Contacts of the strand formed by residues 97 - 104 (chain B) in PDB entry 6RIP
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 GLU 97 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95B LYS* 5.0 5.4 + - - +
96B ASP* 1.3 88.3 - - + +
98B VAL* 1.3 59.9 + - - +
99B ILE* 4.2 1.0 + - - +
145B LYS* 4.4 21.5 + - + -
146B VAL 3.4 9.0 - - - +
147B GLN* 4.1 20.6 - - + +
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Residues in contact with VAL 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B VAL* 4.2 15.0 - - + -
95B LYS* 4.2 28.5 - - + +
96B ASP 4.1 0.4 - - - -
97B GLU* 1.3 74.1 - - - +
99B ILE* 1.3 72.7 + - + +
100B LEU* 4.5 1.3 - - + -
118B ASP* 4.4 12.8 - - - +
121B VAL* 3.6 29.8 - - + -
145B LYS* 3.9 2.2 - - - +
146B VAL* 2.9 57.3 + - + +
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Residues in contact with ILE 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B GLU* 5.3 3.4 - - - +
97B GLU 4.2 1.7 + - - +
98B VAL* 1.3 80.7 - - - +
100B LEU* 1.3 77.1 + - - +
118B ASP* 4.1 9.9 - - - +
143B ARG* 4.2 31.0 - - + +
144B ILE 3.2 20.4 - - - +
145B LYS* 4.6 13.7 - - + +
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Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B VAL* 6.1 2.2 - - + -
98B VAL* 4.3 6.3 - - + +
99B ILE* 1.3 85.2 - - - +
101B THR* 1.3 63.6 + - - +
115B ILE* 3.6 28.3 - - + -
116B THR* 4.3 14.6 - - + +
117B HIS 5.3 2.9 - - - +
118B ASP* 5.5 3.8 - - + +
121B VAL* 4.3 27.8 - - + -
123B ILE* 5.2 7.9 - - + -
143B ARG* 3.4 6.6 - - - +
144B ILE* 2.9 54.8 + - + +
146B VAL* 4.1 25.4 - - + -
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Residues in contact with THR 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B LEU* 1.3 78.1 - - - +
102B LEU* 1.3 65.5 + - - +
103B ASN* 4.5 13.9 + - - +
115B ILE* 3.5 11.2 - - - +
116B THR* 3.2 33.2 + - + +
141B SER* 4.8 2.1 + - - -
142B MET* 2.5 24.2 + - - -
143B ARG* 4.2 11.2 + - - +
144B ILE* 4.8 1.8 - - - +
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Residues in contact with LEU 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B THR* 1.3 79.3 + - - +
103B ASN* 1.3 80.7 + - - +
104B LYS* 5.4 1.6 - - + +
110B VAL* 4.6 16.6 - - + -
111B THR 5.7 0.4 - - - +
114B ASP* 3.1 31.6 - - + +
115B ILE* 3.8 20.6 - - + -
116B THR 5.5 0.2 - - - +
130B ILE* 4.0 26.0 - - + -
131B CYS* 6.5 0.2 - - - -
140B ILE* 3.3 4.6 - - + +
141B SER* 3.0 17.7 - - - -
142B MET* 3.1 45.5 + - + -
144B ILE* 5.8 3.4 - - + -
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Residues in contact with ASN 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B THR* 4.5 15.5 + - - +
102B LEU* 1.3 93.0 - - - +
104B LYS* 1.3 65.0 + - - +
114B ASP* 4.6 8.7 + - - +
139B SER* 5.4 1.6 - - - +
140B ILE 3.0 4.9 - - - +
141B SER* 2.9 27.1 + - - -
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Residues in contact with LYS 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B LEU* 5.4 2.4 - - + +
103B ASN* 1.3 78.6 - - - +
105B SER* 1.3 59.6 + - - +
106B GLY* 3.9 18.4 - - - +
107B ILE 5.2 5.4 + - - +
108B GLY* 5.0 2.4 - - - -
109B PRO 2.9 25.4 + - - -
110B VAL* 4.2 29.1 - - + +
111B THR* 5.2 0.4 - - - +
114B ASP* 4.2 24.9 + - + +
133B LEU* 4.3 7.3 - - + +
139B SER* 2.4 23.6 + - - -
140B ILE* 2.9 23.9 + - + +
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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