Contacts of the helix formed by residues 80 - 92 (chain A) in PDB entry 2XAR
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 ASN 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A VAL* 3.7 11.2 - - - +
78A SER* 3.4 4.5 - - - -
79A PRO* 1.3 88.7 - - - +
81A LYS* 1.3 59.9 + - - +
82A GLU* 3.0 17.3 + - - +
83A VAL* 2.6 34.8 + - - +
84A LEU* 3.1 23.2 + - - +
107A ARG* 4.0 12.5 - - - +
140A HIS* 5.6 2.2 - - + +
141A ASP* 3.8 13.3 + - - +
142A SER* 3.5 22.8 + - - -
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Residues in contact with LYS 81 (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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42A GLN* 3.5 32.7 + - - +
48A ASP* 5.2 7.3 + - - -
59A SER 4.8 4.6 + - - -
60A VAL* 4.2 33.2 - - + +
80A ASN* 1.3 74.6 - - - +
82A GLU* 1.3 60.1 + - - +
84A LEU* 3.4 14.9 - - + +
85A GLU* 2.9 30.3 + - - +
137A ASP* 5.9 0.4 + - - -
140A HIS* 4.0 19.0 + - + +
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Residues in contact with GLU 82 (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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40A ARG 5.5 1.5 - - - +
42A GLN* 3.8 25.6 + - - +
80A ASN* 3.0 12.0 + - - +
81A LYS* 1.3 82.5 + - - +
83A VAL* 1.3 56.8 + - - +
85A GLU* 3.4 5.9 + - - +
86A GLN* 3.0 26.0 + - - +
107A ARG* 4.5 9.9 - - + -
140A HIS* 3.0 34.2 + - - +
142A SER* 3.6 43.7 - - - +
143A ALA* 3.7 13.5 - - - +
144A LEU* 3.9 17.6 - - + +
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Residues in contact with VAL 83 (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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78A SER* 3.5 17.0 - - - +
79A PRO* 3.7 27.1 - - + -
80A ASN* 2.6 17.1 + - - +
82A GLU* 1.3 69.5 - - - +
84A LEU* 1.3 57.1 + - - +
86A GLN* 3.4 22.6 - - - +
87A ARG* 2.7 53.8 + - + +
107A ARG* 3.6 26.0 - - - +
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Residues in contact with LEU 84 (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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60A VAL* 3.6 26.5 - - + +
61A LEU* 4.0 15.3 - - + -
75A LEU* 3.6 36.1 - - + +
78A SER* 3.8 11.2 - - - -
80A ASN 3.1 15.5 + - - +
81A LYS* 3.4 20.2 - - + +
83A VAL* 1.3 78.0 - - - +
85A GLU* 1.3 58.8 + - - +
87A ARG* 4.9 0.9 - - - -
88A TYR* 3.0 29.5 + - - +
410A LEU* 3.7 32.1 - - + -
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Residues in contact with GLU 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ASN* 5.1 2.4 - - - +
40A ARG* 4.5 19.8 + - - +
42A GLN* 4.6 14.2 + - - +
81A LYS 2.9 17.0 + - - +
82A GLU* 3.6 6.1 - - - +
84A LEU* 1.3 75.4 - - - +
86A GLN* 1.3 64.6 + - - +
88A TYR* 3.5 3.7 + - - +
89A VAL* 3.1 31.0 + - + +
144A LEU* 4.5 10.3 - - + -
408A LEU 4.1 8.9 - - - +
409A SER* 3.4 25.4 + - - -
410A LEU* 3.0 38.6 + - - +
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Residues in contact with GLN 86 (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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82A GLU 3.0 14.1 + - - +
83A VAL* 3.4 29.3 - - - +
85A GLU* 1.3 77.7 - - - +
87A ARG* 1.3 61.5 + - + +
89A VAL* 3.3 3.5 + - - +
90A GLN* 3.0 30.5 + - + +
104A ALA* 3.9 21.7 - - + +
105A GLY 2.7 30.6 + - - +
106A VAL* 4.1 2.6 - - - +
107A ARG* 4.0 17.9 - - - +
144A LEU* 4.7 6.5 - - + +
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Residues in contact with ARG 87 (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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74A GLU* 2.8 45.9 + - + +
75A LEU* 3.6 16.6 - - + +
77A SER* 3.3 21.6 + - - -
78A SER* 3.5 9.7 + - - +
79A PRO* 4.4 4.4 - - - +
83A VAL* 2.7 39.4 + - + +
84A LEU 4.1 0.2 - - - +
86A GLN* 1.3 76.4 - - + +
88A TYR* 1.3 57.1 + - - +
90A GLN* 4.2 3.1 - - + -
91A ASN* 2.8 53.8 + - - +
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Residues in contact with TYR 88 (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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69A TRP* 3.6 23.9 - + - -
75A LEU* 3.3 17.2 - - + +
84A LEU 3.0 18.4 + - - +
85A GLU* 3.6 7.2 - - - +
87A ARG* 1.3 73.6 - - - +
89A VAL* 1.3 63.0 + - + +
92A VAL* 2.9 49.8 + - + +
93A ILE* 3.1 28.1 + - + +
361A LEU 3.8 2.3 + - - -
362A ILE* 3.6 16.8 - - - +
365A THR* 2.6 36.1 + - + -
408A LEU 4.2 9.4 - - - -
409A SER 3.8 2.5 - - - -
410A LEU* 3.8 41.8 - - + +
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Residues in contact with VAL 89 (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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85A GLU* 3.1 15.5 + - + +
86A GLN* 3.7 7.0 - - - +
88A TYR* 1.3 79.2 - - + +
90A GLN* 1.3 56.9 + - - +
93A ILE* 3.3 8.5 + - + +
94A ILE* 2.8 36.2 + - + +
102A VAL* 3.7 29.2 - - + -
103A ASP 4.5 1.1 - - - +
104A ALA* 3.8 26.5 - - + +
408A LEU* 3.5 39.3 - - + +
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Residues in contact with GLN 90 (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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86A GLN* 3.0 20.3 + - + +
87A ARG* 3.9 4.9 - - + +
88A TYR 3.2 0.2 - - - -
89A VAL* 1.3 78.1 - - - +
91A ASN* 1.3 69.6 + - - +
94A ILE* 3.6 37.8 - - - +
95A PRO* 3.6 4.2 - - - +
99A PRO* 6.2 0.6 - - - +
104A ALA* 3.6 20.3 + - + +
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Residues in contact with ASN 91 (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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72A ASN* 4.8 4.7 - - - +
74A GLU* 3.4 44.9 - - + +
75A LEU* 5.6 0.4 - - + -
87A ARG* 2.8 39.6 + - - +
90A GLN* 1.3 85.2 - - - +
92A VAL* 1.3 63.3 + - + +
95A PRO* 3.5 16.8 - - - +
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Residues in contact with VAL 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A TRP* 4.2 9.4 - - + -
72A ASN* 4.2 15.9 - - - +
75A LEU* 4.1 17.7 - - + -
88A TYR* 2.9 41.1 + - + +
91A ASN* 1.3 86.8 - - + +
93A ILE* 1.3 65.1 + - + +
94A ILE 3.8 0.2 - - - -
95A PRO* 3.8 2.9 - - - +
96A LEU* 3.3 27.4 - - + +
358A LYS* 6.3 0.4 - - - -
362A ILE* 3.8 31.4 - - + +
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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