Contacts of the helix formed by residues 90 - 102 (chain J) in PDB entry 2XQL
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 THR 90 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44I GLY* 5.0 6.1 - - - +
47I ALA* 4.3 1.8 - - - -
86J ARG* 4.9 8.3 + - - -
88J THR* 3.4 16.1 + - - +
89J ILE* 1.3 76.5 - - - +
91J SER* 1.3 76.5 + - - +
92J ARG* 3.0 19.5 - - + +
93J GLU* 2.8 34.8 + - - +
94J ILE* 3.5 8.8 + - - +
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Residues in contact with SER 91 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46I GLY* 3.8 29.4 - - - -
47I ALA* 4.1 5.0 - - - +
50I TYR* 4.1 19.5 - - - -
90J THR* 1.3 80.6 - - - +
92J ARG* 1.3 64.7 + - - +
93J GLU 3.0 2.9 - - - -
94J ILE* 3.1 13.8 + - - +
95J GLN* 3.0 23.9 + - - +
118J VAL* 4.7 9.0 - - - +
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Residues in contact with ARG 92 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90J THR* 3.0 15.1 - - + +
91J SER* 1.3 84.3 + - - +
93J GLU* 1.3 66.7 + - - +
95J GLN* 3.9 14.2 - - - +
96J THR* 3.2 32.5 + - - +
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Residues in contact with GLU 93 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77J ALA* 3.9 30.9 - - + +
80J LEU* 3.6 22.0 - - + +
81J ALA* 4.3 13.3 - - + +
84J ASN* 5.7 3.5 - - - +
86J ARG* 5.2 10.5 + - - +
88J THR 4.6 5.4 - - - -
89J ILE* 4.3 2.5 - - + -
90J THR* 2.8 54.0 + - - +
91J SER 3.0 0.4 - - - -
92J ARG* 1.3 87.2 + - - +
94J ILE* 1.3 60.3 + - - +
95J GLN 3.1 1.3 - - - -
96J THR 3.4 0.3 + - - -
97J ALA* 2.8 31.7 + - - +
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Residues in contact with ILE 94 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34I LEU* 5.1 5.4 - - + -
47I ALA* 4.0 18.2 - - + +
50I TYR* 3.6 22.9 - - + -
51I LEU* 3.9 40.8 - - + +
54I VAL* 5.2 0.2 - - + -
73J ILE* 4.1 8.5 - - + +
74J ALA* 5.6 0.9 - - - -
77J ALA* 4.0 10.8 - - + -
89J ILE* 3.9 21.8 - - + -
90J THR 3.6 11.4 - - - +
91J SER* 3.1 13.7 + - - +
93J GLU* 1.3 76.0 - - - +
95J GLN* 1.3 57.4 + - - +
97J ALA* 3.5 6.7 + - - +
98J VAL* 2.9 36.8 + - + +
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Residues in contact with GLN 95 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50I TYR* 2.6 40.4 + - + +
91J SER 3.0 15.2 + - - +
92J ARG* 3.9 15.2 - - - +
93J GLU 3.1 0.2 - - - -
94J ILE* 1.3 75.7 - - - +
96J THR* 1.3 61.7 + - - +
98J VAL* 3.0 5.6 + - - +
99J ARG* 2.9 49.2 + - - +
111J VAL* 3.2 23.1 - - + +
115J THR* 3.3 14.5 + - - +
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Residues in contact with THR 96 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80J LEU* 3.5 30.1 - - + -
92J ARG* 3.2 27.7 + - - +
93J GLU* 4.7 0.2 - - - -
95J GLN* 1.3 75.7 - - - +
97J ALA* 1.3 66.3 + - - +
99J ARG* 3.1 14.1 + - + +
100J LEU* 3.0 36.1 + - + +
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Residues in contact with ALA 97 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73J ILE* 3.6 30.1 - - + +
76J GLU* 3.9 10.3 - - + -
77J ALA* 3.7 12.3 - - - +
80J LEU* 3.7 6.0 - - + +
93J GLU 2.8 19.3 + - - +
94J ILE* 3.5 6.1 - - - +
96J THR* 1.3 78.0 - - - +
98J VAL* 1.3 56.6 + - - +
100J LEU* 3.2 4.1 + - - +
101J LEU* 2.9 36.8 + - - +
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Residues in contact with VAL 98 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50I TYR* 4.6 1.8 - - + -
54I VAL* 3.9 23.1 - - + -
73J ILE* 3.9 27.1 - - + -
94J ILE* 2.9 23.0 + - + +
95J GLN* 3.0 10.7 + - - +
97J ALA* 1.3 75.1 - - - +
99J ARG* 1.3 65.1 + - - +
101J LEU* 4.6 0.4 - - - +
102J LEU* 3.0 34.5 + - + +
107J ALA* 4.0 11.5 - - - +
110J ALA* 3.8 26.7 - - + -
111J VAL* 4.1 10.8 - - + +
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Residues in contact with ARG 99 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95J GLN* 2.9 45.2 + - - +
96J THR* 3.1 16.7 + - + +
98J VAL* 1.3 79.3 - - - +
100J LEU* 1.3 65.9 + - + +
102J LEU 3.5 13.0 - - - +
107J ALA* 4.6 9.1 - - + +
108J LYS* 6.0 3.0 - - - +
111J VAL* 3.7 28.3 - - + +
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Residues in contact with LEU 100 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76J GLU* 3.9 24.7 - - + +
80J LEU* 4.4 10.5 - - + -
96J THR* 3.0 38.2 + - + +
97J ALA* 3.6 4.9 - - - +
99J ARG* 1.3 80.8 - - + +
101J LEU* 1.3 66.1 + - + +
102J LEU 4.6 0.9 - - - +
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Residues in contact with LEU 101 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96I LEU* 3.8 9.8 - - + +
72J ARG* 3.3 55.1 + - + +
73J ILE* 3.5 19.1 - - + +
76J GLU* 3.7 24.9 - - + +
97J ALA 2.9 18.3 + - - +
100J LEU* 1.3 80.0 - - + +
102J LEU* 1.3 73.1 + - + +
103J PRO* 3.4 8.8 - - - +
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Residues in contact with LEU 102 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54I VAL* 4.4 2.5 - - + -
58I LEU* 3.9 31.9 - - + -
96I LEU* 3.9 22.7 - - + -
69J ILE* 5.1 2.7 - - + -
73J ILE* 4.8 14.1 - - + -
98J VAL* 3.0 22.7 + - + +
99J ARG 3.5 14.6 - - - +
100J LEU 4.6 1.0 - - - +
101J LEU* 1.3 89.9 - - + +
103J PRO* 1.4 71.8 - - + +
106J LEU* 3.9 12.3 - - + +
107J ALA* 3.6 13.6 - - + +
110J ALA* 3.8 29.6 - - + -
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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