Contacts of the helix formed by residues 76 - 90 (chain J) in PDB entry 2I2X
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 ALA 76 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40J ILE* 3.8 14.4 - - + +
43J ILE* 3.7 43.1 - - + +
44J ALA 4.5 3.5 + - - -
47J ILE* 4.4 0.5 - - - +
59J LEU* 4.9 0.2 - - + -
72J LEU* 2.9 27.1 + - + +
75J ASP* 1.3 80.1 - - - +
77J LEU* 1.3 59.3 + - + +
78J MET 3.7 0.4 - - - -
79J VAL* 4.1 0.6 - - - +
80J GLY* 3.0 25.6 + - - -
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Residues in contact with LEU 77 (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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43J ILE* 3.8 10.8 - - + -
47J ILE* 3.7 25.7 - - + +
55J VAL* 3.8 9.0 - - + -
59J LEU* 3.8 23.1 - - + -
72J LEU 3.1 9.1 + - - +
73J ILE* 3.5 20.0 - - + +
76J ALA* 1.3 72.8 - - - +
78J MET* 1.3 62.3 + - + +
80J GLY* 3.3 1.6 + - - -
81J MET* 2.9 30.5 + - - +
105J MET* 3.9 18.0 - - + +
108J GLY* 3.6 8.3 - - - +
109J ILE* 3.5 41.1 - - + +
112J CYS* 4.4 5.8 - - - -
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Residues in contact with MET 78 (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* 2.8 36.1 + - + +
74J ASP* 3.9 19.3 - - - +
77J LEU* 1.3 70.0 - - + +
79J VAL* 1.3 60.6 + - - +
81J MET* 3.8 2.3 - - - +
82J GLY* 2.9 24.8 + - - -
85J ILE* 5.6 2.5 - - + -
105J MET* 4.2 19.3 - - - +
109J ILE* 5.6 2.9 - - - -
123J LYS* 5.1 8.5 - - - +
148J ARG 5.0 0.4 - - - +
149J ALA 4.1 8.3 - - - +
150J ASN* 3.6 9.0 - - - +
151J GLY* 3.5 40.4 - - - +
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Residues in contact with VAL 79 (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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35J PRO* 4.0 32.5 - - + -
74J ASP 3.4 19.1 + - - +
75J ASP* 3.8 19.3 - - - +
76J ALA 3.9 2.0 + - - +
77J LEU 3.3 0.6 - - - -
78J MET* 1.3 75.5 - - + +
80J GLY* 1.3 65.3 + - - +
82J GLY* 3.4 9.0 + - - +
83J VAL* 3.4 16.4 + - + +
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Residues in contact with GLY 80 (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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44J ALA* 3.6 34.7 - - - +
47J ILE* 3.6 14.1 - - - +
48J PHE* 5.7 0.2 - - - +
76J ALA 3.0 15.8 + - - -
77J LEU 3.7 1.3 - - - -
79J VAL* 1.3 78.3 - - - +
81J MET* 1.3 59.0 + - - +
83J VAL* 3.3 19.7 + - - +
84J VAL* 3.5 6.1 + - - +
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Residues in contact with MET 81 (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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47J ILE* 3.8 8.2 - - + +
77J LEU 2.9 18.2 + - - +
78J MET* 3.9 5.8 - - - +
80J GLY* 1.3 73.5 - - - +
82J GLY* 1.3 60.9 + - - +
84J VAL* 3.1 18.3 + - + +
85J ILE* 2.9 35.9 + - + +
98J VAL* 3.5 30.3 - - + +
101J SER* 3.8 19.7 - - - +
102J ALA* 3.5 20.4 - - - +
105J MET* 4.0 17.9 - - - +
149J ALA* 3.3 44.4 - - + +
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Residues in contact with GLY 82 (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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78J MET 2.9 17.6 + - - -
79J VAL* 3.4 4.9 + - - -
80J GLY 3.2 0.6 - - - -
81J MET* 1.3 74.7 - - - +
83J VAL* 1.3 63.4 + - - +
85J ILE* 3.8 13.6 - - - +
86J ARG* 3.2 23.4 + - - +
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Residues in contact with VAL 83 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30J ALA* 4.3 15.3 - - + +
33J LEU* 3.5 44.6 - - + +
34J TYR* 4.5 15.5 - - + +
35J PRO* 5.0 2.9 - - + -
