Contacts of the strand formed by residues 667 - 680 (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 ASP 667 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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508B ASP* 4.3 1.5 - - - +
664B ASN* 2.9 44.0 + - - +
665B GLU 3.4 1.9 + - - -
666B GLY* 1.3 76.4 - - - +
668B ASP* 1.3 55.2 + - - +
669B PHE* 3.7 9.8 - - - -
715B ALA 5.1 0.7 - - - +
716B LYS* 1.3 47.6 + - - +
717B PRO* 3.8 24.3 - - + +
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Residues in contact with ASP 668 (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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661B LYS* 4.9 7.4 - - - +
662B VAL 3.6 10.2 - - - +
663B LYS* 3.8 30.8 + - + +
666B GLY 3.9 3.1 + - - +
667B ASP* 1.3 74.5 - - - +
669B PHE* 1.3 64.5 + - - +
670B GLY* 2.7 18.4 + - - +
717B PRO* 3.3 15.9 - - - +
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Residues in contact with PHE 669 (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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195A LEU* 3.8 29.8 - - + -
662B VAL* 2.9 31.1 + - + +
664B ASN* 4.4 5.2 - - + -
667B ASP* 3.7 19.3 - - - -
668B ASP* 1.3 78.3 + - - +
670B GLY* 1.3 59.5 + - - +
671B TRP 3.5 5.2 + - - +
700B LEU* 3.7 41.7 - - + -
701B ARG* 4.6 19.3 + - - +
702B CYS* 4.4 5.6 - - - -
715B ALA* 4.1 8.3 - - + -
716B LYS* 3.6 9.9 - - - -
717B PRO* 3.5 41.6 - - + +
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Residues in contact with GLY 670 (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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661B LYS* 3.2 36.2 - - - +
662B VAL 3.4 5.9 + - - -
668B ASP* 2.7 17.4 + - - -
669B PHE* 1.3 78.1 - - - +
671B TRP* 1.3 64.5 + - - -
700B LEU* 5.3 0.2 - - - +
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Residues in contact with TRP 671 (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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659B LEU* 4.0 17.3 - - + -
660B VAL* 3.4 42.0 - - - -
661B LYS* 3.6 34.0 - - + +
669B PHE 3.5 5.4 + - - +
670B GLY* 1.3 77.2 - - - -
672B GLY* 1.3 58.7 + - - +
699B LEU 4.4 1.2 - - - +
700B LEU* 5.2 1.7 - - - -
701B ARG* 4.7 11.3 + - - +
726B MET* 5.2 0.9 - - - +
738B ALA* 4.2 7.6 - - + -
740B SER* 4.2 1.8 - - - -
763B ILE* 3.8 31.5 - - + +
767B GLN* 4.0 24.6 - - + +
774B ILE* 3.3 46.4 - - + +
776B LEU* 4.0 17.9 - - + -
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Residues in contact with GLY 672 (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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659B LEU* 3.4 10.1 - - - +
660B VAL* 2.7 38.3 + - - -
670B GLY 3.8 0.6 + - - -
671B TRP* 1.3 74.5 - - - +
673B VAL* 1.3 57.7 + - - -
698B VAL* 4.0 10.8 - - - -
699B LEU 3.0 17.0 - - - -
700B LEU* 4.5 5.3 - - - +
763B ILE* 4.8 2.7 - - - -
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Residues in contact with VAL 673 (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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657B GLY* 3.4 37.9 - - - +
658B ARG 3.2 3.6 - - - +
659B LEU* 4.8 2.7 - - + -
672B GLY* 1.3 74.6 - - - -
674B VAL* 1.3 60.5 + - - +
675B VAL* 4.3 9.2 - - + -
698B VAL* 3.5 3.2 - - - -
699B LEU* 2.9 54.7 + - + -
744B LEU* 4.1 15.3 - - + +
746B ILE* 5.7 4.3 - - + -
750B LEU* 6.1 0.9 - - + -
759B VAL* 4.2 17.5 - - + -
763B ILE* 5.2 1.5 - - + +
