Contacts of the strand formed by residues 725 - 732 (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 GLU 725 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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701B ARG* 4.1 0.6 - - - +
702B CYS* 2.8 33.7 + - - +
703B SER 5.6 0.4 - - - -
704B LYS* 5.8 3.6 - - + +
707B LEU* 3.3 46.6 - - + +
724B GLY* 1.3 76.3 - - - +
726B MET* 1.3 73.7 + - - +
727B GLN* 3.6 1.6 + - - +
753B VAL* 3.9 27.5 - - - +
757B GLN* 4.0 10.5 - - - +
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Residues in contact with MET 726 (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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671B TRP 5.2 0.9 - - - +
699B LEU* 3.3 50.3 - - + +
700B LEU* 3.3 10.1 - - - +
701B ARG* 3.9 14.4 - - + +
725B GLU* 1.3 80.5 - - - +
727B GLN* 1.3 62.5 + - - +
756B ARG* 3.2 31.7 - - + +
757B GLN* 3.8 14.2 + - - +
759B VAL* 4.3 5.2 - - + -
760B LEU* 4.0 22.9 - - + +
763B ILE* 4.1 24.7 - - + -
1101B CL 3.5 21.3 - - - +
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Residues in contact with GLN 727 (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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188A LYS 5.5 3.0 - - - +
189A ARG 5.3 1.1 - - - -
190A LYS* 3.1 56.6 + - - +
698B VAL 3.4 1.7 - - - +
699B LEU* 3.2 5.5 - - - -
700B LEU 2.9 29.1 + - - +
702B CYS* 4.2 20.2 - - - +
706B SER 6.0 0.2 - - - -
707B LEU* 3.5 34.5 - - + +
715B ALA* 5.2 0.4 - - - +
725B GLU* 3.6 1.1 + - + +
726B MET* 1.3 74.3 - - - +
728B VAL* 1.3 62.2 + - - +
729B VAL* 3.6 7.6 + - - +
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Residues in contact with VAL 728 (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* 3.9 32.3 - - + -
188A LYS 3.2 22.8 + - - +
189A ARG* 3.2 7.1 - - + -
190A LYS* 2.9 23.7 + - - +
675B VAL* 4.4 10.1 - - + -
697B GLU* 3.9 29.8 - - + +
698B VAL 3.4 10.8 - - - +
699B LEU* 4.0 17.7 - - + +
727B GLN* 1.3 75.0 + - - +
729B VAL* 1.3 61.1 + - - +
750B LEU* 5.6 3.1 - - + +
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Residues in contact with VAL 729 (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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190A LYS* 4.0 15.3 - - + -
195A LEU* 4.5 9.0 - - + -
697B GLU* 4.4 0.9 - - - -
698B VAL 3.2 23.4 + - - +
700B LEU* 3.0 36.3 - - + -
702B CYS* 4.7 9.0 - - - -
712B THR* 4.6 6.7 - - + +
715B ALA* 4.3 17.0 - - + -
727B GLN* 3.9 8.5 - - - +
728B VAL* 1.3 76.6 - - - +
730B PRO* 1.3 82.7 - - + +
731B VAL* 3.5 11.3 + - + +
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Residues in contact with PRO 730 (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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189A ARG* 4.0 20.6 - - + -
190A LYS 3.9 13.9 - - - +
193A SER 3.4 21.1 - - - +
194A CYS* 3.6 1.2 - - - -
195A LEU 2.9 20.4 + - - -
206A TRP* 3.8 17.7 - - + -
695B VAL* 3.7 20.9 - - + -
696B VAL 3.4 7.2 - - - +
697B GLU* 3.9 10.3 - - + +
712B THR* 4.1 3.1 - - + +
729B VAL* 1.3 90.7 - - + +
731B VAL* 1.3 62.4 + - - +
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Residues in contact with VAL 731 (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* 3.6 4.7 - - - -
195A LEU* 3.8 23.6 - - + +
662B VAL* 4.3 35.0 - - + -
695B VAL* 3.4 1.9 - - - -
696B VAL* 2.8 44.9 + - + +
698B VAL* 4.7 5.6 - - + -
700B LEU* 4.4 9.6 - - + -
729B VAL* 3.8 15.5 - - + +
730B PRO* 1.3 80.5 - - - +
732B LEU* 1.3 69.0 + - - +
735B LEU* 4.1 10.3 - - + -
736B LEU* 5.6 3.1 - - + +
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Residues in contact with LEU 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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194A CYS* 3.1 33.2 - - + -
196A GLY* 3.7 15.5 - - - +
197A ILE* 3.8 33.9 - - + +
202A GLN* 4.8 7.2 - - - +
693B LEU* 4.3 15.0 - - + -
694B TYR 3.6 5.8 - - - +
695B VAL* 4.0 13.2 - - + -
696B VAL* 4.6 1.0 - - - +
731B VAL* 1.3 85.8 - - - +
733B VAL* 1.3 68.0 + - + +
734B HIS* 3.2 31.2 + - + +
735B LEU* 3.4 10.4 + - + +
736B LEU* 4.6 1.0 + - - +
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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