Contacts of the helix formed by residues 101 - 121 (chain B) in PDB entry 1I1R
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 101 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A SER* 3.2 42.2 - - - +
166A THR 3.6 12.3 - - - +
167A VAL* 3.9 13.2 - - + +
18B TRP* 3.5 33.4 - - + -
98B ASN* 3.3 20.2 - - + +
99B VAL 3.0 0.2 + - - -
100B ASP* 1.3 83.4 + - - +
102B MET* 1.3 61.6 + - - +
103B GLU* 3.2 2.5 - - - -
104B LEU* 3.1 12.8 + - + +
105B LEU* 3.0 25.0 + - - +
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Residues in contact with MET 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B TRP* 5.1 6.3 - - - -
19B MET* 3.2 47.3 - - + -
22B VAL* 4.0 32.3 - - + -
85B PHE* 3.4 34.2 - - + -
98B ASN 3.7 9.4 - - - +
99B VAL* 3.1 15.2 + - - +
101B VAL* 1.3 78.2 - - - +
103B GLU* 1.3 60.4 + - - +
105B LEU* 3.2 31.1 - - + +
106B THR* 2.9 33.8 + - - +
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Residues in contact with GLU 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B GLU* 3.8 28.5 - - + +
85B PHE* 3.8 13.5 - - + +
86B LYS* 2.8 49.3 + - + +
89B THR* 3.6 22.3 + - - +
99B VAL 4.5 0.4 + - - -
100B ASP 3.9 17.5 - - - +
102B MET* 1.3 78.9 - - - +
104B LEU* 1.3 66.7 + - + +
106B THR* 3.5 15.5 - - - +
107B LYS* 3.7 13.3 - - - +
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Residues in contact with LEU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A TRP* 3.8 28.7 - - + -
145A HIS* 4.5 15.7 - - + +
147A PHE* 4.1 20.2 - - + -
164A TYR* 6.1 2.5 - - + -
165A SER 5.3 2.7 - - - +
167A VAL* 4.0 20.6 - - + -
100B ASP 5.8 0.7 - - - +
101B VAL* 3.1 13.4 + - + +
102B MET 3.0 0.6 - - - -
103B GLU* 1.3 88.6 - - + +
105B LEU* 1.3 66.0 + - - +
106B THR 3.3 0.2 - - - -
107B LYS* 3.1 17.8 + - + +
108B THR* 3.0 22.7 + - - -
111B TRP* 5.7 1.3 - - + -
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Residues in contact with LEU 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A VAL* 4.6 8.7 - - + +
168A TYR 4.9 3.6 - - - +
170A VAL* 5.2 0.4 - - + -
15B ARG* 3.3 60.8 - - + +
18B TRP* 3.7 29.6 - - + -
19B MET* 4.0 6.5 - - + +
101B VAL 3.0 16.1 + - - +
102B MET* 3.2 33.0 - - + +
104B LEU* 1.3 76.6 - - - +
106B THR* 1.3 56.9 + - - +
108B THR* 2.8 29.5 + - + -
109B LEU* 3.0 9.0 + - + +
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Residues in contact with THR 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B MET* 3.7 17.0 - - - +
78B PHE* 2.6 48.6 + - - +
81B PHE* 3.3 12.2 - - + +
82B GLU* 3.6 23.3 - - + +
85B PHE* 4.0 5.6 - - + -
102B MET 2.9 19.8 + - - +
103B GLU 3.5 10.8 - - - +
105B LEU* 1.3 76.8 - - - +
107B LYS* 1.3 65.6 + - - +
109B LEU* 3.2 4.7 + - - -
110B GLY 3.0 17.7 + - - -
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Residues in contact with LYS 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B PHE 4.8 0.7 - - - -
79B PHE* 3.9 16.5 - - + +
82B GLU* 3.3 39.5 - - - +
103B GLU 3.7 10.1 - - - +
104B LEU* 3.1 22.5 + - + +
106B THR* 1.3 82.6 - - + +
108B THR* 1.3 58.0 + - - +
110B GLY* 3.3 0.7 + - - -
111B TRP* 2.8 81.7 + - + +
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Residues in contact with THR 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A TRP* 3.7 24.3 - - - -
170A VAL* 3.9 12.3 - - + +
15B ARG* 2.5 52.0 - - - +
104B LEU 3.0 11.9 + - - -
105B LEU* 2.8 16.6 - - + +
107B LYS* 1.3 75.7 - - - +
109B LEU* 1.3 59.5 + - - +
111B TRP* 3.9 10.0 - - - +
112B ASP* 3.1 32.9 + - - +
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Residues in contact with LEU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 3.6 46.4 - - + +
15B ARG* 4.2 18.2 - - + +
16B LEU* 3.7 31.9 - - + +
19B MET* 3.8 26.0 - - + -
78B PHE* 3.9 17.5 - - + -
105B LEU* 3.0 14.3 + - + +
106B THR* 3.2 7.3 + - - +
108B THR* 1.3 73.5 - - - +
110B GLY* 1.3 65.8 + - - +
112B ASP* 4.9 2.0 - - - -
113B ILE* 2.9 37.6 + - + +
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Residues in contact with GLY 110 (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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75B ALA* 4.0 12.6 - - - +
78B PHE* 3.9 5.1 - - - +
79B PHE* 3.3 28.6 - - - -
106B THR 3.0 13.8 + - - -
107B LYS 3.7 1.3 - - - -
109B LEU* 1.3 77.7 - - - +
111B TRP* 1.3 50.8 + - - +
113B ILE* 3.5 0.5 - - - +
114B GLN* 2.6 39.2 + - - +
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Residues in contact with TRP 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A TRP* 3.9 25.6 - + - -
144A THR* 3.2 49.5 - - + -
145A HIS* 4.3 10.3 - + + -
79B PHE* 3.3 15.5 - + - -
104B LEU* 5.7 1.1 - - + -
107B LYS* 2.8 71.1 + - + +
108B THR* 3.9 10.3 - - - +
110B GLY* 1.3 70.4 - - - +
