Contacts of the helix formed by residues 61 - 71 (chain B) in PDB entry 2XGZ
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 VAL 61 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9B SER* 3.7 18.8 + - - +
17B PRO* 3.9 17.1 - - + +
18B THR* 3.7 28.7 - - - +
19B VAL* 4.0 7.9 - - + -
48B MET 4.0 6.5 - - - +
49B ARG* 3.5 29.6 - - - +
50B ASP* 3.6 1.6 - - - -
56B TRP* 5.0 0.8 - - - -
59B LYS 4.2 0.2 - - - +
60B GLY* 1.3 74.0 - - - +
62B LEU* 1.3 64.9 + - - +
63B HIS 3.2 3.1 - - - -
64B ALA* 3.2 4.9 + - + -
65B VAL* 2.9 26.9 + - + +
108B ASN* 3.9 18.8 - - - +
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Residues in contact with LEU 62 (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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9B SER* 3.8 17.3 - - - +
50B ASP* 2.8 19.9 + - - +
55B LYS* 5.7 4.5 - - + -
56B TRP* 3.8 33.0 - - + -
61B VAL* 1.3 77.4 - - - +
63B HIS* 1.3 59.4 + - + +
65B VAL* 3.8 7.5 - - + +
66B LYS* 2.9 29.6 + - - +
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Residues in contact with HIS 63 (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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48B MET* 3.6 24.8 - - + +
49B ARG 4.6 2.2 + - - -
50B ASP* 2.9 44.6 + - + +
62B LEU* 1.3 77.4 - - + +
64B ALA* 1.3 55.4 - - - +
66B LYS* 3.1 19.3 + - - +
67B ASN* 2.8 38.6 + - - +
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Residues in contact with ALA 64 (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 VAL* 3.8 9.9 - - + -
48B MET* 3.9 14.2 + - + +
61B VAL 3.2 8.2 + - - +
63B HIS* 1.3 76.4 - - - +
65B VAL* 1.3 63.4 + - - +
67B ASN* 3.1 5.1 + - - +
68B VAL* 3.0 26.1 + - - +
105B LEU 4.3 11.9 - - - -
108B ASN* 3.6 37.9 - - - +
109B ALA* 3.7 6.3 - - + +
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Residues in contact with VAL 65 (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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7B ALA* 3.4 23.1 - - + +
8B ARG* 3.7 29.4 - - - +
9B SER* 3.8 11.9 - - - +
19B VAL* 4.3 8.3 - - + -
61B VAL* 2.9 27.3 + - + +
62B LEU* 3.8 8.7 - - + +
64B ALA* 1.3 74.2 - - - +
66B LYS* 1.3 59.3 + - - +
68B VAL* 3.2 4.0 + - - +
69B ASN* 3.0 45.2 + - - +
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Residues in contact with LYS 66 (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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62B LEU 2.9 19.2 + - - +
63B HIS* 3.5 19.7 - - - +
65B VAL* 1.3 76.0 - - - +
67B ASN* 1.3 62.4 + - - +
69B ASN* 4.4 5.4 - - - +
70B ASP* 2.7 59.8 + - + +
71B VAL* 6.2 0.4 - - + -
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Residues in contact with ASN 67 (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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48B MET* 3.4 26.5 - - - +
63B HIS* 2.8 15.4 + - - +
64B ALA 3.1 8.0 + - - +
66B LYS* 1.3 76.9 - - - +
68B VAL* 1.3 58.2 + - - +
71B VAL* 3.1 22.1 + - - +
72B ILE* 2.9 28.0 + - - +
104B LYS 3.7 2.8 + - - -
105B LEU* 2.9 51.0 + - + +
109B ALA* 4.5 2.9 - - + -
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Residues in contact with VAL 68 (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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5B VAL* 3.8 26.5 - - + -
6B TYR* 4.3 2.0 - - - -
7B ALA* 3.5 36.1 - - + +
19B VAL* 4.6 2.0 - - + -
21B VAL* 4.2 7.9 - - + -
64B ALA 3.0 14.2 + - - +
65B VAL 3.6 0.4 - - - +
67B ASN* 1.3 75.6 - - - +
69B ASN* 1.3 59.7 + - - +
72B ILE* 4.0 8.5 - - + -
73B ALA* 2.8 33.6 + - - +
109B ALA* 3.7 34.1 - - + +
113B VAL* 4.2 7.0 - - + -
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Residues in contact with ASN 69 (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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5B VAL 4.2 1.4 - - - +
6B TYR* 3.4 24.6 - - - -
7B ALA 2.9 44.5 + - - -
65B VAL* 3.0 28.5 + - - +
66B LYS* 3.1 3.7 + - - +
68B VAL* 1.3 74.0 - - - +
70B ASP* 1.3 69.7 + - - +
73B ALA* 3.7 7.7 - - - +
74B PRO* 3.6 13.9 - - - +
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Residues in contact with ASP 70 (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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66B LYS* 2.7 49.6 + - + +
69B ASN* 1.3 84.9 - - - +
71B VAL* 1.3 64.8 + - + +
74B PRO* 3.4 15.9 - - - +
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Residues in contact with VAL 71 (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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66B LYS* 6.2 0.2 - - + -
67B ASN* 3.1 28.2 + - - +
70B ASP* 1.3 86.2 - - + +
72B ILE* 1.3 70.3 + - - +
73B ALA 3.4 1.1 - - - -
74B PRO* 3.6 8.3 - - - +
75B ALA* 3.7 15.9 + - - +
96B LEU* 4.1 16.9 - - + +
104B LYS* 6.1 2.2 - - - +
105B LEU* 3.9 23.8 - - + -
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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