Contacts of the strand formed by residues 701 - 710 (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 GLY 701 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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700B SER* 1.3 76.3 + - - +
702B HIS* 1.3 65.4 + - - -
703B ARG* 3.3 5.0 + - - +
724B GLN* 3.6 11.2 - - - -
725B ILE 2.8 34.7 + - - -
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Residues in contact with HIS 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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209B ILE* 5.3 0.9 - - - +
701B GLY* 1.3 69.1 - - - -
703B ARG* 1.3 97.5 + - - +
704B LYS* 5.1 5.7 + - + -
722B ASP* 2.9 40.9 + - + +
723B VAL 3.9 5.3 + - - -
724B GLN* 3.5 25.0 + - - +
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Residues in contact with ARG 703 (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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207B ASN* 5.1 3.6 + - - -
208B ASP* 3.0 38.6 + - - -
209B ILE* 4.1 14.9 - - - +
670B PRO* 2.8 40.1 + - - +
671B GLY* 4.5 0.6 - - - -
672B VAL* 3.7 20.0 - - + -
699B VAL* 3.8 37.1 - - - +
700B SER 4.9 1.6 + - - -
701B GLY 3.3 4.9 + - - +
702B HIS* 1.3 107.3 + - - +
704B LYS* 1.3 61.9 + - - +
723B VAL* 2.8 35.7 + - + +
725B ILE* 3.7 22.4 - - + -
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Residues in contact with LYS 704 (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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209B ILE* 3.8 34.6 - - + +
211B VAL* 6.1 0.4 - - - -
224B SER* 3.6 14.1 + - - +
472B ASP* 2.8 32.9 + - - -
669B GLY* 3.3 24.8 - - - -
670B PRO* 4.6 1.8 + - + +
672B VAL* 4.4 4.2 - - - +
702B HIS* 5.1 4.3 + - + -
703B ARG* 1.3 79.5 - - - +
705B LEU* 1.3 65.2 + - - +
706B ILE* 3.2 22.2 - - + -
720B GLU* 3.0 34.1 + - + +
721B LEU 3.4 9.4 - - - +
722B ASP* 3.4 19.3 + - - +
723B VAL* 4.5 2.0 - - - +
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Residues in contact with LEU 705 (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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634B ILE* 3.8 19.7 - - + -
636B VAL* 3.6 32.1 - - + -
646B MET* 4.4 5.6 - - + -
648B VAL* 3.7 23.1 - - + -
667B LEU* 4.2 12.1 - - + -
668B ASP 3.5 12.8 - - - +
672B VAL* 3.7 27.6 - - + -
673B THR* 4.3 9.0 - - + -
695B CYS* 5.0 0.2 - - - -
704B LYS* 1.3 74.8 - - - +
706B ILE* 1.3 59.3 + - - +
720B GLU* 3.0 6.6 - - - +
721B LEU* 2.8 35.4 + - + +
723B VAL* 4.2 15.9 - - + -
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Residues in contact with ILE 706 (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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209B ILE* 5.5 2.2 - - + -
224B SER* 3.7 25.1 - - - +
225B TRP* 4.1 4.9 - - - +
226B SER* 3.6 26.2 - - - +
293B THR* 3.5 28.4 - - + +
634B ILE* 4.0 1.3 - - - -
667B LEU* 3.5 3.1 - - - +
668B ASP* 2.8 58.1 + - + +
669B GLY* 4.8 2.2 - - - +
670B PRO* 5.0 2.2 - - + -
704B LYS* 3.2 31.9 - - + -
705B LEU* 1.3 74.0 - - - +
707B ALA* 1.3 63.5 + - - +
719B GLY 3.6 6.3 - - - +
720B GLU* 4.0 2.7 - - + -
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Residues in contact with ALA 707 (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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293B THR* 4.2 4.7 - - - -
632B ILE* 3.9 26.0 - - + -
634B ILE* 3.8 18.2 - - + -
650B VAL* 4.4 9.0 - - + -
666B HIS 3.1 13.7 - - - +
667B LEU* 4.8 3.1 - - + -
706B ILE* 1.3 77.2 - - - +
708B SER* 1.3 61.4 + - - +
718B TYR* 3.3 8.3 - - - +
719B GLY 2.9 28.2 + - - +
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Residues in contact with SER 708 (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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290B SER 4.2 2.0 - - - -
291B ALA* 2.6 32.9 + - - -
293B THR* 3.7 6.5 - - - +
632B ILE* 3.3 8.9 - - - +
664B TRP 4.5 0.2 - - - -
665B VAL* 3.4 5.0 - - - +
666B HIS* 3.0 39.9 + - - +
707B ALA* 1.3 74.5 - - - +
709B MET* 1.3 60.2 + - - +
717B VAL 3.1 7.6 - - - -
718B TYR* 3.7 22.7 - - - -
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Residues in contact with MET 709 (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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290B SER 5.3 1.6 - - - +
632B ILE* 3.5 15.5 - - + +
652B PHE* 3.9 27.1 - - + -
660B LEU* 5.0 1.6 - - - -
663B VAL* 3.6 27.8 - - + -
664B TRP 3.3 5.2 - - - +
665B VAL* 4.2 7.4 - - + -
708B SER* 1.3 79.0 - - - +
710B SER* 1.3 80.2 + - - +
711B SER* 3.9 6.1 - - - -
714B LEU* 3.8 22.7 - - + +
715B ARG* 3.8 8.8 - - - -
716B HIS 4.0 1.6 + - - -
717B VAL* 2.8 51.1 + - + +
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Residues in contact with SER 710 (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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288B PRO* 3.5 15.1 - - - +
291B ALA* 4.0 28.7 - - - +
662B ASN 3.7 1.4 - - - +
663B VAL* 3.4 1.0 - - - -
664B TRP* 2.6 47.7 + - - +
666B HIS* 5.7 0.2 - - - -
709B MET* 1.3 80.2 - - - +
711B SER* 1.3 61.3 + - - +
715B ARG* 3.3 29.9 + - - -
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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