Contacts of the strand formed by residues 687 - 690 (chain A) in PDB entry 3L7A
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 LEU 687 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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661A ASP 2.9 10.5 + - - +
662A LEU* 3.4 7.2 - - + +
663A SER* 2.8 25.6 + - - -
685A GLY 4.3 0.2 + - - -
686A ALA* 1.3 76.3 - - - +
688A THR* 1.3 61.3 + - - +
707A ASN 4.5 2.2 - - - +
709A PHE* 3.8 24.7 - - + -
790A LEU* 4.0 2.9 - - + -
797A TRP* 3.7 44.4 - - + +
800A MET* 3.9 20.9 - - + -
801A VAL* 3.8 35.0 - - + +
804A ASN* 3.8 24.2 - - - +
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Residues in contact with THR 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662A LEU* 4.2 1.6 - - - -
663A SER* 3.6 17.6 + - - +
665A GLN* 4.0 19.5 - - + -
678A ASN 4.8 2.4 + - - -
682A MET* 5.2 4.3 + - - +
686A ALA 4.2 3.7 + - - -
687A LEU* 1.3 77.6 + - - +
689A ILE* 1.3 70.0 + - - +
690A GLY* 4.3 3.1 - - - +
696A ASN* 5.2 4.5 - - - +
699A MET* 4.1 12.1 - - + +
707A ASN 5.6 0.4 + - - -
708A PHE* 3.5 38.8 - - + +
709A PHE* 2.9 32.2 + - - +
804A ASN* 4.9 4.9 + - - -
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Residues in contact with ILE 689 (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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662A LEU* 3.7 23.3 - - + +
663A SER 3.0 13.4 + - - +
664A GLU* 3.5 27.4 - - - +
665A GLN* 3.0 25.1 + - - -
666A ILE* 3.7 2.4 - - + +
688A THR* 1.3 74.6 - - - +
690A GLY* 1.3 60.4 + - - +
709A PHE* 3.3 14.4 - - + +
711A PHE* 3.8 13.2 - - + -
780A TYR* 3.9 12.6 - - + -
783A CYS* 3.7 22.9 - - + -
784A GLN* 3.7 35.7 - - + +
787A VAL* 4.5 3.6 - - + -
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Residues in contact with GLY 690 (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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665A GLN* 3.1 12.8 - - - -
688A THR* 4.0 4.7 - - - +
689A ILE* 1.3 78.8 - - - +
691A THR* 1.3 64.3 + - - -
696A ASN* 4.1 7.2 - - - -
708A PHE* 5.9 1.7 - - - -
709A PHE 3.0 8.3 + - - -
710A ILE* 3.3 10.5 - - - +
711A PHE* 3.2 32.9 + - - -
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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