Contacts of the strand formed by residues 711 - 720 (chain A) in PDB entry 2W77
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 ASP 711 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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673A TYR* 4.9 1.0 + - - -
691A TYR* 2.7 27.3 + - - +
692A THR 3.5 3.1 - - - -
693A HIS* 3.0 28.5 + - - +
709A PRO* 3.8 3.4 - - - +
710A GLN* 1.3 92.6 + - - +
712A GLN* 1.3 62.4 + - - +
736A TRP* 3.9 20.3 - - + -
737A GLN* 3.5 3.3 - - - +
738A GLY* 2.9 31.0 + - - +
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Residues in contact with GLN 712 (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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194A GLY* 3.5 27.6 + - - +
195A ILE 3.2 8.1 + - - +
196A THR* 3.3 19.8 + - - -
691A TYR* 3.3 11.4 - - - -
692A THR* 2.9 51.9 + - - +
694A LYS* 6.3 1.2 - - - +
708A GLU* 4.8 8.1 + - - +
709A PRO* 4.8 7.7 + - + +
711A ASP* 1.3 76.2 - - - +
713A LEU* 1.3 61.7 + - - +
735A ARG* 2.6 47.0 + - - +
736A TRP* 3.5 11.4 - - - +
737A GLN* 4.3 4.3 - - + -
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Residues in contact with LEU 713 (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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689A ALA* 5.5 1.8 - - + -
690A GLY 3.4 15.5 - - - +
691A TYR* 4.1 16.8 - - + -
712A GLN* 1.3 76.3 - - - +
714A SER* 1.3 79.4 + - - +
715A LEU* 4.5 9.9 - - + +
734A ALA 5.5 1.3 - - - +
735A ARG* 3.3 8.2 - - - -
736A TRP* 2.9 49.1 + - + +
761A TRP* 3.8 32.5 - - + -
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Residues in contact with SER 714 (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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190A ARG 4.8 3.5 + - - -
191A HIS 4.9 1.6 + - - -
192A THR 4.8 1.9 + - - -
193A PRO* 4.5 21.9 - - - +
688A GLN 5.3 0.2 - - - -
689A ALA* 2.9 7.1 - - - +
690A GLY 2.8 39.2 + - - +
713A LEU* 1.3 75.2 + - - +
715A LEU* 1.3 60.5 + - - +
716A TYR* 4.2 16.0 - - - -
734A ALA 3.7 5.2 - - - -
735A ARG* 3.5 30.8 + - - +
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Residues in contact with LEU 715 (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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687A VAL* 5.0 9.9 - - + -
688A GLN 3.6 3.4 - - - -
689A ALA* 3.7 14.4 - - + -
713A LEU* 4.5 9.2 - - + +
714A SER* 1.3 76.6 - - - +
716A TYR* 1.3 68.2 + - - +
717A THR* 4.2 25.6 - - + -
733A GLY* 3.1 7.7 - - - -
734A ALA* 2.9 43.3 + - + +
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Residues in contact with TYR 716 (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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147A TYR* 4.4 4.0 - - + -
176A ASN* 5.0 5.8 - - - +
180A PHE* 3.8 26.2 - + + -
190A ARG 4.9 2.1 + - - -
191A HIS* 3.4 63.3 + + + -
687A VAL* 3.2 5.5 - - - +
688A GLN* 2.8 45.5 + - + +
714A SER* 4.2 16.4 - - - -
715A LEU* 1.3 77.8 - - - +
717A THR* 1.3 62.6 + - - +
732A GLY 3.8 0.4 - - - -
733A GLY* 3.5 24.2 - - - -
734A ALA* 4.2 15.6 + - - -
735A ARG* 4.0 16.8 - - + +
762A LEU* 5.1 1.9 + - - +
764A ASP* 3.6 16.7 + - + -
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Residues in contact with THR 717 (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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147A TYR* 4.5 2.0 - - - -
180A PHE* 3.5 8.6 - - - -
685A TRP* 3.0 27.2 + - + +
686A GLN 2.7 18.3 + - - -
687A VAL* 3.3 13.1 - - - +
715A LEU* 4.2 14.1 - - + -
716A TYR* 1.3 79.3 - - - +
718A SER* 1.3 61.0 + - - +
731A GLY* 3.2 2.9 - - - -
732A GLY 2.9 46.5 + - - +
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Residues in contact with SER 718 (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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147A TYR* 2.8 29.9 + - - -
179A ASP* 3.9 5.4 + - - -
180A PHE* 5.1 1.3 - - - -
684A GLY 3.9 0.9 - - - +
685A TRP* 3.4 6.0 - - - -
686A GLN* 2.9 36.0 + - - +
717A THR* 1.3 76.9 + - - +
719A TYR* 1.3 60.7 + - - +
729A THR* 4.2 13.4 - - - +
730A VAL 3.1 15.3 - - - -
731A GLY* 3.9 4.9 - - - -
766A MET* 4.7 5.2 - - - -
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Residues in contact with TYR 719 (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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682A ALA* 6.1 1.6 - - + -
684A GLY* 3.4 27.2 + - - -
685A TRP* 3.8 25.8 - + + +
718A SER* 1.3 75.4 - - - +
720A LYS* 1.3 76.1 + - - +
721A PHE* 3.6 43.8 + + - -
722A LYS* 4.8 5.4 + - - +
728A LEU 4.1 0.2 - - - +
729A THR* 3.4 5.3 - - - -
730A VAL* 2.8 42.3 + - + +
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Residues in contact with LYS 720 (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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684A GLY* 2.9 26.7 + - - +
719A TYR* 1.3 85.5 - - - +
721A PHE* 1.3 70.1 + - - +
722A LYS* 3.8 2.4 + - + +
726A ASP* 2.9 27.7 + - + +
727A LYS* 4.5 6.9 + - - +
728A LEU 3.9 4.7 - - - +
729A THR* 3.3 24.2 + - + +
770A GLN* 5.6 4.9 - - - +
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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