Contacts of the strand formed by residues 95 - 100 (chain I) in PDB entry 5BRR
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 95 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37I TYR* 5.2 2.6 + - - -
38I GLY* 5.0 0.3 - - - -
41I SER* 3.8 24.3 + - - +
42I VAL* 3.1 22.2 - - + +
45I MET* 4.4 20.4 - - - +
79I TYR* 6.0 2.3 - - - -
93I THR* 3.9 13.8 + - - +
94I THR* 1.3 81.5 + - - +
96I ALA* 1.3 62.2 + - - +
119I SER* 4.9 2.6 + - - -
122I LYS* 3.9 11.3 + - - -
139I TRP* 4.7 1.7 + - - -
166I VAL 3.5 6.3 - - - -
167I ASN* 2.7 28.2 + - - -
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Residues in contact with ALA 96 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42I VAL* 4.4 1.6 - - - +
45I MET* 4.6 1.3 - - - +
94I THR* 4.8 0.4 - - + +
95I ASP* 1.3 76.2 - - - +
97I ILE* 1.3 65.1 + - - +
98I PHE* 4.1 14.6 + - + -
122I LYS* 4.0 14.4 - - + +
139I TRP* 3.5 34.3 - - + +
165I LEU* 3.8 1.6 - - - +
166I VAL* 2.9 42.8 + - + +
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Residues in contact with ILE 97 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45I MET* 3.4 30.7 - - + +
46I LEU* 4.2 31.6 - - + +
49I THR* 4.8 13.2 - - + +
96I ALA* 1.3 76.8 - - - +
98I PHE* 1.3 73.0 + - - +
113I PHE* 5.3 2.9 - - + -
120I THR 5.4 1.0 + - - -
121I VAL* 3.7 20.2 - - + -
122I LYS* 2.8 33.0 + - - +
163I LEU* 4.4 14.1 - - + -
164I VAL 3.8 10.1 - - - +
165I LEU* 3.8 16.6 - - + +
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Residues in contact with PHE 98 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96I ALA* 4.1 25.6 - - + -
97I ILE* 1.3 76.3 - - - +
99I VAL* 1.3 66.2 + - - +
122I LYS* 3.0 30.7 - - + -
124I VAL* 3.9 25.8 - - + -
126I PHE* 4.2 16.8 - - + -
135I ILE* 4.3 7.4 - - + -
136I ILE* 3.5 41.3 - - + -
139I TRP* 4.2 26.2 - + + -
163I LEU* 3.5 8.0 - - - +
164I VAL* 2.9 38.3 + - + +
166I VAL* 4.4 10.1 - - + -
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Residues in contact with VAL 99 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98I PHE* 1.3 78.0 - - - +
100I GLN* 1.3 77.3 + - - +
103I LEU* 4.2 17.9 - - + -
105I LEU* 5.5 3.8 - - + -
121I VAL* 4.2 18.2 - - + -
122I LYS 2.8 15.8 + - - +
123I GLN* 3.4 24.4 - - + +
124I VAL* 2.7 28.1 + - - +
126I PHE* 4.4 5.8 - - - -
162I ARG 3.5 15.7 - - - +
163I LEU* 3.9 15.7 - - + -
309I LEU* 5.1 9.6 - - + -
315I LEU* 4.9 9.0 - - + -
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Residues in contact with GLN 100 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99I VAL* 1.3 80.9 - - + +
101I ARG* 1.3 89.3 + - - +
102I ASP 4.3 2.9 - - - +
103I LEU* 3.4 37.1 - - + +
123I GLN* 2.2 25.1 + - - +
124I VAL 2.6 10.1 + - - -
125I ASP* 3.3 14.3 + - - +
126I PHE* 2.3 42.8 + - + +
127I SER* 3.1 6.7 + - - -
159I GLN 5.0 0.2 - - - +
162I ARG* 3.5 31.3 + - - +
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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