Contacts of the strand formed by residues 779 - 788 (chain B) in PDB entry 2WIN
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 THR 779 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238A LEU 2.7 25.2 + - - -
239A TYR 4.4 0.9 - - - -
577A ASP* 3.7 0.7 - - - +
578A LYS* 3.1 53.7 + - + +
778B THR* 1.3 81.9 + - - +
780B TRP* 1.3 67.9 + - - +
800B GLU* 3.8 17.7 - - + +
801B VAL 3.2 10.8 - - - +
802B THR* 3.2 28.4 + - - +
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Residues in contact with TRP 780 (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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575A ALA* 4.8 10.1 - - + -
576A VAL* 3.7 7.9 - - - -
577A ASP* 3.5 36.8 - - + -
578A LYS* 4.6 0.2 - - - -
746B PRO 3.4 25.8 - - - -
747B GLU 4.4 1.6 - - - -
749B TRP* 3.2 43.0 - + + -
773B LEU* 4.6 13.4 - - + +
774B LYS* 4.0 18.9 + - + +
776B SER* 3.4 39.1 + - - -
778B THR* 4.3 8.4 + - + -
779B THR* 1.3 73.9 - - - +
781B GLU* 1.3 60.6 + - - +
782B ILE* 4.1 4.7 - - + -
799B PHE 3.7 0.4 - - - +
800B GLU* 3.1 7.1 - - - +
801B VAL* 2.8 39.2 + - + +
803B VAL* 3.8 29.4 - - + +
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Residues in contact with GLU 781 (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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574A VAL 3.6 3.6 - - - +
576A VAL* 2.9 36.6 + - - +
578A LYS* 4.3 10.7 - - + +
581A PHE* 3.1 36.5 - - + -
588A LYS* 3.3 16.0 + - - -
780B TRP* 1.3 73.8 - - - +
782B ILE* 1.3 62.9 + - - +
783B LEU* 3.7 3.9 + - + +
798B PRO* 3.7 32.6 - - + +
799B PHE 3.6 2.0 - - - +
800B GLU* 3.9 23.8 - - + +
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Residues in contact with ILE 782 (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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543A VAL* 4.7 14.1 - - + +
561A LEU* 3.8 34.1 - - + -
573A LEU* 4.7 8.5 - - + -
574A VAL 3.4 12.1 - - - +
575A ALA* 4.0 15.7 - - + -
749B TRP* 6.1 1.3 - - + -
750B LEU* 4.2 18.6 - - + -
771B ILE* 4.6 7.9 - - + -
780B TRP* 5.1 3.8 - - + -
781B GLU* 1.3 74.8 - - - +
783B LEU* 1.3 67.5 + - - +
784B ALA* 4.1 1.5 + - + +
797B ASP 4.6 0.7 - - - +
798B PRO* 3.5 5.2 - - - +
799B PHE* 2.8 52.6 + - + +
801B VAL* 4.5 11.9 - - + -
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Residues in contact with LEU 783 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A GLN* 3.8 23.6 + - + +
572A VAL 3.8 1.2 - - - +
573A LEU* 3.7 4.9 - - - +
574A VAL* 3.0 42.3 + - + +
588A LYS* 5.4 11.2 - - - +
589A LEU* 4.2 25.4 - - + +
781B GLU* 3.7 4.2 + - + +
782B ILE* 1.3 73.9 - - - +
784B ALA* 1.3 65.5 - - - +
785B VAL* 4.8 2.7 - - + -
795B VAL* 3.9 15.0 - - + -
796B ALA 3.6 24.2 - - - +
798B PRO* 4.4 17.9 - - + -
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Residues in contact with ALA 784 (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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541A LEU* 3.8 13.9 - - + -
543A VAL* 3.6 30.7 - - + -
571A VAL* 4.1 2.9 - - + -
572A VAL 3.7 3.4 - - - -
573A LEU* 3.7 15.9 - - + -
782B ILE* 4.1 2.5 + - + +
783B LEU* 1.3 77.0 - - - +
785B VAL* 1.3 69.3 + - - +
795B VAL* 3.7 1.4 - - - +
796B ALA* 2.9 32.3 + - + +
797B ASP 5.8 0.4 + - - -
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Residues in contact with VAL 785 (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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111A GLN* 4.5 19.3 - - - +
128A PHE* 3.7 30.9 - - + -
541A LEU* 3.8 1.6 - - - -
570A ARG 3.6 1.7 - - - +
571A VAL* 3.4 3.4 - - - +
572A VAL* 3.1 42.5 + - + +
589A LEU* 4.7 5.6 - - + -
783B LEU* 4.8 3.8 - - + -
784B ALA* 1.3 79.6 - - - +
786B SER* 1.3 62.5 + - - +
787B MET* 4.0 1.2 + - + +
793B ILE* 4.0 24.5 - - + -
794B CYS 3.5 5.2 - - - +
795B VAL* 4.0 22.0 - - + -
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Residues in contact with SER 786 (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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540A SER 4.9 2.5 + - - -
541A LEU* 3.3 24.3 - - - +
565A GLY* 5.9 0.2 - - - -
566A ASP* 5.4 6.4 + - - -
569A ALA* 4.5 12.1 - - - -
570A ARG 3.4 5.2 - - - -
571A VAL* 4.0 13.0 - - - -
785B VAL* 1.3 73.7 - - - +
787B MET* 1.3 61.2 + - - +
788B SER* 3.9 1.5 - - - -
792B GLY 3.6 1.6 + - - +
793B ILE* 3.3 6.9 - - - +
794B CYS* 3.0 47.3 + - - +
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Residues in contact with MET 787 (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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128A PHE* 3.6 35.0 - - + -
130A VAL* 3.8 22.7 - - + -
136A PRO* 4.0 21.1 - - + -
164A LEU* 3.2 40.4 - - + +
165A GLY 3.8 8.5 - - - +
166A VAL* 4.2 10.5 - - + -
568A GLY 5.1 0.3 - - - +
569A ALA* 4.2 0.4 - - - -
570A ARG* 2.9 30.9 + - + +
785B VAL 5.3 0.7 - - - +
786B SER* 1.3 72.7 - - - +
788B SER* 1.3 58.0 + - - +
789B ASP 4.1 0.3 + - - -
792B GLY 4.0 0.2 - - - -
793B ILE* 3.6 33.2 - - + -
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Residues in contact with SER 788 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A PRO* 3.4 8.1 - - - +
566A ASP* 4.6 6.0 - - - +
567A HIS 4.3 9.0 + - - -
568A GLY 5.0 1.6 - - - -
569A ALA* 3.5 26.5 + - - +
786B SER* 3.9 1.1 - - - -
787B MET* 1.3 75.6 - - - +
789B ASP* 1.3 63.0 + - - +
790B LYS* 3.1 15.8 + - - +
791B LYS* 3.5 21.0 + - - +
792B GLY* 2.9 37.2 + - - -
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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