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6A PRO 3.7 0.4 + - - -
8A ASN* 1.3 87.2 + - - +
10A LEU* 1.3 64.3 + - + +
12A GLN* 3.0 23.2 + - - +
13A LEU* 3.0 19.1 + - - +
59A LEU* 3.7 33.7 - - + +
63A GLU* 3.9 26.7 - - + -
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Residues in contact with LEU 10 (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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5A LEU* 3.7 29.6 - - + +
6A PRO* 3.0 35.3 + - + +
9A ALA* 1.3 78.0 - - + +
11A MET* 1.3 58.5 + - - +
13A LEU* 3.4 16.2 + - + +
14A ASN* 2.8 34.1 + - + +
22A TYR* 3.9 19.1 - - + +
58A LYS* 3.6 28.9 - - + +
59A LEU* 3.6 37.9 - - + +
62A ALA* 4.7 0.7 - - + -
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Residues in contact with MET 11 (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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1A PRO 3.4 26.8 + - - +
2A GLY* 4.7 6.5 - - - -
5A LEU* 4.7 2.3 + - - +
7A LYS* 3.0 31.2 + - + +
8A ASN* 3.5 13.0 - - - +
10A LEU* 1.3 75.2 - - - +
12A GLN* 1.3 84.9 + - + +
14A ASN* 3.3 0.7 + - - +
15A GLU* 3.0 40.1 + - + +
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Residues in contact with GLN 12 (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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8A ASN* 3.0 18.5 + - - +
9A ALA* 3.0 13.5 + - - +
11A MET* 1.3 91.0 - - + +
13A LEU* 1.3 62.8 + - + +
15A GLU* 3.6 3.5 - - - +
16A ILE* 3.1 44.9 + - + +
62A ALA 4.9 0.2 + - - -
63A GLU* 3.5 40.4 + - - +
66A LEU* 4.5 3.9 - - + +
67A ARG* 4.4 12.3 - - - +
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Residues in contact with LEU 13 (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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9A ALA 3.0 34.9 + - - +
10A LEU* 3.6 17.5 - - + +
12A GLN* 1.3 76.0 - - + +
14A ASN* 1.3 66.7 + - + +
16A ILE 4.3 0.4 - - - +
17A LYS* 2.8 34.6 + - - +
20A LEU* 3.8 19.3 - - + -
22A TYR* 3.7 22.4 - - - +
62A ALA* 3.4 37.7 - - + +
63A GLU* 4.3 0.9 - - - +
66A LEU* 3.2 35.0 - - + -
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Residues in contact with ASN 14 (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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1A PRO* 2.9 47.6 - - - +
5A LEU* 4.9 14.4 - - + +
10A LEU* 2.8 26.6 + - + +
11A MET* 3.7 4.0 - - - +
13A LEU* 1.3 76.1 - - + +
15A GLU* 1.3 60.7 + - - +
17A LYS 4.1 4.0 - - - -
18A PRO* 3.1 37.7 - - - +
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Residues in contact with GLU 15 (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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1A PRO* 2.8 36.1 - - - +
11A MET* 3.0 32.3 + - - +
12A GLN* 3.6 4.3 - - - +
14A ASN* 1.3 79.3 - - - +
16A ILE* 1.3 67.0 + - + +
18A PRO* 3.8 8.1 - - - +
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Residues in contact with ILE 16 (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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12A GLN* 3.1 37.6 + - + +
13A LEU 4.1 1.8 - - - +
15A GLU* 1.3 83.1 - - + +
17A LYS* 1.3 66.5 + - + +
18A PRO* 4.3 1.9 - - - +
66A LEU* 3.4 33.4 - - + -
69A PHE* 4.7 7.4 - - + -
70A VAL* 4.8 15.9 - - + -
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Residues in contact with LYS 17 (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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13A LEU* 2.8 22.4 + - - +
14A ASN* 3.5 1.8 - - - +
16A ILE* 1.3 80.3 - - + +
18A PRO* 1.3 59.9 - - + +
19A GLY* 2.8 13.5 + - - +
20A LEU* 3.2 28.5 + - + +
42A VAL* 2.8 22.4 + - + +
43A ASN* 2.8 28.2 + - - +
66A LEU* 3.7 19.7 - - + -
69A PHE* 3.6 22.1 - - - -
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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