Contacts of the strand formed by residues 19 - 26 (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 ARG 19 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G PHE* 3.8 13.4 - - + -
13G TYR* 3.4 6.1 - - - -
14G LEU* 2.8 36.7 + - + -
17G ASP* 3.7 28.9 + - + -
18G LYS* 1.3 96.0 + - - +
20G GLY* 1.3 57.3 + - - +
21G GLU* 6.1 0.7 - - + -
36G ILE* 4.0 9.0 - - - +
37G GLU* 2.9 46.7 + - - +
115G PRO 5.7 0.9 - - - +
116G VAL* 4.8 9.9 - - + -
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Residues in contact with GLY 20 (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* 3.2 14.3 - - - -
13G TYR* 4.2 7.2 - - - -
19G ARG* 1.3 77.6 - - - +
21G GLU* 1.3 70.6 + - - +
36G ILE* 2.8 46.6 + - - +
63G ILE* 4.3 1.8 - - - -
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Residues in contact with GLU 21 (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 4.5 0.7 - - - -
11G GLN* 3.2 3.4 - - - -
12G PHE* 3.1 48.6 + - + -
19G ARG* 6.1 0.7 - - + -
20G GLY* 1.3 80.9 - - - +
22G PHE* 1.3 61.8 + - - +
23G MET* 6.2 1.8 - - + -
33G HIS* 6.1 2.5 - - + -
34G VAL 4.4 4.7 - - - +
36G ILE* 4.2 3.1 - - - -
63G ILE* 3.1 10.3 - - - +
136G VAL* 3.3 26.6 - - + +
137G PHE* 3.1 54.5 + - - +
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Residues in contact with PHE 22 (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* 3.5 44.9 - - + -
10G ALA 3.5 4.3 - - - -
11G GLN* 3.6 19.5 - - + -
21G GLU* 1.3 76.0 - - - +
23G MET* 1.3 66.8 + - - +
24G PHE* 3.8 21.3 - + - -
32G PHE* 4.1 3.4 - + - -
33G HIS* 3.0 5.8 - - - +
34G VAL* 2.8 42.2 + - + +
36G ILE* 5.8 0.2 - - + -
54G PHE* 3.8 21.3 - + - -
59G ALA* 3.5 39.0 - - + -
62G ASN* 4.2 9.2 - - + -
63G ILE* 4.3 7.9 - - + -
7H ALA* 3.9 11.7 - - + -
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Residues in contact with MET 23 (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* 3.4 5.0 - - - +
10G ALA* 2.8 52.3 + - + +
21G GLU* 6.2 2.2 - - + -
22G PHE* 1.3 80.5 - - - +
24G PHE* 1.3 89.8 + - - +
25G ASP* 3.9 12.6 - - + +
30G GLU* 3.7 24.7 - - + +
32G PHE* 3.2 15.0 - - - +
33G HIS* 3.6 10.8 - - + +
136G VAL* 4.7 5.8 - - + -
137G PHE 4.6 11.7 - - - +
138G LEU* 3.8 17.9 - - + -
139G PRO* 3.8 22.0 - - + -
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Residues in contact with PHE 24 (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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7G ILE* 4.1 23.8 - - + -
8G ILE 3.2 3.4 - - - -
9G GLN* 3.4 35.9 - - + -
22G PHE* 3.8 12.8 - + - -
23G MET* 1.3 90.2 - - - +
25G ASP* 1.3 60.4 + - - +
31G ILE* 3.0 30.8 + - + -
32G PHE* 3.0 46.0 + + + +
54G PHE* 5.0 0.7 - + - -
5H ILE* 3.9 10.1 - - + -
6H THR 3.6 20.2 - - - -
7H ALA* 4.5 1.6 - - + -
8H PHE* 5.2 5.4 - + - -
108H ASN* 3.7 22.2 - - - -
112H PHE* 4.2 11.9 - + - -
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Residues in contact with ASP 25 (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* 4.6 2.1 - - - +
7G ILE* 3.2 10.9 - - - +
8G ILE* 2.7 55.2 + - + +
23G MET* 3.9 15.2 - - + +
24G PHE* 1.3 76.5 - - - +
26G PHE* 1.3 62.0 + - - +
27G ASP 3.5 1.6 + - - -
28G GLY* 2.7 47.6 + - - +
29G ASP 3.3 10.4 + - - +
30G GLU 4.2 0.7 + - - -
31G ILE* 4.2 3.0 - - - +
138G LEU* 5.7 1.4 - - - +
139G PRO* 4.2 16.5 - - + +
146G ARG* 4.5 2.3 + - - -
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Residues in contact with PHE 26 (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* 3.6 29.6 - + + -
6G THR 3.5 2.0 - - - -
7G ILE* 3.9 26.5 - - + -
25G ASP* 1.3 74.3 + - - +
27G ASP* 1.3 91.8 + - - +
28G GLY 3.1 0.4 - - - -
29G ASP* 2.6 26.8 + - - +
31G ILE* 3.8 14.5 - - + +
109H TYR* 5.2 2.2 - + - -
112H PHE* 4.8 4.3 - + + -
116H LEU* 4.0 27.6 - - + -
117H VAL* 4.0 25.1 - - + -
149H TYR* 3.8 9.4 - - - -
179H TRP* 3.5 31.0 - + + -
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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