Contacts of the strand formed by residues 76 - 84 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64H PHE* 3.5 56.5 - - + -
74H VAL* 4.5 4.5 - - + -
75H LEU* 1.3 78.1 - - - +
77H THR* 1.3 63.9 + - - +
97H ILE* 3.3 4.9 - - - +
98H LYS* 2.8 47.8 + - + +
100H PRO* 3.9 17.0 - - + -
114H TRP* 3.8 18.8 - - + -
116H GLU* 4.3 9.4 - - + -
118H ILE* 4.3 2.8 - - + +
137H ASN* 3.6 1.1 - - - -
138H ARG* 4.0 19.1 - - + -
141H TYR* 4.0 12.8 - - + -
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Residues in contact with THR 77 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64H PHE* 4.1 3.6 - - - -
75H LEU* 4.8 6.3 - - + -
76H LEU* 1.3 82.1 - - - +
78H HIS* 1.3 61.2 + - - +
79H THR* 4.3 13.1 - - - +
95H SER* 5.5 1.3 - - - -
96H ALA 3.4 7.4 - - - -
97H ILE* 4.2 21.8 - - + -
118H ILE* 4.9 0.4 - - - -
136H ILE* 3.2 25.7 - - - +
137H ASN* 2.7 39.2 + - + +
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Residues in contact with HIS 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H TRP* 5.6 0.4 - - - -
60H SER* 2.9 51.6 + - - -
61H GLN* 3.8 1.8 - - - -
62H VAL* 3.4 37.6 - - + +
77H THR* 1.3 74.3 - - - +
79H THR* 1.3 76.7 + - - +
80H ILE* 5.0 0.6 - - - +
95H SER* 3.3 0.9 - - - -
96H ALA 3.0 30.6 + - - +
118H ILE* 3.7 34.9 + - + +
120H LEU* 3.5 16.2 - - + +
134H ALA* 4.6 8.0 - - - +
135H GLU 3.4 14.1 - - - -
136H ILE* 4.0 1.3 - - + -
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Residues in contact with THR 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77H THR* 4.3 12.6 - - - +
78H HIS* 1.3 86.7 - - - +
80H ILE* 1.3 64.3 + - - +
81H SER* 3.8 6.8 + - - -
92H ASN* 3.5 26.4 + - - +
94H LEU 3.2 10.9 + - - -
95H SER* 3.6 15.3 - - - +
120H LEU* 3.8 1.8 - - - -
133H SER 3.6 1.4 - - - +
134H ALA* 3.6 0.6 - - - -
135H GLU* 3.0 40.0 + - + +
136H ILE* 5.7 0.2 - - - -
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Residues in contact with ILE 80 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58H ILE* 3.7 34.5 - - + -
59H TYR 4.0 6.7 - - - +
60H SER* 3.8 30.1 - - - +
78H HIS* 5.0 0.4 - - - +
79H THR* 1.3 75.7 - - - +
81H SER* 1.3 68.2 + - - +
92H ASN* 3.8 1.0 - - - -
93H LEU* 2.9 35.9 + - + +
94H LEU* 2.8 35.9 + - + +
120H LEU* 4.2 12.6 - - + -
132H LEU* 4.9 2.9 - - + -
133H SER 3.0 13.9 - - - +
134H ALA* 4.4 6.3 - - + -
152H PHE* 4.3 7.0 - - + -
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Residues in contact with SER 81 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79H THR* 3.8 6.5 + - - -
80H ILE* 1.3 74.8 - - - +
82H ARG* 1.3 59.7 + - - +
83H ILE* 5.1 0.2 - - - -
90H LYS* 3.9 36.7 - - - +
91H VAL 3.5 9.2 - - - -
92H ASN* 3.1 19.9 + - - -
93H LEU* 4.6 1.3 - - - -
131H ARG 3.7 0.6 - - - +
132H LEU* 3.3 11.0 - - - +
133H SER* 2.8 38.9 + - - -
135H GLU* 5.0 2.6 + - - -
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Residues in contact with ARG 82 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81H SER* 1.3 75.4 - - - +
83H ILE* 1.3 65.3 + - - +
84H ALA* 3.8 21.7 - - + +
89H THR 3.1 3.1 - - - +
90H LYS* 3.6 0.2 - - - -
91H VAL* 2.9 38.0 + - + +
93H LEU* 3.7 25.1 - - + +
125H GLN 3.8 18.0 + - - -
126H LEU* 3.8 17.6 - - - +
127H GLU* 4.0 3.6 + - - +
130H ASP* 2.5 41.6 + - - +
131H ARG 3.5 4.9 - - - +
132H LEU* 4.1 6.1 - - + -
34I ASN* 3.2 21.1 + - - +
160L TYR* 3.3 22.8 + - - -
161L MET* 3.2 28.3 - - - +
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Residues in contact with ILE 83 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47H GLN* 4.6 5.8 - - - +
82H ARG* 1.3 77.6 - - - +
84H ALA* 1.3 64.0 + - - +
85H VAL* 5.4 0.4 - - - -
88H GLN* 3.4 42.4 - - + -
89H THR 3.6 14.1 - - - +
90H LYS* 4.2 20.9 - - + +
129H GLY 4.8 0.3 - - - +
130H ASP* 3.8 0.7 - - - -
131H ARG* 2.9 61.2 + - + +
133H SER* 4.4 10.8 - - - +
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Residues in contact with ALA 84 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82H ARG* 3.8 26.5 + - + +
83H ILE* 1.3 79.4 - - - +
85H VAL* 1.3 65.2 + - - +
86H SER 4.0 2.9 - - - +
87H TYR* 3.1 34.5 + - + +
88H GLN* 3.3 6.4 + - - -
89H THR 4.5 0.2 + - - -
91H VAL* 5.8 0.9 - - + +
127H GLU* 3.8 13.0 - - - +
130H ASP* 3.3 10.1 - - - +
160L TYR* 4.1 9.4 - - + -
161L MET* 4.9 3.4 - - + -
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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