Contacts of the strand formed by residues 715 - 723 (chain B) in PDB entry 1GYW
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 715 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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710B TYR* 3.5 10.8 - - + -
711B SER* 3.3 4.5 - - - -
712B LYS 2.9 33.7 + - - +
713B ASN 3.1 1.8 + - - -
714B GLY* 1.3 79.9 - - - +
716B LYS* 1.3 62.9 + - - +
717B ILE* 4.2 6.5 - - + -
737B ALA* 4.5 4.7 - - + -
738B SER 3.6 14.1 - - - +
745B MET* 3.6 27.4 - - + -
748B PHE* 4.0 22.4 - - + -
770B VAL* 4.4 8.3 - - + -
798B LEU* 3.8 25.8 - - + -
800B TYR* 3.7 28.9 - - + +
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Residues in contact with LYS 716 (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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708B THR* 3.5 28.7 + - + -
710B TYR 3.3 8.1 - - - +
711B SER* 4.4 10.3 - - - +
714B GLY 3.7 2.8 + - - +
715B LEU* 1.3 74.4 - - - +
717B ILE* 1.3 67.0 + - - +
718B GLU* 3.1 25.7 + - + +
736B GLN 3.3 2.1 - - - +
737B ALA* 3.3 3.6 - - - +
738B SER* 2.9 54.4 + - - +
774B ASN* 6.1 0.4 - - - +
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Residues in contact with ILE 717 (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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708B THR* 3.7 2.1 - - - -
709B ALA* 3.0 25.2 + - + -
710B TYR* 2.7 31.2 + - + +
715B LEU* 4.2 9.0 - - + -
716B LYS* 1.3 81.0 - - - +
718B GLU* 1.3 65.5 + - - +
719B PHE* 3.8 25.6 - - + -
735B ILE* 4.1 17.3 - - + -
736B GLN 3.4 4.5 - - - +
737B ALA* 4.3 13.5 - - + -
748B PHE* 4.8 2.9 - - + -
750B PHE* 4.5 5.6 - - + -
796B ILE* 4.6 3.4 - - + -
798B LEU* 3.4 46.7 - - + -
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Residues in contact with GLU 718 (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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706B SER* 5.0 7.7 + - - -
707B ILE 3.2 20.6 - - - +
708B THR* 4.0 5.4 + - - +
716B LYS* 3.1 33.7 + - + +
717B ILE* 1.3 73.8 - - - +
719B PHE* 1.3 69.6 + - - +
720B THR* 4.8 10.1 - - + +
734B THR 3.7 0.4 - - - +
735B ILE* 3.1 5.7 - - - +
736B GLN* 2.7 53.9 + - + +
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Residues in contact with PHE 719 (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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706B SER* 3.5 7.4 + - - -
707B ILE* 3.1 48.8 + - + +
709B ALA* 3.7 29.4 - - + +
717B ILE* 3.8 12.1 - - + -
718B GLU* 1.3 81.7 - - - +
720B THR* 1.3 60.9 + - - +
721B PHE* 3.9 11.0 - + + -
733B ILE* 3.8 16.2 - - + -
734B THR 3.5 3.8 - - - -
735B ILE* 3.7 24.7 - - + -
750B PHE* 4.2 17.3 - + - -
782B ILE* 4.7 1.3 - - + -
794B MET* 4.3 15.0 - - - -
796B ILE* 4.6 7.2 - - + -
813B VAL* 4.5 4.9 - - + -
816B PHE* 4.0 25.1 - + - -
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Residues in contact with THR 720 (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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706B SER* 3.3 22.7 - - - +
718B GLU* 4.8 11.9 - - + +
719B PHE* 1.3 75.0 - - - +
721B PHE* 1.3 65.4 + - - +
733B ILE* 3.3 5.9 - - - +
734B THR* 2.9 55.0 + - - +
736B GLN* 5.3 10.4 + - + +
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Residues in contact with PHE 721 (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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704B ILE* 3.4 41.0 + - + +
705B PRO 3.3 27.1 - - - -
707B ILE* 3.9 19.5 - - + -
719B PHE* 3.9 28.0 - + + -
720B THR* 1.3 79.4 - - - +
722B GLU* 1.3 74.3 + - - +
731B THR* 4.2 6.3 - - + -
732B VAL 3.3 4.7 - - - +
733B ILE* 3.7 32.5 - - + -
792B LEU* 5.1 0.2 - - + -
816B PHE* 3.9 18.8 - + - -
817B PRO* 4.0 12.3 - - + -
820B SER* 3.7 21.8 - - - -
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Residues in contact with GLU 722 (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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704B ILE* 4.1 3.8 - - - -
721B PHE* 1.3 84.7 - - - +
723B ARG* 1.3 69.7 + - - +
724B SER 3.6 0.2 + - - -
731B THR* 3.7 1.0 - - - -
732B VAL* 2.8 52.0 + - + +
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Residues in contact with ARG 723 (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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704B ILE* 3.7 14.5 - - + +
722B GLU* 1.3 83.0 + - - +
724B SER* 1.3 69.4 + - - +
725B ASN* 4.1 6.4 + - - -
728B PRO* 3.9 26.7 + - + +
729B SER* 5.4 1.6 - - - +
730B VAL 3.7 9.9 - - - -
731B THR* 3.4 23.1 + - - +
789B LYS* 5.1 7.9 - - - +
819B GLN 2.7 29.9 + - - -
821B TRP* 3.4 19.2 + - - +
822B GLN* 2.8 32.6 + - - -
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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