Contacts of the strand formed by residues 87 - 91 (chain A) in PDB entry 3PEP
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 ASP 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A ILE* 3.9 17.3 - - + -
21A GLY* 3.1 25.6 - - - -
56A PHE* 3.7 10.2 - - - -
61A SER 3.9 4.2 - - - +
63A THR* 2.6 33.4 + - - -
64A PHE* 3.1 29.8 + - + +
86A TYR* 1.3 71.9 - - - +
88A THR* 1.3 70.0 + - - +
89A VAL* 3.7 2.5 + - - +
98A ASN* 4.2 4.9 - - - +
99A GLN* 2.9 30.9 + - - +
101A PHE* 4.0 8.5 - - + -
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Residues in contact with THR 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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20A ILE* 3.8 0.3 - - - -
21A GLY* 3.0 25.5 + - - -
22A THR* 4.4 13.3 + - - +
63A THR* 4.3 11.0 + - - +
87A ASP* 1.3 81.0 + - - +
89A VAL* 1.3 64.8 + - - +
90A GLN* 3.9 11.1 + - - +
95A SER* 3.5 29.4 - - - +
96A ASP 3.4 13.7 - - - +
97A THR* 4.1 18.1 - - + +
98A ASN 4.1 2.6 + - - +
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Residues in contact with VAL 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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18A ILE* 3.7 30.1 - - + -
19A GLY 3.5 5.6 - - - +
20A ILE* 3.9 23.1 - - + -
38A LEU* 4.4 10.3 - - + -
87A ASP 4.0 3.8 - - - +
88A THR* 1.3 78.8 - - - +
90A GLN* 1.3 67.9 + - - +
91A VAL* 3.5 8.9 + - + +
94A ILE 3.5 0.7 - - - +
96A ASP* 3.0 46.6 + - - +
99A GLN* 3.9 24.5 - - + +
101A PHE* 5.0 2.7 - - + -
121A LEU* 5.8 0.9 - - + -
136A VAL* 5.5 3.4 - - + -
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Residues in contact with GLN 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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17A THR 4.8 0.3 - - - +
18A ILE* 3.3 8.5 - - - +
19A GLY* 2.9 48.9 + - - +
21A GLY 2.8 28.5 + - - -
22A THR* 5.2 0.8 + - - +
24A ALA* 3.5 23.6 + - - +
88A THR* 3.9 10.8 + - + +
89A VAL* 1.3 71.3 - - - +
91A VAL* 1.3 61.1 - - - +
92A GLY 4.3 0.2 - - - -
93A GLY 5.4 0.4 - - - -
94A ILE 3.5 5.4 - - - -
95A SER* 3.4 22.2 - - - +
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Residues in contact with VAL 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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4A GLU* 4.4 3.8 - - - +
17A THR 5.3 0.2 - - - -
18A ILE* 3.9 22.0 - - + +
31A PHE* 4.4 9.4 - - + -
89A VAL* 3.8 17.0 - - + +
90A GLN* 1.3 78.2 - - - +
92A GLY* 1.3 65.8 + - - +
93A GLY 3.1 1.7 - - - +
94A ILE* 2.9 29.9 + - - +
96A ASP* 4.2 13.2 - - + +
121A LEU* 4.4 13.0 - - + -
136A VAL* 4.8 10.3 - - + -
140A LEU* 4.7 12.8 - - + -
167A LEU* 4.1 23.0 - - + +
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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