Contacts of the strand formed by residues 642 - 650 (chain B) in PDB entry 1ED8
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 ALA 642 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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641B LEU* 1.3 75.4 - - - +
643B THR* 1.3 62.3 + - - +
701B ASP* 3.1 14.4 - - + +
810B LEU* 3.7 19.1 - - + +
813B ASN* 3.7 29.0 - - + +
816B GLY 2.8 7.9 + - - -
817B PHE* 3.0 17.4 - - + +
818B PHE 3.0 24.8 + - - -
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Residues in contact with THR 643 (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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633B LEU* 3.8 29.5 - - + +
636B ALA* 3.6 28.9 - - + -
637B LYS* 3.9 14.1 - - + +
641B LEU 3.8 7.0 - - - +
642B ALA* 1.3 81.4 - - - +
644B GLY* 1.3 57.6 + - - +
700B ALA* 3.6 19.1 - - - +
701B ASP* 2.8 31.0 + - - +
702B VAL 3.1 6.2 + - - -
751B GLN* 5.1 0.2 + - - -
810B LEU* 3.6 4.7 - - - +
818B PHE* 3.4 8.7 - - + +
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Residues in contact with GLY 644 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633B LEU* 4.6 5.2 - - - +
643B THR* 1.3 74.0 - - - +
645B ASN* 1.3 60.8 + - - +
659B LEU* 4.9 0.2 - - - +
700B ALA* 5.0 0.7 - - - -
702B VAL* 3.2 11.9 - - - -
810B LEU* 3.9 9.0 - - - +
818B PHE* 3.0 13.9 + - - +
819B LEU* 3.5 21.1 - - - -
820B GLN* 3.1 23.0 + - - +
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Residues in contact with ASN 645 (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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633B LEU* 4.7 6.3 - - + -
644B GLY* 1.3 73.0 - - - +
646B VAL* 1.3 65.4 + - - +
651B LEU* 4.4 2.4 - - - +
656B PRO* 3.0 47.7 + - - +
659B LEU* 3.5 27.3 - - + +
660B VAL* 4.3 12.5 - - - +
695B LEU* 5.8 3.0 - - - +
700B ALA* 5.2 1.6 - - + -
702B VAL 2.9 9.9 + - - +
703B THR* 3.4 19.3 - - + +
704B LEU 3.0 24.8 + - - +
819B LEU* 4.2 0.6 - - - +
820B GLN* 3.6 8.0 + - - +
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Residues in contact with VAL 646 (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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645B ASN* 1.3 85.2 + - - +
647B SER* 1.3 66.7 + - - +
651B LEU* 5.3 0.2 - - - -
656B PRO* 5.6 0.2 - - - +
702B VAL* 4.8 1.6 - - + -
704B LEU* 3.2 28.3 - - + +
799B LEU* 3.7 24.7 - - + -
802B MET* 3.9 27.4 - - + +
803B THR* 4.8 1.3 - - - +
806B ALA* 4.2 10.1 - - + -
819B LEU* 4.2 17.5 - - + -
820B GLN* 2.8 14.7 + - - +
821B VAL* 3.3 11.2 - - + -
822B GLU* 2.8 23.6 + - - +
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Residues in contact with SER 647 (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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646B VAL* 1.3 78.1 - - - +
648B THR* 1.3 63.8 + - - +
649B ALA* 3.0 18.7 + - - +
651B LEU* 4.7 3.8 - - - -
656B PRO* 3.8 21.5 - - - -
704B LEU 3.1 6.1 + - - +
705B GLY* 3.2 24.1 - - - -
799B LEU* 4.8 0.2 - - - -
802B MET* 3.9 9.5 - - - +
822B GLU* 2.7 39.9 + - - -
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Residues in contact with THR 648 (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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647B SER* 1.3 76.0 + - - +
649B ALA* 1.4 61.8 + - - +
763B ASN* 3.7 2.1 - - - +
764B MET* 2.7 50.4 + - + +
765B PRO 6.2 0.2 - - - -
799B LEU* 4.2 27.8 - - + +
802B MET* 4.4 7.0 - - + -
822B GLU 3.3 7.8 + - - +
823B GLY* 4.1 1.0 - - - -
824B ALA* 3.1 26.0 + - - +
825B SER* 3.7 8.8 + - - -
841B GLU* 4.7 9.3 + - - +
844B ASP* 4.4 9.0 - - - +
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Residues in contact with ALA 649 (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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647B SER* 3.0 19.0 + - - +
648B THR* 1.4 83.4 + - - +
650B GLU* 1.3 73.7 + - - +
651B LEU* 3.4 1.4 + - - -
653B ASP* 3.7 21.3 - - + +
705B GLY* 4.2 0.7 - - - -
706B GLY* 2.9 23.8 + - - -
763B ASN* 3.2 14.8 - - - +
822B GLU* 4.3 1.6 - - - +
824B ALA* 3.6 16.4 - - + +
825B SER* 5.7 0.2 - - - -
828B LYS* 4.1 2.9 - - - +
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Residues in contact with GLU 650 (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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649B ALA* 1.3 76.1 - - - +
651B LEU* 1.3 58.6 + - - +
652B GLN* 3.0 15.9 - - - +
653B ASP* 2.8 33.2 + - + +
656B PRO* 4.1 2.1 - - - +
669B TYR* 3.0 33.6 + - - +
707B GLY* 3.5 15.4 - - - +
709B LYS* 5.9 2.9 - - - +
761B ASP 4.6 2.1 - - - +
762B GLY* 3.4 29.8 + - - +
763B ASN* 3.0 24.4 + - - +
828B LYS* 5.7 0.7 + - - -
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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