112B ASP* 1.3 63.6 + - - +
114B GLN* 3.1 25.1 + - - +
115B GLU* 2.9 28.9 + - - +
127B PRO* 5.0 8.0 - - + +
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Residues in contact with ASP 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B PHE* 4.0 13.6 - - + -
8B GLU* 5.5 4.5 - - - +
11B LEU* 5.5 0.9 - - - +
12B LEU* 3.5 22.1 - - + +
15B ARG* 3.1 26.1 + - - -
108B THR* 3.1 20.4 + - - +
109B LEU 4.2 0.4 - - - +
111B TRP* 1.3 80.4 - - - +
113B ILE* 1.3 62.0 + - - +
115B GLU* 3.3 26.6 + - - +
116B GLU* 3.4 5.4 + - - +
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Residues in contact with ILE 113 (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 PHE* 4.6 10.5 - - + -
12B LEU* 3.8 22.4 - - + -
16B LEU* 6.2 0.2 - - + -
71B LEU* 3.4 42.8 - - + +
74B LEU* 4.1 14.4 - - + -
75B ALA* 3.5 10.1 - - + +
78B PHE* 3.9 30.1 - - + -
109B LEU* 2.9 26.9 + - + +
110B GLY 3.8 1.1 - - - +
112B ASP* 1.3 71.7 - - - +
114B GLN* 1.3 58.5 + - - +
115B GLU 3.0 5.2 - - - -
116B GLU* 3.0 19.7 + - - +
117B LEU* 3.2 11.5 + - + +
164B ALA* 6.0 0.2 - - + -
168B LEU* 5.2 7.6 - - + -
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Residues in contact with GLN 114 (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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75B ALA* 4.3 9.0 - - + -
79B PHE* 4.2 10.5 - - + -
110B GLY 2.6 24.6 + - - +
111B TRP* 3.5 29.5 + - - +
113B ILE* 1.3 72.8 - - - +
115B GLU* 1.3 69.1 + - - +
117B LEU* 3.8 9.0 + - + +
118B ASN* 3.1 37.7 + - - +
124B HIS* 6.1 0.2 - - - -
125B TYR* 4.4 17.4 + - + +
127B PRO* 4.6 17.2 - - + +
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Residues in contact with GLU 115 (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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6B GLU* 4.1 17.8 - - - +
111B TRP 2.9 11.0 + - - +
112B ASP* 3.4 21.4 - - - +
113B ILE 3.0 0.4 - - - -
114B GLN* 1.3 88.1 - - - +
116B GLU* 1.3 65.3 + - + +
118B ASN* 3.7 4.4 + - - +
119B LYS* 3.4 25.2 + - - +
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Residues in contact with GLU 116 (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 PHE* 3.1 62.6 - - + +
67B GLU* 4.6 6.8 - - - +
71B LEU* 4.0 16.1 - - + +
112B ASP 3.4 1.6 + - - +
113B ILE 3.0 10.2 + - - +
115B GLU* 1.3 78.3 - - - +
117B LEU* 1.3 53.8 + - - +
119B LYS* 2.9 43.2 + - - +
120B LEU* 2.7 42.4 + - + +
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Residues in contact with LEU 117 (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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68B THR* 3.3 33.7 - - + +
71B LEU* 4.0 17.2 - - + +
72B LYS* 3.4 41.3 - - + +
75B ALA* 5.1 7.0 - - + -
113B ILE 3.2 6.8 + - - +
114B GLN* 3.9 10.5 - - + +
116B GLU* 1.3 77.3 - - - +
118B ASN* 1.3 53.3 + - - +
120B LEU* 2.6 27.3 + - + +
121B THR* 2.7 29.5 + - - +
125B TYR* 4.0 29.4 - - + -
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Residues in contact with ASN 118 (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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114B GLN* 3.1 38.5 + - - +
115B GLU* 4.1 4.9 - - - +
116B GLU 3.4 0.4 - - - -
117B LEU* 1.3 78.0 - - - +
119B LYS* 1.3 57.9 + - - +
121B THR 2.8 20.6 - - - +
122B LYS* 4.9 1.1 - - - -
123B THR 3.6 5.4 - - - +
124B HIS* 3.3 30.2 + - + -
125B TYR* 2.8 41.3 + - - +
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Residues in contact with LYS 119 (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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6B GLU* 3.2 41.4 + - - +
7B PHE* 4.5 1.4 - - - +
115B GLU* 3.4 14.9 + - - +
116B GLU* 2.9 39.2 + - - +
118B ASN* 1.3 79.0 - - - +
120B LEU* 1.3 60.4 + - + +
121B THR 4.2 2.1 - - - +
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Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B GLU* 3.6 37.0 - - + +
68B THR* 3.5 31.4 - - + +
71B LEU* 5.4 2.7 - - + -
116B GLU* 2.7 17.2 + - - +
117B LEU* 2.6 21.0 + - + +
119B LYS* 1.3 74.9 - - + +
121B THR* 1.3 58.5 + - - +
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Residues in contact with THR 121 (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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68B THR* 4.1 23.6 - - + +
117B LEU* 2.7 28.1 + - - +
118B ASN 2.8 20.8 - - - +
119B LYS 4.1 2.4 - - - +
120B LEU* 1.3 77.5 + - - +
122B LYS* 1.3 75.5 + - + +
123B THR* 3.2 34.8 - - - +
125B TYR* 4.6 5.9 - - + +
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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
------------------------------------------------------------
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