Contacts of the helix formed by residues 94 - 114 (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 PHE 94 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235I ASN 3.5 17.7 - - - -
236I LYS* 3.2 33.7 - - + -
237I ASN 4.2 0.2 - - - -
238I LEU 3.6 9.6 - - - -
239I ALA* 3.5 35.2 - - - +
240I HIS* 5.1 3.1 - + - -
417I PHE* 3.5 34.0 - + + -
418I GLU* 6.1 4.5 - - + -
88J TYR* 4.0 4.5 - - - -
91J GLY 4.5 9.6 - - - -
93J ILE* 1.3 81.1 - - - +
95J LEU* 1.3 67.4 + - - +
96J PRO* 3.4 8.3 - - + -
97J ASN* 3.1 33.4 + - - +
98J VAL* 3.5 6.4 + - - +
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Residues in contact with LEU 95 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177I LEU* 4.4 15.5 - - + +
229I ILE* 5.1 1.3 - - + -
236I LYS 2.9 9.5 + - - -
237I ASN* 3.4 29.4 - - + +
88J TYR* 3.6 23.1 - - + +
94J PHE* 1.3 70.2 - - - +
96J PRO* 1.4 69.8 - - + +
98J VAL* 2.9 19.7 + - + +
99J MET* 3.0 27.1 + - + +
142J ILE* 3.7 50.0 - - + -
146J LEU* 4.3 15.7 - - + -
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Residues in contact with PRO 96 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176I VAL 4.3 3.4 - - - +
177I LEU* 3.2 23.5 - - - +
178I ARG* 4.3 0.2 - - - -
179I ASN* 3.3 43.3 - - - +
237I ASN 3.3 21.8 - - - +
238I LEU* 4.1 15.0 - - + -
239I ALA 5.5 0.4 - - - +
94J PHE* 3.5 13.5 - - + -
95J LEU* 1.4 89.3 - - + +
97J ASN* 1.3 55.1 + - - +
99J MET* 3.2 2.8 + - - +
100J MET* 3.0 33.7 + - - +
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Residues in contact with ASN 97 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179I ASN* 4.2 14.0 + - - +
417I PHE* 3.4 21.9 - - - -
48J PHE* 4.8 4.8 - - + +
93J ILE* 3.9 22.7 - - + -
94J PHE* 3.1 39.7 + - - +
96J PRO* 1.3 76.8 - - - +
98J VAL* 1.3 57.6 + - - +
100J MET* 3.5 11.4 + - - +
101J SER* 2.9 32.9 + - - -
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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
----------------------------------------------------------
81J MET* 3.5 17.7 - - + +
84J VAL* 3.8 11.9 - - + -
85J ILE* 5.7 5.2 - - + +
88J TYR* 3.6 40.6 - - + -
93J ILE* 3.8 9.2 - - + -
94J PHE 3.8 10.1 - - - +
95J LEU* 2.9 12.9 + - + +
97J ASN* 1.3 72.7 - - - +
99J MET* 1.3 57.6 + - - +
101J SER 3.4 0.7 + - - -
102J ALA* 2.7 33.5 + - + +
145J ALA 5.9 0.2 - - - +
146J LEU* 3.7 26.5 - - + -
149J ALA* 4.9 5.2 - - + -
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Residues in contact with MET 99 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177I LEU* 3.1 45.5 - - + +
178I ARG* 3.7 39.0 - - + +
95J LEU* 3.0 31.0 + - + +
96J PRO 3.4 2.2 - - - +
98J VAL* 1.3 73.6 - - - +
100J MET* 1.3 55.5 - - - +
102J ALA* 3.2 5.2 + - + +
103J ASP* 2.8 42.1 + - - +
141J ASN* 5.0 3.1 - - + +
142J ILE* 5.1 4.7 - - - -
145J ALA* 3.6 33.2 - - + -
146J LEU* 5.3 3.4 - - - -
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Residues in contact with MET 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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178I ARG* 3.3 34.3 - - + +
179I ASN* 4.4 13.2 - - - +
49J GLU 4.0 19.1 - - - +
50J GLY* 3.9 17.5 - - - +
52J GLU* 5.4 0.3 - - - +
96J PRO 3.0 17.6 + - - +
97J ASN* 3.8 10.5 - - - +
98J VAL 3.4 0.2 - - - -
99J MET* 1.3 74.8 - - - +
