Contacts of the strand formed by residues 86 - 91 (chain A) in PDB entry 5C7G
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 TYR 86 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A VAL* 4.2 9.6 + - + +
69A THR* 3.7 30.0 + - + +
83A VAL* 4.2 13.0 - - + -
85A THR* 1.3 82.5 - - - +
87A LYS* 1.3 71.3 + - - +
88A ILE* 3.9 21.5 - - + -
108A LEU* 3.6 3.7 - - - +
109A PHE* 2.8 50.0 + - + +
110A GLN 4.6 0.7 + - - -
111A GLY* 3.9 23.5 - - - -
119A VAL 5.0 1.6 + - - -
121A ALA* 3.3 24.1 - - - +
134A ILE* 3.8 18.8 - - + -
135A LYS 3.4 17.3 - - - +
136A PRO* 3.9 8.3 - - + -
137A ALA* 3.9 3.6 - - - +
145A MET* 4.3 4.3 - - + -
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Residues in contact with LYS 87 (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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86A TYR* 1.3 77.3 - - - +
88A ILE* 1.3 68.9 + - - +
99A THR* 4.9 7.4 - - + -
106A PRO* 4.4 21.7 - - + +
107A VAL 3.7 19.7 - - - +
108A LEU* 4.2 24.9 - - + -
109A PHE* 4.3 0.7 - - - -
134A ILE* 3.6 0.7 - - - -
135A LYS* 2.8 58.7 + - + +
137A ALA* 5.2 6.7 - - + -
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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
----------------------------------------------------------
67A VAL* 4.0 15.0 - - + -
86A TYR* 3.9 20.6 - - + -
87A LYS* 1.3 82.1 - - - +
89A ASP* 1.3 76.5 + - - +
90A VAL* 4.0 1.1 - - + -
99A THR* 3.5 2.6 - - - +
100A ILE* 2.9 48.5 + - + +
107A VAL 4.7 0.6 + - - -
109A PHE* 3.6 23.1 - - + -
121A ALA* 6.1 0.2 - - + -
123A PHE* 3.6 27.4 - - + -
132A VAL* 3.9 17.7 - - + -
133A ARG 3.2 11.4 - - - +
134A ILE* 4.5 6.7 - - + -
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Residues in contact with ASP 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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88A ILE* 1.3 74.0 - - - +
90A VAL* 1.3 63.7 + - - +
97A TRP* 3.8 26.1 - - + +
98A ILE 3.3 7.4 - - - +
99A THR* 2.7 33.7 + - - +
133A ARG* 2.8 44.3 + - + +
135A LYS* 2.9 36.5 + - + +
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Residues in contact with VAL 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ILE* 4.0 6.1 - - + -
89A ASP* 1.3 80.1 - - - +
91A SER* 1.3 61.3 + - - +
96A ASP 3.8 0.3 - - - +
97A TRP* 3.4 6.4 - - - -
98A ILE* 2.9 50.3 + - + +
100A ILE* 4.0 24.9 - - + -
123A PHE* 5.2 2.0 - - + -
127A LEU* 4.3 17.3 - - + -
129A THR* 3.3 29.4 - - + +
131A PHE 3.2 10.8 - - - +
132A VAL* 4.5 6.5 - - + -
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Residues in contact with SER 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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90A VAL* 1.3 75.7 - - - +
92A SER* 1.3 61.2 + - - +
93A ASN* 3.3 2.1 + - - -
94A GLY* 2.9 27.1 + - - -
95A GLU 3.6 0.7 + - - -
96A ASP 2.7 25.2 + - - -
97A TRP* 3.6 25.1 - - - -
129A THR* 3.1 7.5 + - - -
130A ARG 3.1 1.0 + - - -
131A PHE* 2.9 38.8 + - - -
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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