Contacts of the strand formed by residues 87 - 95 (chain A) in PDB entry 5EXU
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 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A ASN* 2.8 24.3 + - - -
66A ARG 3.2 15.9 + - - -
78A TYR* 4.8 2.2 - + + -
79A PHE* 3.8 22.9 - + + -
82A ALA* 4.0 8.3 - - + -
83A PHE* 3.7 31.9 - + - -
86A GLY* 1.3 75.8 - - - +
88A SER* 1.3 66.9 + - - +
89A TRP* 3.8 11.9 - + - -
106A ASP* 4.3 0.2 - - - +
107A ILE* 2.9 53.8 + - + +
177A TYR* 3.8 28.0 - + + -
178A LYS* 2.9 32.8 + - - +
179A ALA* 3.7 4.5 - - - +
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Residues in contact with SER 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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87A TYR* 1.3 80.1 - - - +
89A TRP* 1.3 65.7 + - - +
90A GLU* 6.5 0.2 - - - -
105A SER 3.2 14.8 - - - -
106A ASP* 3.8 10.8 - - - -
177A TYR* 3.4 1.4 - - - -
178A LYS* 2.6 67.8 + - - +
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Residues in contact with TRP 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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60A ALA* 3.4 42.8 - - + -
62A CRQ 2.7 33.2 + - - -
87A TYR* 3.8 23.8 - + - -
88A SER* 1.3 76.4 - - - +
90A GLU* 1.3 66.3 + - - +
91A ARG* 3.7 35.0 - - + -
103A ALA* 3.8 28.3 - - + -
104A THR* 3.3 9.3 - - - -
105A SER* 2.9 58.1 + - - +
107A ILE* 3.6 6.6 - - + +
118A ILE* 4.9 1.3 - - + -
175A THR* 3.8 2.7 - - + -
176A THR 3.3 7.4 - - - +
177A TYR* 3.4 27.6 - + + -
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Residues in contact with GLU 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 TRP* 1.3 78.0 - - - +
91A ARG* 1.3 60.7 + - - +
103A ALA 3.5 6.7 - - - +
104A THR* 4.6 12.3 - - + +
174A LYS 3.9 0.7 - - - +
175A THR* 3.2 4.0 - - - +
176A THR* 3.0 51.6 + - + +
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Residues in contact with ARG 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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59A PRO* 3.1 24.2 + - - +
60A ALA* 4.0 2.2 - - - +
62A CRQ 2.7 60.8 + - - -
89A TRP* 3.7 39.1 - - + -
90A GLU* 1.3 75.1 - - - +
92A SER* 1.3 70.8 + - - +
93A MET* 4.0 12.4 - - + +
101A CYS 4.1 0.3 - - - +
102A ILE* 3.3 6.8 - - - +
103A ALA* 2.9 35.9 + - + +
173A PHE* 3.7 16.6 - - + -
174A LYS 3.3 6.7 - - - +
175A THR* 2.6 23.3 + - - +
177A TYR* 3.9 12.7 + - - -
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Residues in contact with SER 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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91A ARG* 1.3 73.3 - - - +
93A MET* 1.3 65.4 + - - +
94A THR* 4.2 6.4 + - - -
100A ILE* 6.0 1.8 - - - -
101A CYS 3.7 4.5 - - - -
102A ILE* 4.4 12.3 - - - -
172A ASP 3.5 2.2 + - - +
173A PHE* 3.3 5.0 - - - -
174A LYS* 2.9 54.2 + - - +
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Residues in contact with MET 93 (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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56A ILE 4.7 7.6 - - - +
59A PRO* 5.7 1.8 - - - -
60A ALA* 5.7 1.8 - - + -
91A ARG* 4.0 15.9 - - + +
92A SER* 1.3 80.2 - - - +
94A THR* 1.3 60.7 + - - +
95A TYR* 3.8 9.1 + - + -
100A ILE* 3.4 5.7 - - - +
101A CYS* 2.9 64.9 + - + +
103A ALA* 3.6 33.0 - - + +
120A PHE* 3.8 14.1 - - + -
171A CYS* 3.8 14.6 - - - -
172A ASP 3.4 4.7 - - - -
173A PHE* 3.6 36.3 - - + -
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Residues in contact with THR 94 (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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92A SER* 5.3 5.0 + - - -
93A MET* 1.3 71.9 + - - +
95A TYR* 1.3 70.3 + - - +
98A GLN* 6.1 1.3 - - - -
99A GLY 4.0 4.5 - - - +
100A ILE* 4.5 13.1 - - + +
170A ARG 4.7 0.2 - - - -
171A CYS* 3.4 2.3 - - - -
172A ASP* 2.9 49.6 + - - +
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Residues in contact with TYR 95 (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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56A ILE* 3.6 27.1 + - + +
93A MET* 3.8 14.4 - - + +
94A THR* 1.3 81.3 - - - +
96A GLU* 1.3 65.8 + - - +
97A ASP* 3.1 4.4 + - - +
98A GLN* 3.3 13.9 + - - -
99A GLY 2.9 21.0 + - - +
101A CYS* 4.1 10.2 - - - -
125A PHE* 3.7 24.7 - + - -
139A TRP* 3.4 26.1 - + - -
161A LEU* 4.1 6.5 - - + -
169A TYR* 3.3 44.0 - + + +
170A ARG 3.3 7.9 - - - -
171A CYS* 3.4 33.2 - - + -
173A PHE* 4.6 3.1 - - - -
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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