101J SER* 1.3 57.2 + - - +
103J ASP* 3.4 10.1 + - - +
104J ALA* 2.9 29.1 + - - +
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Residues in contact with SER 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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47J ILE* 2.7 31.2 + - - +
48J PHE 3.4 10.6 + - - -
50J GLY* 4.2 1.7 - - - -
81J MET* 3.8 16.4 - - - -
84J VAL* 3.6 19.3 - - - +
97J ASN 2.9 18.8 + - - -
98J VAL 3.5 4.0 - - - -
100J MET* 1.3 74.5 - - - +
102J ALA* 1.3 60.1 + - - +
104J ALA* 3.0 3.9 + - - +
105J MET* 2.8 30.1 + - - +
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Residues in contact with ALA 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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81J MET* 3.5 18.1 - - + +
98J VAL* 2.7 22.7 + - + +
99J MET* 3.5 9.0 - - + +
101J SER* 1.3 71.1 - - - +
103J ASP* 1.3 60.6 + - - +
105J MET* 3.1 7.1 + - + +
106J LEU* 2.9 36.2 + - + +
145J ALA* 4.4 14.4 - - + +
148J ARG* 6.3 0.7 - - + -
149J ALA* 4.2 13.9 - - + +
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Residues in contact with ASP 103 (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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174I TYR* 4.6 3.8 + - - -
178I ARG* 2.7 47.7 + - - +
52J GLU* 5.1 6.7 - - - +
99J MET* 2.8 24.4 + - - +
100J MET* 3.5 8.0 - - - +
102J ALA* 1.3 75.6 - - - +
104J ALA* 1.3 60.0 + - - +
105J MET 3.3 0.9 + - - -
106J LEU* 3.6 11.7 + - - +
107J GLU* 3.4 25.8 + - - +
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Residues in contact with ALA 104 (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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46J ALA 4.6 1.1 - - - +
47J ILE* 4.9 2.2 - - - +
50J GLY* 3.8 28.5 - - - +
51J GLU 4.2 0.9 - - - +
52J GLU* 3.9 23.2 + - + +
55J VAL* 3.6 25.8 - - + +
100J MET 2.9 16.4 + - - +
101J SER* 3.5 5.4 - - - +
103J ASP* 1.3 75.8 - - - +
105J MET* 1.3 59.1 + - - +
107J GLU* 3.9 4.2 - - - +
108J GLY 3.5 12.6 + - - -
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Residues in contact with MET 105 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47J ILE* 4.2 13.5 - - + -
77J LEU* 3.9 29.2 - - + +
78J MET* 4.2 19.5 - - - +
81J MET* 4.0 26.9 - - + -
101J SER 2.8 14.8 + - - +
102J ALA* 3.1 10.3 + - + +
104J ALA* 1.3 76.8 - - - +
106J LEU* 1.3 85.8 + - + +
107J GLU 3.0 1.6 - - - -
108J GLY* 2.9 4.4 + - - -
109J ILE* 2.8 40.7 + - + +
148J ARG 3.9 20.4 - - - +
149J ALA* 4.5 6.1 - - - -
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Residues in contact with LEU 106 (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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102J ALA* 2.9 20.7 + - + +
103J ASP* 4.1 11.2 - - - +
105J MET* 1.3 89.4 - - + +
107J GLU* 1.3 56.3 + - - +
109J ILE* 3.4 17.9 + - + +
110J GLU* 3.0 31.0 + - - +
148J ARG* 4.4 36.3 - - + +
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Residues in contact with GLU 107 (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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52J GLU* 3.4 36.7 - - + +
56J VAL* 4.6 12.7 - - + +
103J ASP 3.4 16.1 + - - +
104J ALA 3.9 6.3 - - - +
105J MET 3.0 0.4 - - - -
106J LEU* 1.3 77.6 - - - +
108J GLY* 1.3 62.8 + - - +
