Contacts of the strand formed by residues 740 - 746 (chain B) 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 SER 740 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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706B THR 3.4 6.5 - - - -
707B TRP* 2.9 48.2 + - - -
709B PRO* 4.2 9.9 - - - -
737B GLN* 4.3 9.9 + - - -
738B GLY 3.3 2.3 + - - -
739B LYS* 1.3 74.9 - - - +
741B TRP* 1.3 67.3 + - - +
756B SER* 3.9 1.2 - - - -
757B GLN* 2.9 39.2 + - - +
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Residues in contact with TRP 741 (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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703B LYS* 4.4 20.4 - - + -
706B THR* 2.4 76.7 + - + +
707B TRP* 3.4 9.9 + - - -
710B GLN* 4.3 24.2 - - + -
739B LYS* 4.0 27.6 - - + -
740B SER* 1.3 84.1 - - - +
742B GLN* 1.3 66.3 + - - +
743B MET* 4.1 27.6 - - + +
754B LYS* 4.4 19.0 - - + +
755B PHE 3.1 16.4 - - - +
756B SER* 4.1 11.4 - - - +
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Residues in contact with GLN 742 (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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208B TYR* 5.1 2.6 + - - -
705B SER* 5.6 2.6 - - - +
706B THR* 4.3 7.7 + - - +
707B TRP* 3.5 34.4 - - + +
741B TRP* 1.3 79.7 + - - +
743B MET* 1.3 76.5 + - - +
744B VAL* 3.8 12.0 + - + -
753B GLU 3.7 0.7 - - - +
754B LYS* 3.5 1.9 - - - +
755B PHE* 2.7 40.0 + - - +
793B ILE* 3.0 35.0 - - + +
794B GLY* 4.7 2.7 - - - -
1C PVE 5.8 1.4 + - - -
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Residues in contact with MET 743 (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 THR* 5.3 0.6 + - - +
741B TRP* 4.1 24.7 - - + +
742B GLN* 1.3 83.4 + - - +
744B VAL* 1.3 61.3 + - - +
752B TRP* 3.8 26.2 - - + -
753B GLU 3.5 4.3 - - - +
754B LYS* 3.9 35.0 - - + -
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Residues in contact with VAL 744 (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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368B LEU* 4.1 6.1 - - + -
369B PHE* 4.1 17.3 - - + -
742B GLN* 4.0 10.1 - - + -
743B MET* 1.3 79.1 - - - +
745B TYR* 1.3 60.4 + - - +
746B ASN 3.6 0.7 + - - -
752B TRP* 3.4 9.1 - - - -
753B GLU* 2.9 31.3 + - + -
755B PHE* 2.7 47.3 - - + -
793B ILE* 4.5 0.2 - - + -
794B GLY* 3.6 33.4 - - - +
797B THR* 5.3 4.9 - - + +
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Residues in contact with TYR 745 (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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369B PHE* 4.3 5.9 - - - -
744B VAL* 1.3 72.4 - - - +
746B ASN* 1.3 61.7 + - - +
747B ASN* 3.2 43.2 + - - +
750B SER* 3.5 27.4 + - - -
751B ARG* 3.6 22.2 - - - -
752B TRP* 3.6 45.3 - + + -
797B THR* 4.5 13.5 + - - +
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Residues in contact with ASN 746 (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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369B PHE* 3.4 25.3 - - + -
373B GLY* 3.0 26.3 + - - -
744B VAL 3.6 3.2 + - - -
745B TYR* 1.3 70.5 - - - +
747B ASN* 1.3 55.2 + - - +
748B PRO* 3.1 10.6 - - - +
749B ARG* 2.9 32.0 + - - +
750B SER* 2.8 22.3 + - - -
751B ARG* 2.9 27.2 + - + +
753B GLU* 2.9 28.9 + - - +
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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