Contacts of the strand formed by residues 697 - 702 (chain A) in PDB entry 3AR2
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 ILE 697 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A THR* 3.7 30.3 - - + +
344A CYS* 3.4 23.9 + - + +
345A THR* 3.5 26.0 - - - +
346A SER* 3.1 28.0 + - - -
347A VAL 3.7 1.7 + - - -
695A ASP 4.9 1.3 - - - +
696A GLU* 1.3 75.2 - - - +
698A THR* 1.3 60.0 + - - +
715A GLU* 3.6 19.7 - - + -
716A ILE* 5.3 0.7 - - + -
824A PRO* 3.7 37.4 - - + +
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Residues in contact with THR 698 (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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345A THR* 4.7 0.9 - - - -
347A VAL* 3.7 12.5 - - + +
349A CYS* 4.2 15.3 - - - -
688A VAL* 4.1 20.2 - - + -
691A LEU* 3.8 20.3 - - + +
692A GLN* 3.3 25.4 - - - +
696A GLU* 3.3 7.8 + - - +
697A ILE* 1.3 75.3 - - - +
699A ALA* 1.3 73.0 + - - +
714A ALA* 3.5 0.8 - - - +
715A GLU* 2.8 44.1 + - - +
716A ILE* 3.4 2.9 + - - +
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Residues in contact with ALA 699 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A LEU* 4.4 6.3 - - + -
345A THR* 4.1 12.5 - - + +
347A VAL 3.1 11.6 + - - +
348A ILE* 4.3 13.5 - - + -
349A CYS* 3.0 27.5 + - - +
698A THR* 1.3 80.2 - - - +
700A MET* 1.3 62.3 + - - +
714A ALA* 3.8 2.2 - - - +
716A ILE* 3.0 27.1 - - + +
718A ILE* 4.8 7.9 - - + -
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Residues in contact with MET 700 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A CYS* 3.3 23.3 - - - +
350A SER 4.3 1.6 - - - -
351A ASP 3.8 11.9 - - - +
624A ILE* 4.8 6.3 - - + -
684A LYS* 4.2 10.8 - - + -
688A VAL* 4.3 5.4 - - + -
699A ALA* 1.3 77.4 - - - +
701A THR* 1.3 83.4 + - - +
707A ASP* 4.1 21.1 - - - +
710A ALA* 3.5 33.2 - - + +
711A LEU* 3.4 22.3 - - + +
714A ALA* 3.7 17.9 - - + -
716A ILE 3.1 4.8 + - - -
717A GLY* 3.3 1.4 - - - -
718A ILE* 2.8 27.5 + - - +
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Residues in contact with THR 701 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ILE* 4.1 10.0 - - - +
349A CYS 2.8 12.9 + - - -
350A SER* 3.9 12.6 - - - -
351A ASP* 2.7 33.3 + - - +
355A THR* 3.7 17.5 - - + +
699A ALA* 5.5 0.2 - - - +
700A MET* 1.3 83.2 + - - +
702A GLY* 1.3 56.1 + - - +
718A ILE* 3.1 24.6 - - + +
720A MET* 4.4 11.4 - - - -
740A PHE* 4.4 2.7 - - + -
743A ILE* 3.9 31.1 - - + +
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Residues in contact with GLY 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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351A ASP* 3.8 0.2 - - - -
355A THR* 3.3 13.0 - - - -
700A MET 4.3 0.6 - - - -
701A THR* 1.3 75.6 - - - +
703A ASP* 1.3 60.1 + - - -
707A ASP* 3.1 20.2 - - - -
711A LEU* 4.3 10.4 - - - +
718A ILE 3.1 6.7 + - - -
719A ALA* 3.2 9.0 - - - +
720A MET* 3.0 24.5 + - - -
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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