110J GLU* 3.9 16.0 - - + +
111J TYR* 3.2 23.6 + - - +
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Residues in contact with GLY 108 (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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55J VAL* 3.9 12.5 - - - +
56J VAL* 5.2 1.6 - - - -
59J LEU* 3.7 20.7 - - - +
77J LEU* 3.6 9.0 - - - -
104J ALA 3.5 4.9 + - - -
105J MET 2.9 7.3 + - - -
107J GLU* 1.3 77.1 - - - +
109J ILE* 1.3 64.8 + - - +
111J TYR* 3.3 5.4 + - - +
112J CYS* 3.1 26.2 + - - -
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Residues in contact with ILE 109 (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* 4.3 28.5 - - + +
77J LEU* 3.5 16.5 - - + +
78J MET* 5.6 4.0 - - - -
105J MET* 2.8 41.4 + - + +
106J LEU* 3.5 22.4 - - + +
108J GLY* 1.3 75.0 - - - +
110J GLU* 1.3 58.5 + - - +
112J CYS* 3.0 21.6 + - - +
113J LYS* 3.1 34.5 + - + +
120J PRO* 5.3 3.6 - - + -
148J ARG 5.6 1.1 - - - +
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Residues in contact with GLU 110 (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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106J LEU 3.0 20.0 + - - +
107J GLU* 3.9 18.8 - - + +
109J ILE* 1.3 72.5 - - - +
111J TYR* 1.3 64.6 + - - +
113J LYS* 3.7 35.4 - - + +
114J GLU* 3.8 16.8 - - - +
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Residues in contact with TYR 111 (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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56J VAL* 3.7 33.2 - - + -
59J LEU* 4.5 16.4 - - + -
60J GLN* 2.7 43.0 + - + +
63J ILE* 4.3 14.2 - - + +
107J GLU 3.2 18.5 + - - +
108J GLY* 3.5 7.0 - - - +
109J ILE 3.2 0.4 - - - -
110J GLU* 1.3 76.7 - - - +
112J CYS* 1.3 66.0 + - - +
113J LYS 3.2 0.2 - - - -
114J GLU* 3.3 32.7 + - - +
115J ASN* 2.9 39.6 + - - -
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Residues in contact with CYS 112 (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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59J LEU* 3.9 27.8 - - - -
63J ILE* 6.3 4.0 - - - -
69J PRO* 3.7 26.9 - - - +
70J ILE* 5.4 1.1 - - - +
72J LEU* 4.5 4.9 - - - -
73J ILE* 4.3 21.1 - - + -
77J LEU* 4.4 3.1 - - - -
108J GLY 3.1 19.1 + - - -
109J ILE 3.0 9.9 + - - +
111J TYR* 1.3 79.7 - - - +
113J LYS* 1.3 61.6 + - - +
115J ASN* 3.2 19.2 + - - +
116J SER* 3.5 14.5 + - - -
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Residues in contact with LYS 113 (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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70J ILE* 6.0 0.2 - - - -
73J ILE* 5.9 0.2 - - - +
109J ILE* 3.1 33.8 + - + +
110J GLU* 3.7 25.9 - - + +
112J CYS* 1.3 77.2 - - - +
114J GLU* 1.3 61.5 + - + +
116J SER* 3.2 22.4 + - - +
117J GLY 3.9 3.8 + - - -
120J PRO* 4.5 29.2 - - + -
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Residues in contact with GLU 114 (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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110J GLU* 3.8 17.9 + - - +
111J TYR* 3.3 34.7 + - - +
112J CYS 3.2 0.4 - - - -
113J LYS* 1.3 78.0 - - + +
115J ASN* 1.3 66.0 + - - +
116J SER 3.5 0.9 + - - -
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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