48J PHE* 5.2 3.1 - - + -
79J VAL* 3.4 15.3 + - + +
80J GLY* 3.3 12.0 + - - +
81J MET 3.2 0.4 - - - -
82J GLY* 1.3 76.2 - - - +
84J VAL* 1.3 63.4 + - + +
86J ARG* 3.4 5.0 + - - +
87J LEU* 3.1 46.7 + - + +
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Residues in contact with VAL 84 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47J ILE* 3.9 13.7 - - + -
48J PHE* 3.9 20.6 - - + -
80J GLY 3.7 13.5 - - - +
81J MET* 3.1 15.8 + - + +
83J VAL* 1.3 74.5 - - + +
85J ILE* 1.3 65.2 + - - +
87J LEU* 3.2 5.3 + - - -
88J TYR* 3.0 22.9 + - - +
93J ILE* 3.6 25.5 - - + +
98J VAL* 3.8 18.8 - - + -
101J SER* 3.6 30.1 - - - +
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Residues in contact with ILE 85 (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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78J MET* 5.4 3.4 - - + +
81J MET* 2.9 33.6 + - + +
82J GLY* 3.8 10.5 - - - +
84J VAL* 1.3 75.7 - - - +
86J ARG* 1.3 61.3 + - - +
88J TYR* 3.6 9.6 + - + +
89J ASP* 3.0 41.5 + - - +
98J VAL* 5.6 4.5 - - + -
146J LEU* 6.1 3.6 - - + -
149J ALA* 3.4 26.5 - - + +
150J ASN* 3.7 37.5 - - - +
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Residues in contact with ARG 86 (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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33J LEU* 3.4 48.1 - - + +
82J GLY 3.2 16.9 + - - +
83J VAL* 3.6 4.3 - - - +
84J VAL 3.2 0.6 - - - -
85J ILE* 1.3 81.6 - - - +
87J LEU* 1.3 58.2 + - - +
89J ASP* 3.1 22.7 + - - +
90J GLU* 2.8 41.0 + - - +
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Residues in contact with LEU 87 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26J PRO 4.5 0.4 - - - +
29J ALA* 3.9 16.8 - - + +
30J ALA* 4.0 9.2 - - + +
33J LEU* 3.7 24.0 - - + -
48J PHE* 3.7 30.7 - - + -
83J VAL* 3.1 34.3 + - + +
84J VAL* 3.2 4.0 + - - +
86J ARG* 1.3 72.6 - - + +
88J TYR* 1.3 58.6 + - - +
90J GLU* 3.6 13.8 + - - +
91J GLY 3.1 5.2 + - - -
92J VAL* 2.8 57.3 + - + +
93J ILE* 3.3 9.1 + - + -
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Residues in contact with TYR 88 (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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236I LYS* 2.9 56.1 + - + -
237I ASN* 2.8 19.6 + - - -
84J VAL 3.0 15.8 + - - +
85J ILE* 3.7 9.0 - - + +
87J LEU* 1.3 77.5 - - - +
89J ASP* 1.3 60.1 + - - +
91J GLY* 2.9 12.6 + - - -
93J ILE* 3.5 19.6 - - + +
94J PHE 4.0 1.3 - - - -
95J LEU* 3.6 24.4 - - + +
98J VAL* 3.6 22.4 - - + -
142J ILE* 5.4 2.6 - - - +
146J LEU* 4.3 31.0 - - + -
230J GLU* 3.8 10.7 + - + +
231J ALA* 5.6 2.8 - - + +
232J ALA* 4.4 15.2 + - + -
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Residues in contact with ASP 89 (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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236I LYS* 3.2 18.0 + - - +
85J ILE* 3.0 30.0 + - - +
86J ARG* 3.1 12.6 + - - +
88J TYR* 1.3 82.1 - - - +
90J GLU* 1.3 60.9 + - + +
232J ALA* 4.7 16.5 - - - +
236J LYS* 4.7 17.9 - - - +
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Residues in contact with GLU 90 (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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236I LYS* 4.8 0.4 - - - -
22J LYS* 3.9 28.5 + - - +
33J LEU* 5.7 0.9 - - - +
86J ARG* 2.8 54.6 + - - +
87J LEU* 4.1 8.2 - - - +
89J ASP* 1.3 77.5 - - + +
91J GLY* 1.3 62.1 + - - +
92J VAL* 3.4 21.8 + - + +
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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