Contacts of the strand formed by residues 76 - 84 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64C PHE* 3.5 57.7 - - + -
74C VAL* 4.5 5.2 - - + -
75C LEU* 1.3 77.5 - - - +
77C THR* 1.3 61.8 - - - +
97C ILE* 3.3 5.2 - - - +
98C LYS* 2.8 43.9 + - + +
100C PRO* 4.0 17.3 - - + -
114C TRP* 3.8 18.4 - - + -
116C GLU* 4.3 9.2 - - + -
118C ILE* 4.3 1.8 - - - +
137C ASN* 3.6 1.6 - - - -
138C ARG* 4.0 19.5 - - + -
141C TYR* 4.0 12.8 - - + -
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Residues in contact with THR 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C PHE* 4.1 3.9 - - - -
75C LEU* 4.8 5.6 - - + -
76C LEU* 1.3 80.8 - - - +
78C HIS* 1.3 60.2 + - - +
79C THR* 4.3 13.2 - - - +
95C SER* 5.5 1.3 - - - -
96C ALA 3.4 8.5 - - - -
97C ILE* 4.2 21.3 - - + -
118C ILE* 4.9 0.4 - - - -
136C ILE* 3.2 25.2 - - - +
137C ASN* 2.8 40.4 + - + +
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Residues in contact with HIS 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C SER* 2.9 51.3 + - - -
61C GLN* 3.8 1.3 - - - -
62C VAL* 3.4 38.1 - - + +
77C THR* 1.3 74.1 - - - +
79C THR* 1.3 76.5 + - - +
80C ILE* 5.0 0.6 - - - +
95C SER* 3.4 1.6 + - - -
96C ALA 3.0 30.5 + - - +
118C ILE* 3.7 34.6 + - + +
120C LEU* 3.5 16.7 - - + +
134C ALA* 4.6 7.4 - - - +
135C GLU 3.4 13.9 - - - -
136C ILE* 4.0 1.6 - - + -
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Residues in contact with THR 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C THR* 4.3 11.7 - - - +
78C HIS* 1.3 86.8 - - - +
80C ILE* 1.3 63.7 + - - +
81C SER* 3.8 7.6 + - - -
92C ASN* 3.6 24.1 + - - +
94C LEU 3.2 11.7 + - - -
95C SER* 3.7 14.6 - - - +
120C LEU* 3.8 1.3 - - - -
133C SER 3.5 1.6 - - - +
134C ALA* 3.6 0.6 - - - -
135C GLU* 3.1 39.8 + - + +
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Residues in contact with ILE 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C ILE* 3.7 33.9 - - + -
59C TYR* 3.9 7.4 - - - +
60C SER* 3.7 29.6 - - - +
78C HIS* 5.0 0.2 - - - +
79C THR* 1.3 75.7 - - - +
81C SER* 1.3 68.4 + - - +
92C ASN* 3.8 1.2 - - - -
93C LEU* 2.9 35.2 + - + +
94C LEU* 2.8 35.6 + - + +
120C LEU* 4.2 12.8 - - + -
132C LEU* 4.9 3.1 - - + -
133C SER 3.0 12.8 - - - +
134C ALA* 4.4 5.8 - - + -
152C PHE* 4.3 9.0 - - + -
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Residues in contact with SER 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C THR* 3.8 6.4 + - - -
80C ILE* 1.3 75.0 - - - +
82C ARG* 1.3 61.6 + - - +
83C ILE* 5.1 0.2 - - - -
90C LYS* 3.9 36.6 - - - +
91C VAL 3.5 8.5 - - - -
92C ASN* 3.2 19.6 + - - -
93C LEU* 4.5 2.2 - - - -
131C ARG 3.7 0.6 - - - +
132C LEU* 3.3 9.6 - - - +
133C SER* 2.8 39.1 + - - -
135C GLU* 5.1 2.8 + - - -
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Residues in contact with ARG 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ASN* 3.2 20.4 + - - +
81C SER* 1.3 76.6 - - - +
83C ILE* 1.3 64.7 + - - +
84C ALA* 3.8 18.2 + - + +
89C THR 3.2 2.9 - - - +
90C LYS* 3.6 0.2 - - - -
91C VAL* 3.0 38.6 + - + +
93C LEU* 3.7 24.7 - - + -
125C GLN 3.8 18.6 + - - -
126C LEU* 3.8 19.2 - - - +
127C GLU* 3.9 3.0 + - - +
130C ASP* 2.4 43.6 + - - +
131C ARG 3.5 4.3 - - - +
132C LEU* 4.0 5.6 - - + -
160E TYR* 3.3 24.7 + - - -
161E MET* 3.1 30.1 - - - +
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Residues in contact with ILE 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C GLN* 4.6 6.5 - - - +
82C ARG* 1.3 78.0 - - - +
84C ALA* 1.3 64.6 + - - +
85C VAL* 5.4 0.2 - - - -
88C GLN* 3.4 42.6 - - + -
89C THR* 3.7 14.1 - - - +
90C LYS* 4.2 20.0 - - + +
129C GLY 4.8 0.5 - - - +
130C ASP* 3.8 0.7 - - - -
131C ARG* 3.0 62.0 + - + +
133C SER* 4.4 10.1 - - - +
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Residues in contact with ALA 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C ARG* 3.8 25.8 + - + +
83C ILE* 1.3 78.0 - - - +
85C VAL* 1.3 66.3 + - - +
86C SER 3.1 3.4 - - - +
87C TYR* 3.1 34.5 + - + +
88C GLN* 3.2 6.6 + - - -
89C THR 4.6 0.2 + - - -
91C VAL* 5.8 0.8 - - + +
127C GLU* 3.7 11.0 - - - +
130C ASP* 3.3 13.9 - - - +
160E TYR* 4.1 9.2 - - + -
161E MET* 4.8 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