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Residues in contact with VAL 674 (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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653B PHE 5.5 0.2 - - - +
654B LEU* 4.3 22.0 - - + +
655B GLN 3.8 23.6 - - - +
656B PRO* 3.2 3.0 - - - +
657B GLY* 3.0 21.5 + - - -
658B ARG* 2.9 22.6 + - + +
660B VAL* 4.2 24.9 - - + -
673B VAL* 1.3 72.9 - - - +
675B VAL* 1.3 63.3 + - - +
676B ASN* 4.0 18.8 - - - +
696B VAL* 4.2 14.6 - - + -
697B GLU 4.1 3.1 - - - -
698B VAL* 4.3 7.4 - - + -
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Residues in contact with VAL 675 (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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184A ILE* 4.2 7.4 - - - +
185A ALA* 4.4 14.8 + - + +
187A TYR* 3.1 39.7 - - + -
656B PRO* 3.6 19.4 - - - +
673B VAL* 4.1 12.3 - - + +
674B VAL* 1.3 78.8 - - - +
676B ASN* 1.3 61.7 + - - +
697B GLU 2.9 13.7 + - - +
699B LEU* 4.2 19.5 - - + +
728B VAL* 4.4 9.4 - - + -
750B LEU* 4.1 17.7 - - + -
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Residues in contact with ASN 676 (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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179A LEU* 3.9 18.3 - - - +
184A ILE* 3.4 29.8 - - - +
187A TYR* 3.4 30.6 + - + +
654B LEU 5.8 0.4 - - - -
656B PRO* 5.0 1.3 - - - -
674B VAL* 3.8 5.9 - - - +
675B VAL* 1.3 78.7 - - - +
677B PHE* 1.3 85.7 + - - +
678B SER* 6.1 1.1 - - - -
696B VAL* 3.8 4.7 - - - +
697B GLU* 3.1 31.6 + - + +
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Residues in contact with PHE 677 (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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173A ASN* 3.6 33.2 - - + -
177A LYS 4.0 13.5 - - - -
178A SER* 3.7 6.4 - - - -
179A LEU* 3.5 43.6 + - + +
651B LEU* 3.6 33.2 - - + -
654B LEU* 3.8 39.7 - - + -
676B ASN* 1.3 90.3 + - - +
678B SER* 1.3 74.1 + - - +
694B TYR* 5.1 3.1 - + - -
695B VAL 3.6 12.1 - - - +
696B VAL* 4.2 3.1 - - + -
697B GLU* 4.7 1.8 - - - +
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Residues in contact with SER 678 (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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178A SER* 6.0 2.9 - - - +
206A TRP* 4.0 10.8 - - - -
676B ASN* 6.1 0.4 - - - -
677B PHE* 1.3 84.4 - - - +
679B LYS* 1.3 59.1 + - - +
680B LYS* 2.9 34.6 - - - +
694B TYR* 4.0 2.1 - - - -
695B VAL* 3.0 32.9 + - - +
697B GLU* 5.5 4.7 - - - +
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Residues in contact with LYS 679 (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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177A LYS* 4.1 35.0 + - + +
178A SER* 6.1 0.4 - - - -
677B PHE* 5.7 0.2 - - + -
678B SER* 1.3 75.1 - - - +
680B LYS* 1.3 77.7 + - - +
681B SER* 5.8 3.6 - - - -
692B PRO* 4.4 19.7 - - + -
693B LEU 3.8 7.0 - - - +
694B TYR* 4.2 32.5 - - + +
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Residues in contact with LYS 680 (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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204A ILE* 3.9 33.7 - - + -
205A SER 4.0 19.2 + - - +
206A TRP* 3.5 33.0 + - + +
678B SER* 2.9 31.3 - - - +
679B LYS* 1.3 81.9 + - - +
681B SER* 1.3 61.5 + - - +
692B PRO* 3.4 7.2 - - - +
693B LEU* 2.9 31.5 + - - +
695B VAL* 3.9 18.8 - - + -
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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