Contacts of the strand formed by residues 691 - 696 (chain B) in PDB entry 5L73
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 ASN 691 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651B GLU 3.2 1.2 - - - +
652B PHE* 2.9 30.3 + - + +
653B GLY 3.6 11.0 - - - +
654B TRP 3.1 35.2 + - - +
657B HIS 3.4 4.8 + - - -
658B LYS* 3.9 9.9 - - - +
675B VAL* 4.2 0.8 - - + +
676B LEU 3.2 5.8 - - - +
677B THR* 2.8 34.5 + - - +
685B ASP* 3.5 3.5 + - - +
688B GLY 4.4 0.2 + - - -
689B ASP 3.7 1.1 - - - +
690B GLY* 1.3 78.4 - - - +
692B PHE* 1.3 59.9 - - - +
796B ASP* 3.1 5.5 - - - +
901B CA 2.3 31.7 - - - -
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Residues in contact with PHE 692 (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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652B PHE* 4.2 5.8 - - - -
675B VAL* 3.4 4.0 - - - +
676B LEU* 2.9 42.6 + - + +
678B SER* 3.8 24.7 - - - -
683B ILE* 3.5 38.6 - - + -
684B GLN* 4.2 4.3 - - - -
685B ASP* 4.4 7.0 - - + -
690B GLY 3.9 7.9 - - - -
691B ASN* 1.3 77.2 - - - +
693B ILE* 1.3 82.0 + - - +
694B TYR* 4.0 15.5 - + - -
763B TRP* 4.1 11.9 - + + -
794B ALA* 3.6 20.0 - - + -
795B VAL 3.3 13.5 - - - +
796B ASP* 3.7 17.5 - - + -
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Residues in contact with ILE 693 (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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652B PHE* 3.3 45.9 - - + -
660B PHE* 3.9 17.9 - - + -
673B TRP* 3.6 39.3 - - + -
674B SER 3.1 5.4 - - - +
675B VAL* 3.9 6.1 - - + -
692B PHE* 1.3 77.5 - - - +
694B TYR* 1.3 61.7 + - - +
708B LEU* 4.1 13.5 - - + -
781B PHE* 5.3 4.0 - - + -
794B ALA* 3.3 5.2 - - - -
795B VAL* 2.9 57.2 + - + +
798B ILE* 5.3 0.9 - - + -
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Residues in contact with TYR 694 (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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672B LYS 4.8 0.5 - - - +
673B TRP* 3.6 2.9 - - - -
674B SER* 2.8 38.8 + - - +
676B LEU* 3.6 34.5 - - + -
683B ILE* 4.3 16.5 - - + +
692B PHE* 4.0 16.4 - + + -
693B ILE* 1.3 76.5 - - - +
695B SER* 1.3 63.3 + - - +
696B GLN* 3.8 35.2 + - + +
791B GLY* 2.9 35.6 + - - -
792B GLY* 3.9 20.2 - - - -
793B ILE 3.3 15.0 - - - -
794B ALA* 4.1 1.1 - - + -
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Residues in contact with SER 695 (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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672B LYS 5.1 1.4 + - - -
673B TRP* 3.1 40.2 - - - -
694B TYR* 1.3 71.5 + - - +
696B GLN* 1.3 65.7 + - - +
697B ALA* 3.5 0.3 + - - -
706B ALA* 4.3 9.9 - - - +
733B VAL 4.7 1.6 - - - +
783B GLY* 4.4 6.9 - - - -
785B ILE* 3.9 20.7 - - - +
792B GLY* 3.3 0.9 - - - -
793B ILE* 2.9 39.8 + - - +
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Residues in contact with GLN 696 (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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694B TYR* 3.8 26.5 + - + -
695B SER* 1.3 72.5 - - - +
697B ALA* 1.3 78.6 + - - +
698B ASP* 3.5 14.1 + - + +
701B GLN* 5.7 0.3 - - - +
785B ILE* 3.5 20.2 - - - +
791B GLY 3.8 10.5 - - - +
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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