Contacts of the strand formed by residues 731 - 736 (chain B) in PDB entry 3LJ1
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 TYR 731 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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716B ILE* 3.4 33.4 - - + +
719B LEU* 4.0 27.4 - - + -
720B THR* 4.0 17.7 - - - -
723B ASP* 3.6 20.3 + - - +
729B ILE 4.0 1.8 + - - -
730B ARG* 1.3 81.8 + - - +
732B TYR* 1.3 71.2 + - - +
733B CYS* 3.5 27.4 - - - -
734B SER* 3.2 34.6 + - - -
743B ILE* 4.0 16.2 - - + -
744B ALA 3.7 7.6 - - - -
745B LEU* 4.1 6.3 - - + -
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Residues in contact with TYR 732 (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 PHE* 4.4 19.5 - + + -
697B ARG* 3.4 46.8 + - + -
698B PRO 5.1 2.1 + - - -
699B VAL* 3.4 27.8 - - + -
730B ARG* 3.5 29.5 + - + -
731B TYR* 1.3 84.0 - - - +
733B CYS* 1.3 65.4 + - - +
744B ALA* 3.2 18.6 + - + +
745B LEU 3.6 13.2 - - - -
746B GLU* 2.7 46.5 + - + -
747B LEU 5.1 0.4 - - - -
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Residues in contact with CYS 733 (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 ASN* 4.9 4.5 - - - -
673B LEU* 4.1 19.2 - - - +
694B PHE* 3.6 46.2 - - + -
731B TYR* 3.4 19.8 - - - -
732B TYR* 1.3 83.2 - - - +
734B SER* 1.3 64.0 + - - +
744B ALA* 2.8 29.2 + - - +
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Residues in contact with SER 734 (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 ASN* 5.7 1.6 - - - +
673B LEU* 4.8 1.6 - - - -
716B ILE* 3.1 29.4 - - - +
731B TYR* 3.2 11.1 + - - -
733B CYS* 1.3 80.6 - - - +
735B GLU* 1.3 64.3 + - - +
736B THR* 5.8 0.4 - - - -
741B LEU* 4.6 9.1 - - - +
742B TYR 3.3 13.9 + - - -
743B ILE* 3.6 9.2 - - - +
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Residues in contact with GLU 735 (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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669B SER 4.6 1.2 - - - +
670B LEU* 3.3 24.3 - - + +
671B LYS* 2.6 32.4 + - - +
672B ASN* 2.8 30.4 + - + +
673B LEU* 3.1 26.8 + - + +
734B SER* 1.3 77.6 - - - +
736B THR* 1.3 70.0 + - - +
737B THR* 5.4 0.5 - - - +
741B LEU* 3.8 1.5 - - - +
742B TYR* 2.9 37.5 + - + +
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Residues in contact with THR 736 (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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706B ILE* 5.7 3.6 - - + -
734B SER* 5.8 0.3 - - - -
735B GLU* 1.3 80.5 - - - +
737B THR* 1.3 78.9 + - - +
740B PHE 3.7 8.3 - - - +
741B LEU* 3.4 22.9 - - + +
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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