Contacts of the strand formed by residues 693 - 702 (chain B) in PDB entry 6IEH
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 LEU 693 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197A ILE* 5.1 4.5 - - + -
202A GLN* 5.7 7.2 - - + +
204A ILE* 4.8 16.8 - - + -
679B LYS* 3.8 1.7 - - - +
680B LYS* 2.9 33.4 + - - +
681B SER* 4.8 2.3 - - - +
682B ASN* 6.3 2.0 - - + -
691B ASP 4.2 0.8 + - - +
692B PRO* 1.3 73.2 - - - +
694B TYR* 1.3 63.4 + - - +
695B VAL* 3.7 2.2 + - + -
732B LEU* 4.3 23.1 - - + -
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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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174A TRP* 3.4 23.7 - + - -
177A LYS* 5.4 4.6 - - - +
647B PRO* 3.7 23.8 - - + -
651B LEU* 3.3 37.0 - - + -
677B PHE* 5.1 2.9 - + + -
678B SER 4.0 3.8 - - - -
679B LYS* 4.2 34.4 - - + +
692B PRO* 4.1 18.8 - - + +
693B LEU* 1.3 74.5 - - - +
695B VAL* 1.3 60.8 + - - +
696B VAL* 5.8 0.2 - - + -
732B LEU* 3.6 5.0 - - - +
733B VAL* 2.8 48.7 + - + +
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Residues in contact with VAL 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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194A CYS* 3.5 33.9 - - - -
204A ILE* 4.3 6.5 - - + -
206A TRP* 4.0 11.9 - - + -
677B PHE* 3.6 3.7 - - - +
678B SER* 3.0 38.2 + - - +
680B LYS* 3.9 24.2 - - + -
693B LEU* 4.1 5.6 - - + +
694B TYR* 1.3 77.0 - - - +
696B VAL* 1.3 65.3 + - - +
697B GLU* 4.2 1.8 + - + +
730B PRO* 3.7 21.3 - - + -
731B VAL 3.4 5.4 - - - +
732B LEU* 4.0 5.8 - - + +
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Residues in contact with VAL 696 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654B LEU* 4.2 25.1 - - + -
674B VAL* 4.2 10.3 - - + -
676B ASN 3.8 11.7 - - - +
677B PHE* 4.2 7.6 - - + -
694B TYR 5.0 0.2 - - - -
695B VAL* 1.3 77.9 - - - +
697B GLU* 1.3 63.7 + - - +
698B VAL* 3.7 20.8 + - + -
730B PRO* 4.2 0.7 - - - -
731B VAL* 2.8 38.3 + - + +
732B LEU 4.6 0.9 - - - +
733B VAL* 4.1 31.6 - - + -
736B LEU* 4.4 12.1 - - + -
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Residues in contact with GLU 697 (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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187A TYR* 2.3 35.4 + - + +
189A ARG* 3.3 33.5 + - - +
206A TRP* 4.1 19.3 - - + -
674B VAL* 4.1 0.3 - - - -
675B VAL* 2.9 23.9 + - - +
676B ASN* 3.1 30.5 + - + +
677B PHE* 5.1 0.9 - - - -
678B SER* 5.4 4.8 + - - +
695B VAL 5.0 2.7 - - - +
696B VAL* 1.3 73.4 - - - +
698B VAL* 1.3 61.5 + - - +
728B VAL* 3.9 14.5 - - + +
729B VAL 3.8 5.4 - - - -
730B PRO* 3.9 10.9 - - + +
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Residues in contact with VAL 698 (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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660B VAL* 3.9 29.6 - - + -
662B VAL* 4.2 5.2 - - + -
672B GLY* 4.0 0.7 - - - -
673B VAL 3.5 14.8 - - - +
674B VAL* 4.3 4.3 - - + -
696B VAL* 3.7 25.3 + - + +
697B GLU* 1.3 78.7 - - - +
699B LEU* 1.3 67.9 + - - +
700B LEU* 3.3 29.1 + - + -
728B VAL* 4.0 4.7 - - - +
729B VAL* 3.2 34.1 + - - +
731B VAL* 4.7 8.5 - - + -
736B LEU* 5.7 1.3 - - + -
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Residues in contact with LEU 699 (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 GLY* 3.0 24.4 - - - -
673B VAL* 2.9 28.9 + - + -
675B VAL* 4.2 5.1 - - + +
698B VAL* 1.3 70.6 - - - +
700B LEU* 1.3 58.9 + - - +
726B MET* 3.3 47.9 - - + +
727B GLN 3.2 20.0 - - - +
728B VAL* 4.0 12.1 - - + +
750B LEU* 4.3 17.9 - - + +
756B ARG* 4.2 12.3 - - + +
759B VAL* 3.6 27.8 - - + -
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Residues in contact with LEU 700 (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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662B VAL* 3.6 29.2 - - + +
669B PHE* 3.7 43.3 - - + +
671B TRP 4.7 0.9 - - - -
672B GLY* 4.5 11.0 - - - +
698B VAL* 3.7 19.5 - - + +
699B LEU* 1.3 74.2 - - - +
701B ARG* 1.3 60.1 + - - +
702B CYS* 3.4 6.8 + - - -
725B GLU 3.4 1.0 - - - +
726B MET* 3.3 8.8 - - - -
727B GLN 2.9 28.2 + - - +
729B VAL* 3.0 30.3 - - + -
731B VAL* 4.4 15.5 - - + -
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Residues in contact with ARG 701 (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 PHE* 4.6 16.0 + - - +
671B TRP 4.7 7.9 + - - +
700B LEU* 1.3 73.1 - - - +
702B CYS* 1.3 59.8 + - - +
717B PRO* 3.7 6.8 - - - +
718B ALA* 3.2 44.3 + - - +
719B LYS 5.0 2.0 + - - -
720B PRO* 6.2 0.4 - - - +
722B GLU 3.6 11.7 + - - -
723B LYS 2.8 37.4 + - - -
724B GLY* 3.9 15.9 - - - -
725B GLU 3.5 6.7 - - - +
726B MET* 3.9 13.8 - - + +
760B LEU* 3.8 25.1 - - + +
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Residues in contact with CYS 702 (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 PHE* 4.4 5.6 - - - -
700B LEU* 4.0 21.1 - - - -
701B ARG* 1.3 75.4 - - - +
703B SER* 1.3 63.3 + - - +
706B SER* 4.2 9.9 - - - -
707B LEU* 4.4 11.4 - - + -
715B ALA* 4.4 20.2 - - - -
716B LYS 3.3 13.9 - - - +
718B ALA 4.1 3.8 - - - -
724B GLY* 3.6 4.9 - - - -
725B GLU* 2.8 35.7 + - - +
727B GLN* 4.2 17.3 - - + +
729B VAL* 4.7 3.8 - - - -
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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