Contacts of the strand formed by residues 79 - 85 (chain B) in PDB entry 7CE1
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 VAL 79 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A HIS* 6.2 0.4 - - - +
113A VAL* 5.9 1.8 - - + -
67B ARG* 5.3 2.9 - - - +
71B ARG* 4.3 8.3 - - - +
77B THR* 3.2 30.5 + - - +
78B ASN* 1.3 78.6 - - - +
80B ILE* 1.3 65.5 + - - +
110B TYR* 4.1 0.4 - - - -
111B HIS* 3.5 15.9 - - + +
113B VAL* 3.5 37.0 - - + +
135B SER 3.3 22.0 - - - +
136B ALA* 3.5 2.8 - - - -
137B ASP* 2.8 31.9 + - - +
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Residues in contact with ILE 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B VAL* 1.3 74.8 - - - +
81B ALA* 1.3 66.1 + - - +
101B ILE* 5.4 1.1 - - + -
105B LEU* 3.8 21.3 - - + -
110B TYR* 3.6 22.7 - - + -
111B HIS 2.7 14.0 + - - +
112B LEU* 3.3 22.6 - - + +
113B VAL 2.9 26.4 + - - +
138B GLY 3.6 9.4 - - - +
140B ILE* 4.2 8.5 - - + -
323B LEU* 3.9 26.7 - - + -
324B LEU* 4.9 5.4 - - + -
327B ILE* 3.5 32.5 - - + -
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Residues in contact with ALA 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B VAL 4.1 1.2 + - - -
80B ILE* 1.3 74.1 - - - +
82B LEU* 1.3 54.1 + - - +
83B VAL* 3.9 0.9 - - + -
113B VAL* 3.4 12.8 - - + -
115B THR* 4.0 15.9 - - - +
130B ILE* 4.0 15.5 - - + -
136B ALA* 3.9 17.9 - - + +
138B GLY 2.9 15.2 + - - +
139B VAL* 3.2 8.9 - - + +
140B ILE* 2.7 34.0 + - - +
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Residues in contact with LEU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B ILE 3.8 0.4 + - - -
81B ALA* 1.3 71.4 - - - +
83B VAL* 1.3 69.6 + - - +
84B LEU* 3.9 20.4 + - + +
97B MET* 4.4 15.0 - - + -
98B VAL* 4.2 22.9 - - + -
101B ILE* 3.7 25.1 - - + -
112B LEU* 4.0 23.6 - - + -
113B VAL 2.9 12.3 + - - +
114B VAL* 3.5 12.0 - - + +
115B THR 2.9 24.8 + - - +
140B ILE* 3.6 31.9 - - + +
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Residues in contact with VAL 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B ALA 4.7 1.6 - - - +
82B LEU* 1.3 81.5 - - - +
84B LEU* 1.3 63.1 + - - +
115B THR* 3.2 27.4 - - - +
117B HIS* 4.1 13.7 - - + +
126B PRO* 3.9 23.3 - - + -
127B ILE* 4.1 15.0 - - + -
130B ILE* 5.0 7.9 - - + -
139B VAL* 3.8 22.4 - - + -
140B ILE 2.7 25.1 + - - +
141B ILE* 3.9 20.0 - - + +
142B SER* 4.1 6.8 + - - -
150B ARG* 5.6 2.5 - - - +
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Residues in contact with LEU 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A SER* 5.9 1.3 - - - -
98A VAL* 5.4 10.1 - - + -
99A PHE* 3.9 32.5 - - + -
82B LEU* 3.9 22.4 + - + +
83B VAL* 1.3 81.8 - - - +
85B SER* 1.3 65.6 + - - +
86B VAL 3.3 2.9 + - - -
88B GLU* 5.0 2.7 - - - +
94B THR* 3.6 31.0 - - + -
97B MET* 4.0 18.2 - - + -
98B VAL* 5.2 4.7 - - + -
114B VAL* 5.5 7.6 - - + -
115B THR 3.4 5.3 + - - +
116B PRO* 3.9 14.0 - - + +
117B HIS* 3.6 15.8 + - - -
142B SER* 4.7 6.7 - - - +
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Residues in contact with SER 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A PHE* 3.4 12.2 - - - -
83B VAL 4.4 0.2 + - - -
84B LEU* 1.3 74.9 - - - +
86B VAL* 1.3 63.8 + - - +
87B ASP* 2.4 34.6 + - - +
88B GLU* 4.1 8.4 - - - +
117B HIS* 3.7 20.4 + - - -
142B SER* 4.2 9.9 + - - -
143B LYS* 3.5 32.0 - - - +
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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