Contacts of the strand formed by residues 85 - 89 (chain A) in PDB entry 3R6O
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 VAL 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A PRO* 3.4 27.6 - - + -
84A GLN* 1.3 78.6 - - - +
86A ILE* 1.3 64.2 + - - +
112A MET* 3.2 9.0 - - - +
113A LYS* 2.9 62.2 + - + +
114A SER 4.8 0.4 - - - +
115A PRO* 4.2 13.2 - - + -
117A SER* 5.7 0.2 - - - +
118A ILE* 4.2 9.6 - - + -
199A CYS* 4.1 11.4 - - - -
258A ILE* 3.5 10.8 - - + +
260A LEU* 4.1 24.7 - - + -
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Residues in contact with ILE 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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84A GLN* 4.0 27.8 - - + +
85A VAL* 1.3 74.5 - - - +
87A ALA* 1.3 58.6 + - - +
88A LEU* 4.3 13.5 - - + -
110A VAL* 3.6 26.2 - - + -
111A PHE 3.5 2.9 - - - +
112A MET* 3.6 26.0 - - + -
247A VAL* 4.2 23.6 - - + -
251A ILE* 4.2 14.6 - - + -
253A LEU* 4.9 4.0 - - + -
257A ASP* 6.2 0.4 - - + -
258A ILE 2.9 11.0 + - - +
259A ILE* 3.3 14.2 - - + -
260A LEU* 2.8 33.8 + - - +
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Residues in contact with ALA 87 (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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85A VAL 4.1 0.4 + - - -
86A ILE* 1.3 75.1 - - - +
88A LEU* 1.3 63.6 + - - +
110A VAL* 3.7 1.2 - - - -
111A PHE* 2.7 51.9 + - + +
113A LYS* 4.4 15.0 - - + -
168A ASP* 3.5 30.1 - - - +
260A LEU* 3.6 15.7 - - + -
400A MG 4.4 1.3 - - - -
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Residues in contact with LEU 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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86A ILE* 4.3 8.3 - - + -
87A ALA* 1.3 77.0 - - - +
89A GLY* 1.3 58.7 + - - +
91A ASN* 3.8 23.3 - - + +
108A PRO* 4.2 15.5 - - + -
109A VAL 3.5 7.0 - - - +
110A VAL* 4.4 11.0 - - + -
111A PHE* 4.3 0.4 - - - -
139A GLU* 4.6 0.2 + - - -
238A LEU* 4.9 5.2 - - + -
243A VAL* 3.8 31.6 - - + -
247A VAL* 3.7 28.3 - - + -
259A ILE* 4.3 4.0 - - + -
260A LEU 2.9 18.9 + - - +
261A THR 4.1 7.9 - - - +
262A GLY* 3.5 16.1 - - - -
263A THR 4.7 0.2 + - - -
400A MG 3.2 17.1 - - - -
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Residues in contact with GLY 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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88A LEU* 1.3 74.2 - - - +
90A PHE* 1.3 76.5 + - - -
91A ASN 3.3 1.2 + - - -
95A HIS* 6.0 0.7 - - - -
108A PRO* 3.2 5.5 - - - +
109A VAL 2.9 31.6 + - - -
111A PHE* 3.6 23.5 - - - -
400A MG 4.7 2.7 - - - -
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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