Contacts of the strand formed by residues 673 - 683 (chain B) in PDB entry 1EX0
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 THR 673 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231B GLU* 4.5 1.0 - - - +
667B LEU* 4.4 10.3 - - + +
668B ASP* 3.7 29.8 - - - +
669B GLY 2.9 22.1 + - - +
670B PRO* 4.4 3.1 - - - +
672B VAL* 1.3 79.5 - - - +
674B ARG* 1.3 81.7 + - - +
675B PRO* 4.0 0.5 - - - +
676B MET* 3.7 19.1 - - - -
695B CYS* 3.9 15.9 - - - -
698B TRP* 3.5 12.7 - - - -
705B LEU* 4.3 12.6 - - + -
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Residues in contact with ARG 674 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B GLU* 4.0 16.6 + - - +
232B ASP* 2.7 51.7 + - - +
296B VAL* 3.8 10.2 - - - +
300B LEU* 3.1 29.5 - - - +
668B ASP* 4.5 0.2 - - - -
673B THR* 1.3 95.4 + - - +
675B PRO* 1.3 89.0 - - + +
676B MET* 3.4 7.5 + - + +
698B TRP* 3.7 14.3 - - + -
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Residues in contact with PRO 675 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B THR* 4.9 2.0 - - - +
296B VAL* 4.1 11.7 - - + -
297B ASP* 3.5 49.9 - - + +
666B HIS* 6.3 0.4 - - - +
667B LEU 3.4 8.5 - - - +
668B ASP* 3.5 29.4 - - + +
673B THR 4.4 0.4 - - - +
674B ARG* 1.3 108.9 - - + +
676B MET* 1.3 60.8 + - - +
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Residues in contact with MET 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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666B HIS* 3.3 6.4 - - - +
667B LEU* 2.7 36.3 + - + +
673B THR* 3.7 16.4 - - - +
674B ARG* 3.6 10.8 - - + +
675B PRO* 1.3 80.7 - - - +
677B LYS* 1.3 65.5 + - - +
691B TRP* 3.8 12.1 - - + -
693B GLU* 3.3 46.7 - - - +
695B CYS* 5.9 1.1 - - - -
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Residues in contact with LYS 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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287B VAL* 4.5 19.0 - - - +
664B TRP* 3.5 37.8 - - + -
665B VAL 3.1 12.8 - - - +
666B HIS* 3.8 30.8 - - + +
676B MET* 1.3 79.7 - - - +
678B LYS* 1.3 65.0 + - - +
691B TRP* 3.7 6.5 - - - -
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Residues in contact with LYS 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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663B VAL 3.7 0.9 - - - +
664B TRP* 3.5 7.1 - - - -
665B VAL* 2.8 33.5 + - - +
677B LYS* 1.3 77.2 + - - +
679B MET* 1.3 69.4 + - - +
680B PHE* 3.6 29.0 - - + -
690B GLN 5.6 0.2 - - - +
691B TRP* 3.6 48.1 - - + +
693B GLU* 4.6 4.0 + - - -
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Residues in contact with MET 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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662B ASN* 3.8 25.4 - - - +
663B VAL 3.2 12.8 - - - +
664B TRP* 3.5 50.1 - - + +
678B LYS* 1.3 82.2 - - - +
680B PHE* 1.3 68.7 + - - +
681B ARG* 3.2 56.2 + - - +
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Residues in contact with PHE 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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663B VAL* 2.8 46.4 + - + +
665B VAL* 3.9 26.2 - - + -
678B LYS* 3.6 37.0 - - + -
679B MET* 1.3 77.8 - - - +
681B ARG* 1.3 65.9 + - - +
682B GLU 3.1 4.8 + - - +
683B ILE* 4.3 6.1 - - + -
689B VAL* 3.6 46.2 - - + -
690B GLN 4.1 16.6 - - - -
691B TRP* 4.2 7.9 - - + -
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Residues in contact with ARG 681 (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 ARG* 3.5 5.4 - - - +
662B ASN* 2.9 37.5 + - - +
679B MET* 3.2 31.2 + - - +
680B PHE* 1.3 69.7 - - - +
682B GLU* 1.3 66.1 + - + +
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Residues in contact with GLU 682 (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 THR* 4.9 2.4 + - - +
660B LEU 3.2 11.4 - - - +
661B ARG* 2.6 39.9 + - - +
663B VAL* 5.2 0.2 - - - -
680B PHE* 3.1 6.3 + - - +
681B ARG* 1.3 87.6 - - + +
683B ILE* 1.3 69.3 + - - +
684B ARG* 2.9 45.9 + - + +
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Residues in contact with ILE 683 (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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652B PHE* 4.1 16.2 - - + +
654B ASN* 3.4 14.6 + - + +
659B THR* 3.3 3.4 - - - -
660B LEU* 2.8 41.0 + - + +
663B VAL* 3.8 35.0 - - + -
680B PHE* 4.3 3.1 - - + -
682B GLU* 1.3 79.4 - - - +
684B ARG* 1.3 65.3 + - - +
687B SER* 3.6 32.3 - - - +
689B VAL* 3.6 42.2 - - + +
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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