Contacts of the strand formed by residues 701 - 710 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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700A SER* 1.3 76.8 - - - +
702A HIS* 1.3 66.9 + - - -
703A ARG* 3.1 8.8 + - - +
724A GLN* 3.5 20.9 - - - -
725A ILE* 2.8 32.4 + - - +
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Residues in contact with HIS 702 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A ILE* 5.1 1.7 - - + +
472A ASP* 5.8 0.4 + - - -
701A GLY* 1.3 69.5 - - - -
703A ARG* 1.3 114.5 + - - +
704A LYS* 4.7 5.8 - - + -
722A ASP* 3.0 36.9 + - + -
723A VAL 3.3 6.0 + - - -
724A GLN* 3.4 20.7 + - - +
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Residues in contact with ARG 703 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A LYS* 5.8 3.8 - - - +
207A ASN* 4.9 3.4 + - - +
208A ASP* 2.8 41.1 + - - +
209A ILE* 4.1 14.9 - - - +
670A PRO* 2.9 32.2 + - - +
671A GLY* 4.6 0.4 - - - -
672A VAL* 3.8 16.4 - - + -
699A VAL* 3.8 43.8 - - - +
700A SER 4.7 1.4 + - - -
701A GLY 3.1 11.6 + - - +
702A HIS* 1.3 115.9 + - - +
704A LYS* 1.3 63.2 + - - +
723A VAL* 2.7 29.0 + - + +
725A ILE* 3.8 4.9 - - + -
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Residues in contact with LYS 704 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A ILE* 3.8 34.7 - - + +
211A VAL* 5.0 0.6 - - - +
224A SER* 3.5 24.7 + - - +
472A ASP* 2.5 38.0 + - - -
669A GLY* 3.3 24.4 - - - -
670A PRO* 4.7 1.6 + - - +
672A VAL* 4.5 4.3 - - - +
702A HIS* 4.7 5.6 - - + -
703A ARG* 1.3 80.4 - - - +
705A LEU* 1.3 75.3 + - - +
706A ILE* 4.2 6.0 - - + +
720A GLU* 3.0 19.2 + - + +
721A LEU 3.4 12.3 - - - +
722A ASP* 2.9 23.3 + - - +
723A VAL* 4.0 2.8 - - - +
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Residues in contact with LEU 705 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634A ILE* 3.9 20.4 - - + -
636A VAL* 3.7 22.0 - - + -
646A MET* 4.4 4.3 - - + -
648A VAL* 3.6 35.2 - - + -
667A LEU* 4.3 12.1 - - + -
668A ASP 3.5 11.2 - - - +
672A VAL* 3.9 28.3 - - + -
673A THR* 4.4 9.0 - - + -
695A CYS* 4.9 0.4 - - - -
704A LYS* 1.3 75.9 - - - +
706A ILE* 1.3 60.0 + - - +
720A GLU* 3.2 6.6 - - - +
721A LEU* 2.7 35.5 + - + +
723A VAL* 4.2 15.3 - - + -
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Residues in contact with ILE 706 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A ILE* 4.6 7.0 - - + -
224A SER* 3.6 42.4 - - - +
225A TRP 4.4 1.6 - - - +
226A SER* 4.3 19.3 - - - +
293A THR* 3.9 26.6 - - + +
634A ILE* 3.9 2.6 - - - +
666A HIS 4.4 0.2 - - - -
667A LEU* 3.3 4.4 - - - +
668A ASP* 2.6 44.1 + - + +
669A GLY* 4.7 7.9 - - - -
670A PRO* 4.8 5.8 - - + -
704A LYS* 4.2 19.1 - - + +
705A LEU* 1.3 78.7 - - - +
707A ALA* 1.3 66.5 + - - +
718A TYR* 6.4 0.7 - - + -
719A GLY 3.6 6.5 - - - +
720A GLU* 4.4 2.5 - - + -
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Residues in contact with ALA 707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A THR* 4.2 4.5 - - - -
632A ILE* 3.8 17.0 - - + -
634A ILE* 3.8 15.0 - - + -
650A VAL* 3.8 16.8 - - + -
666A HIS 2.9 13.9 - - - +
667A LEU* 4.7 1.6 - - + -
706A ILE* 1.3 79.5 - - - +
708A SER* 1.3 61.8 + - - +
718A TYR* 3.3 8.5 - - - +
719A GLY 2.8 32.1 + - - +
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Residues in contact with SER 708 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A SER 4.2 3.1 - - - -
291A ALA* 2.7 31.7 + - - -
293A THR* 4.0 4.4 - - - +
632A ILE* 3.5 4.0 - - - -
664A TRP 4.6 0.2 - - - -
665A VAL* 3.4 9.0 - - - +
666A HIS* 2.8 37.0 + - - +
707A ALA* 1.3 75.0 - - - +
709A MET* 1.3 62.4 + - - +
717A VAL 3.0 13.7 - - - -
718A TYR* 3.5 21.3 - - - -
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Residues in contact with MET 709 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A SER 5.4 0.7 - - - +
291A ALA* 5.6 0.2 - - - -
632A ILE* 4.0 8.1 - - + -
652A PHE* 3.4 33.2 - - + -
660A LEU* 4.8 1.3 - - + -
663A VAL* 3.5 28.7 - - + -
664A TRP 3.4 6.5 - - - +
665A VAL* 4.2 6.5 - - + -
708A SER* 1.3 80.9 - - - +
710A SER* 1.3 82.1 + - - +
711A SER* 3.6 7.2 - - - -
714A LEU* 3.7 17.5 - - + +
715A ARG* 3.8 3.8 - - - -
716A HIS 3.9 0.9 + - - -
717A VAL* 2.8 63.7 + - + +
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Residues in contact with SER 710 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A PRO* 4.2 13.4 - - - +
290A SER 4.4 0.9 - - - -
291A ALA* 3.7 32.5 + - - +
662A ASN 3.5 2.1 - - - +
663A VAL* 3.6 0.3 - - - -
664A TRP* 2.8 41.5 + - - +
708A SER* 5.2 0.2 + - - -
709A MET* 1.3 75.7 + - - +
711A SER* 1.3 64.2 - - - +
715A ARG* 3.4 26.7 - - - +
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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