Contacts of the strand formed by residues 85 - 92 (chain A) in PDB entry 5V8V
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 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A THR 3.4 2.8 - - - +
80A ASN* 3.7 0.9 - - - -
81A TYR* 2.9 55.6 + - + +
84A THR* 1.3 88.8 + - - +
86A TYR* 1.3 62.9 + - - +
87A TYR* 4.0 9.9 - - + -
187A LEU 3.0 23.6 + - - -
189A GLU* 2.7 36.7 + - - +
190A PHE* 3.5 17.7 - - + -
502A 90D 5.3 4.4 + - - +
503A 90D 3.2 33.0 - - + +
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Residues in contact with TYR 86 (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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78A LEU* 4.5 7.9 - - + +
79A THR 3.2 6.3 - - - +
80A ASN* 3.0 32.7 + - + -
83A ASP* 3.3 26.6 + - - -
84A THR 4.2 0.2 - - - -
85A GLN* 1.3 73.7 - - - +
87A TYR* 1.3 61.6 + - - +
102A VAL* 3.6 21.7 - - - +
103A PHE* 4.6 1.7 + - - -
228A TYR* 3.5 54.9 + + + -
229A ASN 2.8 20.7 + - - -
239A GLY 3.7 13.7 - - - -
240A GLY* 4.8 2.0 - - - -
383A ALA* 3.9 11.9 - - + -
387A ARG* 3.2 19.0 + - - +
503A 90D 2.8 27.6 + - - +
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Residues in contact with TYR 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU* 3.2 7.9 - - - +
79A THR* 2.7 66.9 + - + +
81A TYR* 4.3 10.4 - - + +
85A GLN* 4.0 20.2 - - + -
86A TYR* 1.3 77.0 - - - +
88A GLY* 1.3 59.9 + - - +
100A LYS* 3.5 41.1 + - + +
101A VAL 3.2 22.0 - - - +
102A VAL* 4.2 1.3 - - + -
103A PHE* 5.4 0.4 - - - -
189A GLU* 3.8 32.7 + - + +
190A PHE* 4.1 17.9 - + + -
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Residues in contact with GLY 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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76A VAL* 4.3 0.9 - - - -
77A ILE 3.6 17.5 - - - -
78A LEU* 3.6 12.0 - - - +
79A THR* 5.7 0.4 - - - -
87A TYR* 1.3 75.0 - - - +
89A GLU* 1.3 59.8 + - - -
100A LYS* 3.2 8.7 - - - -
101A VAL 2.8 33.0 + - - -
103A PHE* 4.0 7.6 - - - -
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Residues in contact with GLU 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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76A VAL* 4.1 17.2 - - + +
77A ILE 4.6 1.2 + - - -
88A GLY* 1.3 74.1 - - - +
90A ILE* 1.3 72.2 + - - +
98A THR* 3.2 41.9 + - + +
99A PHE 3.4 7.0 - - - +
100A LYS* 4.8 6.5 - - + +
103A PHE* 4.6 0.9 - - - -
164A THR 4.7 0.5 - - - +
165A VAL* 4.8 5.4 - - - -
166A GLY 5.0 1.9 + - - -
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Residues in contact with ILE 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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89A GLU* 1.3 82.5 - - - +
91A GLY* 1.3 59.9 + - - +
92A ILE* 4.1 26.2 - - + -
97A GLN 3.6 0.7 - - - +
98A THR* 3.5 6.0 + - - -
99A PHE* 3.0 38.4 + - + +
101A VAL* 3.9 33.4 - - + -
103A PHE* 4.0 8.7 - - + -
110A VAL* 4.8 5.6 - - + -
112A VAL* 4.7 3.8 - - + -
163A ILE* 4.3 13.9 - - + -
164A THR 3.3 14.8 - - - +
165A VAL* 3.9 17.0 - - + -
194A VAL* 3.9 17.0 - - + -
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Residues in contact with GLY 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 ILE* 1.3 73.4 - - - +
92A ILE* 1.3 63.0 + - - +
93A GLY 4.2 0.2 - - - -
96A PRO* 4.2 14.4 - - - -
97A GLN 3.2 8.1 - - - -
98A THR* 4.7 2.2 - - - -
162A ILE 3.7 0.9 - - - +
163A ILE* 3.2 5.1 - - - +
164A THR* 2.7 51.9 + - - +
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Residues in contact with ILE 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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90A ILE* 4.1 14.4 - - + -
91A GLY* 1.3 77.3 - - - +
93A GLY* 1.3 62.5 + - - +
97A GLN* 2.8 41.3 + - - +
99A PHE* 3.7 30.3 - - + -
110A VAL* 5.6 0.7 - - + -
112A VAL* 3.9 27.4 - - + -
130A PHE* 3.5 26.3 - - + -
161A ASP* 4.0 7.2 - - + -
162A ILE 3.3 7.9 - - - +
163A ILE* 4.0 19.7 - - + -
174A PHE* 3.8 21.8 - - + -
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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