Contacts of the strand formed by residues 87 - 92 (chain A) in PDB entry 3CBG
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 GLN 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A LYS 2.7 11.1 + - - +
63A GLN* 3.7 20.4 - - - +
64A VAL* 2.9 28.6 + - - +
82A LEU* 3.8 1.2 - - - +
85A ASP 3.7 6.0 + - - +
86A GLY* 1.3 78.6 - - - +
88A ILE* 1.3 77.7 + - - +
89A ILE* 4.3 5.8 - - + +
112A GLU 3.8 15.1 - - - +
113A LYS 3.4 12.0 + - - -
114A ILE 4.7 0.4 - - - -
115A SER* 4.3 13.9 - - - +
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Residues in contact with ILE 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A VAL* 3.3 24.0 - - + +
66A GLU* 4.4 12.3 - - + -
75A ALA* 3.5 31.9 - - + +
78A MET* 4.1 13.2 - - + -
79A ALA* 3.8 21.8 - - + +
82A LEU* 3.4 18.2 - - + -
87A GLN* 1.3 75.3 + - - +
89A ILE* 1.3 71.7 + - - +
90A ALA* 3.6 3.5 + - + +
113A LYS 2.6 14.7 + - - +
114A ILE* 3.3 14.8 - - + -
115A SER* 2.6 34.1 + - - -
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Residues in contact with ILE 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A VAL 2.9 9.5 + - - +
65A LEU* 3.3 24.5 - - + +
66A GLU 2.8 26.5 + - - +
87A GLN* 5.2 5.6 - - + +
88A ILE* 1.3 74.3 - - - +
90A ALA* 1.3 59.5 + - - +
91A CYS* 4.3 5.4 - - - -
115A SER* 3.4 7.2 - - - -
117A ARG* 3.6 50.9 - - + +
128A LEU* 3.8 16.6 - - + -
135A PRO* 5.9 2.0 - - + -
137A PHE* 3.7 26.9 - - + -
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Residues in contact with ALA 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A GLU* 3.7 8.7 - - + +
69A VAL* 3.3 21.5 - - + -
75A ALA* 5.2 0.4 - - + -
88A ILE* 3.6 6.1 + - + -
89A ILE* 1.3 72.3 - - - +
91A CYS* 1.3 57.8 + - - +
105A TRP* 4.2 9.4 - - + -
114A ILE* 3.9 24.5 - - + -
115A SER 2.9 9.7 + - - +
116A LEU* 3.3 7.3 - - + +
117A ARG* 2.6 33.7 + - - -
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Residues in contact with CYS 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A LEU* 3.9 21.3 - - - -
66A GLU 2.8 20.1 + - - +
67A ILE* 4.4 10.5 - - + +
68A GLY 3.0 24.8 + - - -
69A VAL* 3.7 3.0 - - - +
89A ILE* 4.3 3.8 - - - -
90A ALA* 1.3 74.8 - - - +
92A ASP* 1.3 63.1 + - - +
117A ARG 3.5 6.5 - - - +
121A ALA* 4.5 20.4 - - + -
124A THR* 3.6 31.2 - - + -
125A LEU* 5.4 2.7 - - - -
128A LEU* 5.0 1.1 - - - -
301A SAH 4.3 4.4 + - - -
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Residues in contact with ASP 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A VAL* 2.8 36.2 + - + -
70A PHE* 2.9 8.0 + - - -
90A ALA 4.0 1.2 + - - -
91A CYS* 1.3 73.4 - - - +
93A GLN* 1.3 57.8 + - - +
94A ASP* 2.9 26.8 + - - +
98A THR* 4.0 13.5 - - - +
116A LEU* 4.6 1.0 - - + +
117A ARG 3.2 5.9 + - - -
118A LEU* 3.0 16.2 - - - +
119A GLY 3.0 23.9 + - - -
301A SAH 2.8 49.3 + - - -
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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