Contacts of the strand formed by residues 5 - 15 (chain G) in PDB entry 1I3R
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 HIS 5 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3G GLU* 3.1 28.8 + - - -
4G GLU* 1.3 85.9 + - - +
6G THR* 1.3 66.5 + - - +
26G PHE* 3.6 23.5 - + + -
27G ASP* 2.7 30.1 + - - +
43H PHE* 2.8 37.3 + - + +
109H TYR* 3.7 35.9 - + + -
117H VAL* 3.7 16.6 - - + +
120H ARG* 6.2 0.7 - - - -
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Residues in contact with THR 6 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G HIS* 1.3 78.8 + - - +
7G ILE* 1.3 67.8 + - - +
8G ILE* 3.6 29.4 - - + -
25G ASP* 3.7 1.8 - - - +
26G PHE* 3.5 4.9 - - - -
27G ASP* 2.9 41.1 + - - +
28G GLY 6.2 0.2 - - - +
40H GLU* 4.6 7.4 - - + -
41H CYS 3.2 9.9 - - - +
42H HIS* 3.7 21.5 + - + -
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Residues in contact with ILE 7 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G THR* 1.3 78.3 - - - +
8G ILE* 1.3 67.5 + - - +
24G PHE* 4.1 27.6 - - + -
25G ASP 3.2 7.9 - - - +
26G PHE* 3.9 18.4 - - + -
31G ILE* 5.4 0.2 - - + -
8H PHE* 6.0 2.0 - - + -
39H SER 3.7 1.3 - - - +
40H GLU* 3.3 1.7 - - - -
41H CYS* 2.7 47.5 + - + +
43H PHE* 3.6 29.6 - - + -
105H CYS* 4.9 0.7 - - - +
108H ASN* 4.5 5.2 - - + +
109H TYR* 4.1 15.3 - - + +
112H PHE* 3.6 30.5 - - + -
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Residues in contact with ILE 8 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G THR* 3.6 20.9 - - + -
7G ILE* 1.3 84.6 - - - +
9G GLN* 1.3 72.6 + - - +
10G ALA* 3.8 6.0 + - + +
23G MET 3.5 1.4 - - - +
24G PHE* 3.2 6.7 - - - +
25G ASP* 2.7 57.8 + - + +
139G PRO* 4.9 13.5 - - + -
140G ARG 5.7 3.8 - - - +
38H LYS* 4.0 24.0 - - + -
39H SER 3.4 9.2 - - - +
40H GLU* 3.9 22.4 - - + +
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Residues in contact with GLN 9 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G ILE* 1.3 74.0 - - - +
10G ALA* 1.3 60.1 + - - +
11G GLN* 2.7 26.4 + - - +
22G PHE* 3.5 28.7 - - + -
23G MET 3.4 4.3 - - - +
24G PHE* 3.4 16.4 - - + -
62G ASN* 3.6 0.4 - - - +
7H ALA* 3.3 11.4 - - - +
8H PHE* 2.8 67.9 + - + +
10H GLU* 5.5 1.2 + - - -
37H CYS 3.6 1.7 - - - +
38H LYS* 3.3 3.1 - - - -
39H SER* 2.8 36.0 + - - +
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Residues in contact with ALA 10 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G ILE* 3.8 2.6 - - + -
9G GLN* 1.3 74.8 - - - +
11G GLN* 1.3 61.1 + - - +
12G PHE* 6.1 0.4 - - - -
21G GLU 4.0 0.9 - - - +
22G PHE* 3.5 1.6 - - - -
23G MET* 2.8 58.0 + - + +
137G PHE 5.9 0.7 - - - +
139G PRO* 4.3 15.9 - - + -
36H TYR* 4.4 7.6 - - + +
37H CYS 3.5 4.0 - - - -
38H LYS* 4.0 18.4 - - + -
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Residues in contact with GLN 11 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G GLN* 2.7 34.3 + - - +
10G ALA* 1.3 77.0 - - - +
12G PHE* 1.3 64.0 + - - +
21G GLU 3.2 13.0 - - - +
22G PHE* 3.6 13.1 - - + -
62G ASN* 3.4 31.7 + - - +
63G ILE* 4.3 2.2 - - + -
66G ASN* 2.6 35.8 + - - +
10H GLU* 3.7 15.3 + - - +
35H GLU 4.0 0.3 - - - +
36H TYR* 3.3 4.4 - - - -
37H CYS* 2.9 43.9 + - + +
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Residues in contact with PHE 12 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G ALA 6.1 0.2 - - - -
11G GLN* 1.3 79.3 - - - +
13G TYR* 1.3 66.7 + - - +
14G LEU* 4.3 5.4 - - + -
19G ARG* 3.8 21.8 - - + -
20G GLY* 3.2 7.8 - - - -
21G GLU* 3.1 63.7 + - + -
63G ILE* 3.6 9.1 - - - +
66G ASN* 4.2 4.7 + - - -
115G PRO* 3.8 31.6 - - + -
137G PHE* 4.2 8.7 - + + -
145G PHE* 4.0 19.7 - + - -
34H LEU* 3.8 18.8 - - + -
35H GLU 3.1 13.0 - - - +
36H TYR* 3.7 13.0 - + + -
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Residues in contact with TYR 13 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G PHE* 1.3 77.4 - - - +
14G LEU* 1.3 63.5 + - - +
15G LEU* 4.2 21.3 - - + +
18G LYS* 3.5 40.4 + - - +
19G ARG 3.4 17.3 - - - -
20G GLY* 4.7 0.4 - - - -
36G ILE* 5.3 3.4 - - + -
63G ILE* 3.9 21.8 - - + +
66G ASN* 4.0 21.8 - - + +
67G LYS* 3.3 57.9 - - + +
70G LEU* 3.7 16.3 - - + +
33H PHE 3.9 1.0 - - - +
34H LEU* 3.6 2.8 - - - +
35H GLU* 3.1 27.4 + - + +
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Residues in contact with LEU 14 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G PHE* 4.3 4.5 - - + -
13G TYR* 1.3 78.3 - - - +
15G LEU* 1.3 72.4 + - - +
17G ASP* 3.8 18.2 - - + +
18G LYS* 2.8 26.0 + - - -
19G ARG* 2.8 25.2 + - + +
70G LEU* 4.4 0.4 - - - -
114G PRO* 4.0 18.6 - - + -
115G PRO* 4.2 14.6 - - + +
116G VAL* 3.5 35.9 - - + -
30H ARG* 5.8 0.2 - - - +
32H TRP* 4.3 5.8 - - + -
33H PHE 3.5 22.7 - - - +
34H LEU* 3.9 15.5 - - + -
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Residues in contact with LEU 15 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G TYR* 4.2 10.5 - - + -
14G LEU* 1.3 80.4 - - - +
16G PRO* 1.3 74.9 - - + +
17G ASP* 3.4 5.4 - - - -
18G LYS* 3.7 34.3 - - + -
70G LEU* 3.6 26.0 - - + +
71G ASP* 4.3 14.4 - - - +
74G LYS* 4.2 20.0 - - + +
32H TRP* 3.4 2.9 - - - +
33H PHE* 2.9 41.6 + - + +
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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