Contacts of the strand formed by residues 151 - 156 (chain G) in PDB entry 3IT8
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 TYR 151 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G HIS* 3.4 33.9 - + + +
16G VAL 3.3 10.5 - - - +
17G VAL* 4.6 3.4 - - + -
28G TRP* 3.6 5.2 - - - -
59G TYR* 3.7 13.9 - + - -
60G SER* 3.0 6.8 + - - -
61G GLN* 2.8 72.1 + - + +
119G TYR* 3.6 6.3 - + - -
148G GLY* 3.5 29.6 - - - -
150G VAL* 1.3 79.6 - - - +
152G PHE* 1.3 62.2 + - - +
93I LEU 5.0 0.2 - - - -
94I LEU* 3.4 18.0 - - + +
120I LEU* 4.1 2.1 - - - +
121I GLY 3.0 40.7 + - - -
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Residues in contact with PHE 152 (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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15G HIS* 4.5 1.3 - - - -
16G VAL* 2.7 46.1 + - + +
28G TRP* 3.6 33.9 - + + -
46G ASN 5.3 0.2 - - - -
47G GLN* 5.2 1.3 - - - -
48G LEU* 3.4 36.9 - - + +
58G ILE* 4.2 20.2 - - + -
59G TYR* 3.3 16.8 - - - -
60G SER* 4.0 2.5 - - - +
80G ILE* 4.3 5.4 - - + -
132G LEU* 3.9 33.9 - - + -
133G SER* 4.1 1.1 - - - -
134G ALA* 3.5 32.8 - - + -
151G TYR* 1.3 78.7 - - - +
153G GLY* 1.3 67.6 - - - +
154G ILE* 4.6 0.7 - - + -
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Residues in contact with GLY 153 (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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14G ALA 2.9 13.9 - - - -
15G HIS* 4.0 0.4 - - - -
48G LEU* 4.4 2.7 - - - -
58G ILE* 4.1 0.3 - - - +
59G TYR* 2.9 51.8 + - - +
152G PHE* 1.3 78.8 - - - +
154G ILE* 1.3 72.6 + - - +
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Residues in contact with ILE 154 (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 VAL* 3.3 6.0 - - - +
14G ALA* 2.8 40.6 + - + +
41G VAL* 4.8 12.8 - - + -
48G LEU* 4.0 27.4 - - + -
50G VAL* 4.1 11.2 - - + -
56G TYR* 4.0 23.1 - - + -
57G LEU 3.0 9.9 - - - +
58G ILE* 3.9 17.7 - - + -
59G TYR* 4.0 2.8 - - - -
132G LEU* 3.8 33.4 - - + -
152G PHE* 4.6 1.3 - - + -
153G GLY* 1.3 80.9 - - - +
155G ILE* 1.3 61.8 + - - +
123I VAL* 5.6 0.2 - - - -
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Residues in contact with ILE 155 (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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11G LYS* 4.1 14.8 - - + -
12G PRO 3.8 4.0 - - - +
13G VAL* 3.5 28.9 - - + -
56G TYR* 3.5 4.5 - - - -
57G LEU* 2.9 55.2 + - + +
59G TYR* 5.3 0.4 - - + -
154G ILE* 1.3 75.1 - - - +
156G ALA* 1.3 72.8 + - - +
157G LEU* 3.4 5.0 + - + -
55I LEU* 3.9 17.9 - - + -
123I VAL* 3.9 28.7 - - + -
157I LEU* 3.9 22.2 - - + -
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Residues in contact with ALA 156 (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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11G LYS* 3.2 28.3 + - + +
12G PRO* 3.0 46.9 + - + +
54G GLY* 6.5 0.2 - - - -
55G LEU 3.7 7.4 - - - +
56G TYR* 3.7 17.4 - - + -
155G ILE* 1.3 74.1 - - - +
157G LEU* 1.3 61.0 + - - +
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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