Contacts of the helix formed by residues 77 - 93 (chain P) in PDB entry 2IMW
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 ARG 77 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16P GLU* 2.8 33.0 + - - +
19P LEU* 3.6 28.4 - - - +
75P PRO* 3.6 20.8 + - + +
76P MET* 1.3 71.7 - - - +
78P LYS* 1.3 58.6 + - - +
79P GLU* 3.2 15.3 - - - +
80P VAL* 2.9 43.3 + - + +
81P TYR* 3.1 29.3 + - + +
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Residues in contact with LYS 78 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12P TYR* 3.0 37.1 + - + +
76P MET* 3.7 11.8 - - + +
77P ARG* 1.3 75.4 - - - +
79P GLU* 1.3 60.3 + - + +
81P TYR* 3.2 7.6 + - - +
82P GLN* 2.8 40.5 + - + +
104P ILE* 3.8 20.9 - - + -
502P EDO 2.0 50.4 + - - +
1801S G 5.9 2.6 - - - +
1802S G 5.2 3.0 + - - -
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Residues in contact with GLU 79 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76P MET 4.4 2.6 - - - +
77P ARG* 3.4 15.2 - - - +
78P LYS* 1.3 96.7 + - + +
80P VAL* 1.3 75.8 + - + +
82P GLN* 3.5 6.5 + - - +
83P GLN* 3.2 26.7 + - - +
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Residues in contact with VAL 80 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15P VAL* 4.1 13.7 - - + -
19P LEU* 3.8 27.6 - - + -
77P ARG* 2.9 42.2 + - + +
79P GLU* 1.3 82.5 - - + +
81P TYR* 1.3 68.6 + - + +
83P GLN* 3.2 15.1 + - - +
84P VAL* 3.2 16.6 + - + +
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Residues in contact with TYR 81 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11P PHE* 3.5 22.0 - - + -
12P TYR* 3.3 62.8 - + + -
15P VAL* 3.6 24.2 - - + -
16P GLU* 2.6 35.9 + - - +
30P VAL* 3.8 6.6 - - - +
75P PRO 3.8 1.0 + - - -
76P MET* 3.8 9.9 - - + -
77P ARG* 3.1 43.4 + - + -
78P LYS* 3.7 8.5 - - - +
80P VAL* 1.3 78.2 - - + +
82P GLN* 1.3 58.3 + - - +
84P VAL* 3.4 5.2 + - - -
85P SER* 2.8 30.0 + - - -
104P ILE* 4.0 3.6 - - + -
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Residues in contact with GLN 82 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78P LYS* 2.8 22.2 + - + +
79P GLU* 3.7 7.9 - - - +
81P TYR* 1.3 78.3 - - - +
83P GLN* 1.3 65.2 + - - +
85P SER* 3.3 10.3 + - - -
86P SER* 2.9 42.6 + - - +
104P ILE* 3.7 25.1 - - + +
242P ARG* 5.3 8.9 + - - -
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Residues in contact with GLN 83 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79P GLU 3.2 11.1 + - - +
80P VAL* 3.2 11.2 + - - +
82P GLN* 1.3 83.2 - - - +
84P VAL* 1.3 65.9 + - + +
86P SER* 3.3 15.0 + - - -
87P ARG* 3.2 42.5 + - - +
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Residues in contact with VAL 84 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11P PHE* 4.1 11.4 - - + -
15P VAL* 3.9 28.0 - - + -
18P VAL* 6.5 0.7 - - + -
19P LEU* 5.2 6.7 - - + -
80P VAL* 3.2 18.2 + - + +
81P TYR 3.7 5.6 - - - +
83P GLN* 1.3 74.5 - - + +
85P SER* 1.3 63.5 + - - +
87P ARG* 3.2 26.7 + - - +
88P ILE* 3.1 37.1 + - + +
136P GLU* 4.0 16.8 - - - +
138P ILE* 4.5 7.4 - - + -
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Residues in contact with SER 85 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8P PHE* 4.3 5.6 - - - -
11P PHE* 3.8 9.6 - - - -
81P TYR 2.8 21.9 + - - -
82P GLN* 3.5 10.4 + - - -
84P VAL* 1.3 74.0 - - - +
86P SER* 1.3 63.0 + - - +
88P ILE* 3.0 4.3 + - - +
89P MET* 2.9 33.7 + - - +
101P ILE* 5.9 0.2 - - - +
