Contacts of the strand formed by residues 863 - 866 (chain A) in PDB entry 1B0P
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 ALA 863 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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832A MET 3.0 13.6 + - - +
833A PHE* 4.1 6.3 - - + -
834A ILE 2.8 27.4 + - - -
861A GLY 3.4 2.2 + - - -
862A PRO* 1.3 67.6 - - - +
864A TRP* 1.3 60.0 + - - +
208B MET* 3.3 24.2 - - + +
209B ASN 3.8 36.8 - - - +
210B PRO 4.0 0.4 - - - -
213B PRO* 4.1 6.7 - - + -
214B HIS 4.1 7.2 - - - +
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Residues in contact with TRP 864 (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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834A ILE* 3.5 23.5 - - + +
836A ASN* 3.2 41.6 - - + +
841A SER 4.1 3.1 - - - -
842A SER* 3.8 21.8 - - - -
845A GLY* 4.4 4.7 - - - -
846A ALA* 3.6 18.8 - - + -
853A TYR* 3.4 43.2 - + + -
862A PRO 3.1 10.2 + - - +
863A ALA* 1.3 74.5 - - - +
865A GLY* 1.3 75.5 + - - +
866A ASN* 3.5 26.7 - - + -
208B MET* 4.0 3.8 - - - +
214B HIS 3.3 9.4 + - - +
215B VAL* 4.1 20.2 - - + -
216B ARG* 3.0 47.8 + - - +
217B GLY 3.6 6.7 - - - -
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Residues in contact with GLY 865 (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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834A ILE 3.0 12.8 + - - +
836A ASN* 2.9 28.1 + - - +
864A TRP* 1.3 82.9 - - - +
866A ASN* 1.3 60.0 + - - -
875A TYR* 3.5 16.2 - - - -
208B MET* 4.0 3.2 - - - +
216B ARG* 3.3 18.8 - - - -
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Residues in contact with ASN 866 (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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121A LEU* 4.6 18.8 - - - +
836A ASN 3.3 16.7 - - - +
838A THR* 3.3 26.5 + - - -
842A SER* 4.2 14.2 + - - -
864A TRP* 3.6 15.5 - - + -
865A GLY* 1.3 71.9 - - - -
867A SER* 1.3 66.9 + - - +
868A LEU 3.9 0.2 - - - +
875A TYR* 3.9 2.6 + - - -
99B LYS* 3.0 24.1 + - - +
103B GLU* 4.3 4.3 - - - +
216B ARG 3.0 7.5 + - - -
217B GLY* 3.1 29.7 + - - +
218B THR 5.4 1.0 + - - -
219B ALA* 5.8 1.6 - - - +
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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