Contacts of the strand formed by residues 76 - 84 (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 LEU 76 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64G PHE* 3.5 57.4 - - + -
74G VAL* 4.4 4.7 - - + -
75G LEU* 1.3 77.9 - - - +
77G THR* 1.3 63.6 + - - +
96G ALA 4.0 0.2 - - - +
97G ILE* 3.3 5.0 - - - +
98G LYS* 2.8 44.7 + - + +
100G PRO* 3.9 17.0 - - + -
114G TRP* 3.8 18.2 - - + -
116G GLU* 4.3 9.2 - - + -
118G ILE* 4.3 2.8 - - - +
137G ASN* 3.5 1.6 - - - -
138G ARG* 4.0 18.8 - - + -
141G TYR* 4.0 13.5 - - + -
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Residues in contact with THR 77 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G PHE* 4.0 3.8 - - - -
75G LEU* 4.8 5.6 - - + -
76G LEU* 1.3 81.1 - - - +
78G HIS* 1.3 60.4 + - - +
79G THR* 4.3 13.2 - - - +
95G SER* 5.5 1.3 - - - -
96G ALA 3.4 8.5 - - - -
97G ILE* 4.2 22.0 - - + -
118G ILE* 4.9 1.1 - - - -
136G ILE* 3.2 25.1 - - - +
137G ASN* 2.7 39.7 + - + +
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Residues in contact with HIS 78 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G TRP* 5.6 0.4 - - - -
60G SER* 2.8 51.5 + - - -
61G GLN* 3.8 1.8 - - - -
62G VAL* 3.4 36.3 - - + +
77G THR* 1.3 75.0 - - - +
79G THR* 1.3 77.0 + - - +
80G ILE* 5.0 0.4 - - - +
95G SER* 3.3 1.0 - - - -
96G ALA 3.0 30.0 + - - +
118G ILE* 3.7 35.3 + - + +
120G LEU* 3.5 16.1 - - + +
134G ALA* 4.5 7.4 - - - +
135G GLU 3.4 13.9 - - - -
136G ILE* 4.0 2.0 - - + -
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Residues in contact with THR 79 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77G THR* 4.3 13.0 - - - +
78G HIS* 1.3 86.4 - - - +
80G ILE* 1.3 63.9 + - - +
81G SER* 3.8 7.1 + - - -
92G ASN* 3.6 23.9 + - - +
94G LEU 3.3 11.9 + - - -
95G SER* 3.6 14.8 - - - +
120G LEU* 3.8 1.6 - - - -
133G SER 3.6 1.6 - - - +
134G ALA* 3.6 0.6 - - - -
135G GLU* 3.0 40.2 + - + +
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Residues in contact with ILE 80 (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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58G ILE* 3.7 34.3 - - + -
59G TYR* 3.9 7.0 - - - +
60G SER* 3.7 30.1 - - - +
78G HIS* 5.0 0.4 - - - +
79G THR* 1.3 75.7 - - - +
81G SER* 1.3 68.2 + - - +
92G ASN* 3.8 1.0 - - - -
93G LEU* 2.8 37.0 + - + +
94G LEU* 2.8 34.8 + - + +
120G LEU* 4.2 12.1 - - + -
132G LEU* 4.9 2.2 - - + -
133G SER 3.0 15.0 - - - +
134G ALA* 4.4 5.6 - - + -
152G PHE* 4.3 7.0 - - + -
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Residues in contact with SER 81 (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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79G THR* 3.8 6.8 + - - -
80G ILE* 1.3 74.9 - - - +
82G ARG* 1.3 61.6 + - - +
83G ILE* 5.1 0.2 - - - -
90G LYS* 3.9 35.7 - - - +
91G VAL 3.5 10.1 - - - -
92G ASN* 3.2 19.9 + - - -
93G LEU* 4.5 2.2 - - - -
131G ARG 4.4 0.2 - - - -
132G LEU* 3.3 9.8 - - - +
133G SER* 2.8 38.2 + - - -
135G GLU* 5.1 2.4 + - - -
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Residues in contact with ARG 82 (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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81G SER* 1.3 75.4 - - - +
83G ILE* 1.3 64.7 + - - +
84G ALA* 3.8 18.3 - - + +
89G THR 3.1 2.8 - - - +
90G LYS* 3.6 0.4 - - - -
91G VAL* 3.0 37.1 + - + +
93G LEU* 3.7 24.6 - - + +
125G GLN 3.9 16.9 + - - -
126G LEU* 3.9 18.1 - - - +
127G GLU* 3.9 2.2 - - - +
130G ASP* 2.4 43.8 + - - +
131G ARG 3.5 4.5 - - - +
132G LEU* 4.0 5.8 - - + -
34H ASN* 3.1 20.3 + - - +
160K TYR* 3.2 25.7 + - - -
161K MET* 3.0 30.3 - - - +
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Residues in contact with ILE 83 (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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47G GLN* 4.6 5.8 - - - +
81G SER 5.1 0.2 - - - +
82G ARG* 1.3 79.0 - - - +
84G ALA* 1.3 63.9 + - - +
85G VAL* 5.4 0.4 - - - -
88G GLN* 3.4 43.3 - - + -
89G THR* 3.7 14.6 - - - +
90G LYS* 4.2 19.7 - - + +
129G GLY 4.8 0.3 - - - +
130G ASP* 3.8 0.5 - - - -
131G ARG* 3.0 60.9 + - + +
133G SER* 4.4 10.3 - - - +
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Residues in contact with ALA 84 (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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82G ARG* 3.8 25.4 + - + +
83G ILE* 1.3 78.4 - - - +
85G VAL* 1.3 65.7 + - - +
86G SER 4.0 2.2 - - - +
87G TYR* 3.1 32.7 + - + +
88G GLN* 3.2 6.6 + - - -
89G THR 4.6 0.4 + - - -
91G VAL* 5.8 1.3 - - + +
127G GLU* 3.7 13.2 - - - +
130G ASP* 3.3 10.1 - - - +
160K TYR* 4.0 11.7 - - + -
161K MET* 4.9 3.6 - - + -
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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