104P ILE* 2.5 44.9 + - - +
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Residues in contact with SER 86 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82P GLN* 2.9 35.4 + - - +
83P GLN* 3.3 19.6 + - - -
85P SER* 1.3 75.3 - - - +
87P ARG* 1.3 59.1 + - - +
89P MET* 3.8 8.0 - - - +
90P ASN* 3.0 39.4 + - - +
93P ARG* 5.1 1.1 + - - +
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Residues in contact with ARG 87 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19P LEU* 6.3 0.4 - - - +
83P GLN* 3.4 31.8 + - - +
84P VAL* 3.2 28.6 + - - +
86P SER* 1.3 78.4 - - - +
88P ILE* 1.3 62.1 + - - +
90P ASN* 3.4 11.3 + - - +
91P LEU* 3.2 27.4 + - - +
136P GLU* 2.8 44.4 + - - +
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Residues in contact with ILE 88 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8P PHE* 3.3 41.7 - - + -
11P PHE* 4.2 2.0 - - + -
84P VAL* 3.3 28.7 - - + +
85P SER 3.0 6.5 + - - +
87P ARG* 1.3 75.0 - - - +
89P MET* 1.3 64.5 + - - +
91P LEU* 3.0 11.7 + - + +
92P LEU* 3.0 22.4 + - + +
132P ILE* 3.9 28.3 - - + -
136P GLU* 3.9 18.6 - - + -
138P ILE* 4.1 30.5 - - + -
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Residues in contact with MET 89 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8P PHE* 3.5 27.6 - - + -
85P SER* 2.9 22.4 + - - +
86P SER* 3.8 7.0 - - - +
88P ILE* 1.3 75.5 - - - +
90P ASN* 1.3 62.0 + - - +
92P LEU* 3.1 19.8 + - - +
93P ARG* 3.2 35.8 + - - +
99P ILE* 4.2 2.2 - - + +
101P ILE* 3.9 23.3 - - + -
103P SER 3.6 16.6 - - - +
104P ILE 3.6 18.2 - - - +
106P GLU 3.9 16.8 - - - +
107P ALA* 3.8 20.6 - - + -
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Residues in contact with ASN 90 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86P SER* 3.0 29.3 + - - +
87P ARG* 3.6 9.0 - - - +
88P ILE 3.2 0.4 - - - -
89P MET* 1.3 76.4 - - - +
91P LEU* 1.3 62.0 + - + +
92P LEU 3.5 0.3 + - - -
93P ARG* 3.1 38.2 + - - +
94P GLU* 3.4 19.3 - - - +
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Residues in contact with LEU 91 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87P ARG 3.2 17.0 + - - +
88P ILE* 3.0 17.3 + - + +
90P ASN* 1.3 78.6 - - + +
92P LEU* 1.3 58.4 + - + +
94P GLU* 3.0 31.7 - - + +
95P TYR* 3.4 12.7 - - - -
131P LYS* 4.5 20.9 - - + +
132P ILE* 4.6 13.5 - - + -
135P LYS* 3.8 44.2 - - + -
136P GLU* 4.5 10.5 - - + +
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Residues in contact with LEU 92 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6P VAL* 4.1 18.6 - - + -
8P PHE* 4.6 9.2 - - + -
88P ILE* 3.0 16.2 + - + +
89P MET* 3.1 22.2 + - - +
91P LEU* 1.3 73.2 - - - +
93P ARG* 1.3 56.9 + - - +
94P GLU 3.0 5.8 - - - -
95P TYR* 2.9 28.0 + - + +
96P SER 3.6 4.3 + - - +
99P ILE* 3.9 10.1 - - + -
107P ALA* 3.9 28.5 - - + -
109P LEU* 3.6 21.4 - - + +
128P ILE* 3.6 32.3 - - + -
132P ILE* 4.0 12.1 - - + -
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Residues in contact with ARG 93 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86P SER* 5.1 1.2 + - - +
89P MET* 3.2 21.4 + - - +
90P ASN* 3.1 35.3 + - - +
91P LEU 3.3 0.6 - - - -
92P LEU* 1.3 75.0 - - - +
94P GLU* 1.3 60.2 + - - +
95P TYR 3.2 1.8 - - - -
96P SER 3.2 24.4 - - - +
97P GLU* 4.4 5.2 + - - +
99P ILE* 4.1 27.1 - - + +
101P ILE* 3.5 33.0 - - - +
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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