Contacts of the strand formed by residues 76 - 84 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64I PHE* 3.5 57.2 - - + -
74I VAL* 4.4 5.2 - - + -
75I LEU* 1.3 78.9 - - - +
77I THR* 1.3 63.9 + - - +
97I ILE* 3.3 5.0 - - - +
98I LYS* 2.8 46.9 + - + +
100I PRO* 3.9 16.6 - - + -
114I TRP* 3.8 18.8 - - + -
116I GLU* 4.3 9.0 - - + -
118I ILE* 4.2 2.6 - - - +
137I ASN* 3.6 1.8 - - - -
138I ARG* 4.0 18.8 - - + -
141I TYR* 4.0 13.2 - - + -
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Residues in contact with THR 77 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64I PHE* 4.1 3.3 - - - -
75I LEU* 4.8 5.6 - - + -
76I LEU* 1.3 80.6 - - - +
78I HIS* 1.3 60.6 + - - +
79I THR* 4.3 14.5 - - - +
95I SER* 5.5 1.3 - - - -
96I ALA 3.4 8.5 - - - -
97I ILE* 4.2 22.2 - - + -
118I ILE* 4.9 0.4 - - - -
136I ILE* 3.2 24.6 - - - +
137I ASN* 2.7 40.0 + - + +
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Residues in contact with HIS 78 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28I TRP* 5.6 0.2 - - - -
60I SER* 2.9 51.0 + - - -
61I GLN* 3.8 1.8 - - - -
62I VAL* 3.4 36.5 - - + +
77I THR* 1.3 74.9 - - - +
79I THR* 1.3 77.6 + - - +
80I ILE* 5.0 0.6 - - - +
95I SER* 3.3 0.9 - - - -
96I ALA 3.0 31.2 + - - +
118I ILE* 3.7 35.2 + - + +
120I LEU* 3.5 15.2 - - + +
134I ALA* 4.6 7.4 - - - +
135I GLU 3.4 13.7 - - - -
136I ILE* 4.0 2.0 - - + -
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Residues in contact with THR 79 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77I THR* 4.3 11.9 - - - +
78I HIS* 1.3 87.0 - - - +
80I ILE* 1.3 64.5 + - - +
81I SER* 3.8 7.6 + - - -
92I ASN* 3.6 24.6 + - - +
94I LEU 3.2 11.3 + - - -
95I SER* 3.6 15.3 - - - +
120I LEU* 3.8 1.8 - - - -
133I SER 3.6 1.4 - - - +
134I ALA* 3.6 0.9 - - - -
135I GLU* 3.0 40.0 + - + +
136I ILE* 5.7 0.2 - - - -
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Residues in contact with ILE 80 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58I ILE* 3.7 35.0 - - + -
59I TYR 3.9 6.7 - - - +
60I SER* 3.8 29.6 - - - +
78I HIS* 5.0 0.2 - - - +
79I THR* 1.3 75.1 - - - +
81I SER* 1.3 68.5 + - - +
92I ASN* 3.8 1.7 - - - -
93I LEU* 2.9 35.8 + - + +
94I LEU* 2.8 35.8 + - + +
120I LEU* 4.2 12.8 - - + -
132I LEU* 4.9 2.7 - - + -
133I SER 3.0 14.1 - - - +
134I ALA* 4.4 5.8 - - + -
152I PHE* 4.3 6.3 - - + -
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Residues in contact with SER 81 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79I THR* 3.8 5.9 + - - -
80I ILE* 1.3 75.6 - - - +
82I ARG* 1.3 61.5 + - - +
90I LYS* 3.8 35.8 - - - +
91I VAL 3.5 10.3 - - - -
92I ASN* 3.1 19.4 + - - -
93I LEU* 4.5 2.2 - - - -
131I ARG 3.7 0.6 - - - +
132I LEU* 3.3 9.1 - - - +
133I SER* 2.8 39.0 + - - -
135I GLU* 5.0 2.6 + - - -
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Residues in contact with ARG 82 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34G ASN* 3.3 18.9 + - - +
81I SER* 1.3 74.8 - - - +
83I ILE* 1.3 65.5 + - - +
84I ALA* 3.7 20.4 + - + +
89I THR 3.1 3.1 - - - +
90I LYS* 3.6 0.5 - - - -
91I VAL* 3.0 37.4 + - + +
93I LEU* 3.7 25.5 - - + +
125I GLN 3.9 17.6 + - - -
126I LEU* 3.8 18.7 - - - +
127I GLU* 3.9 4.9 + - - +
130I ASP* 2.4 43.6 + - - -
131I ARG 3.5 5.6 - - - +
132I LEU* 4.0 4.7 - - + -
160J TYR* 3.5 21.2 + - - -
161J MET* 3.0 31.7 - - - +
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Residues in contact with ILE 83 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47I GLN* 4.6 6.5 - - - +
82I ARG* 1.3 78.1 - - - +
84I ALA* 1.3 63.9 + - - +
85I VAL* 5.5 0.4 - - - -
88I GLN* 3.4 44.0 - - + -
89I THR* 3.7 14.8 - - - +
90I LYS* 4.2 20.2 - - + +
129I GLY 4.8 0.3 - - - +
130I ASP* 3.8 1.0 - - - -
131I ARG* 2.9 60.0 + - + +
133I SER* 4.4 10.5 - - - +
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Residues in contact with ALA 84 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82I ARG* 3.7 27.4 + - + +
83I ILE* 1.3 78.8 - - - +
85I VAL* 1.3 65.3 - - - +
86I SER 3.1 3.6 - - - +
87I TYR* 3.1 37.6 + - + +
88I GLN* 3.2 6.2 + - - -
89I THR 4.6 0.2 + - - -
91I VAL* 5.8 1.5 - - + +
127I GLU* 3.7 10.8 - - - +
130I ASP* 3.2 13.7 - - - +
160J TYR* 4.5 4.5 - - + -
161J MET* 5.0 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