Contacts of the strand formed by residues 740 - 746 (chain A) in PDB entry 2HWK
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 PHE 740 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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708A CYS* 3.8 13.9 - - - -
711A LEU* 3.5 33.7 - - + -
715A GLY 3.8 3.1 - - - -
717A CYS* 4.0 5.6 - - + -
736A ILE* 3.1 37.9 - - + -
737A ALA 3.3 11.4 + - - +
738A ARG* 4.8 0.9 - - - -
739A GLN* 1.3 86.9 + - + +
741A LYS* 1.3 65.7 + - - +
742A PHE* 3.3 13.9 + - - +
743A SER* 4.5 0.8 + - - +
761A PHE* 3.5 46.9 - + + -
762A ILE 3.4 9.0 - - - +
763A GLY 3.1 4.0 - - - -
764A TYR* 3.5 27.1 - + + -
769A ARG* 3.4 16.5 + - - -
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Residues in contact with LYS 741 (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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714A GLY* 4.7 9.7 + - - -
740A PHE* 1.3 73.7 - - - +
742A PHE* 1.3 95.8 + - + +
762A ILE* 3.6 6.3 - - - +
763A GLY* 2.7 40.9 + - - +
765A ASP* 3.7 9.2 - - + +
769A ARG* 3.6 36.3 + - - +
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Residues in contact with PHE 742 (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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740A PHE* 3.2 5.6 - - - +
741A LYS* 1.3 120.2 - - + +
743A SER* 1.3 68.4 + - - +
744A ARG* 4.3 6.7 - - + -
761A PHE* 3.6 0.7 - - - -
762A ILE* 3.0 56.2 + - + +
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Residues in contact with SER 743 (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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737A ALA* 3.4 37.4 + - - +
740A PHE 4.7 0.5 + - - -
742A PHE* 1.3 79.1 + - - +
744A ARG* 1.3 64.4 + - - +
760A VAL 3.5 4.9 - - - -
761A PHE* 3.7 12.4 - - - -
772A ASN* 3.9 27.5 + - - +
775A LYS* 5.9 0.9 - - - +
776A LEU* 3.2 23.2 - - - +
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Residues in contact with ARG 744 (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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742A PHE* 4.3 6.7 - - + -
743A SER* 1.3 79.4 - - - +
745A VAL* 1.3 88.9 + - - +
746A CYS* 4.1 25.3 - - - +
759A PHE* 3.8 2.6 - - - +
760A VAL* 2.8 44.2 + - + +
761A PHE* 5.8 1.4 - - - -
762A ILE* 5.9 5.2 - - + -
776A LEU* 3.9 4.7 - - - +
779A THR* 4.3 19.6 + - - +
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Residues in contact with VAL 745 (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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744A ARG* 1.3 101.6 + - - +
746A CYS* 1.3 63.0 + - - +
757A VAL* 3.8 15.7 - - + -
758A LEU 3.4 9.6 - - - +
759A PHE* 3.9 24.2 - - + -
776A LEU* 3.9 24.1 - - + +
779A THR* 3.6 20.5 - - + +
780A LEU* 3.6 33.4 - - + -
783A ILE* 3.8 13.7 - - + +
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Residues in contact with CYS 746 (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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625A PHE* 4.3 26.9 - - + -
744A ARG* 4.1 27.1 - - - +
745A VAL* 1.3 82.1 - - - +
747A LYS* 1.3 60.2 + - - +
748A PRO* 3.9 3.6 - - + -
757A VAL* 3.7 2.9 - - - +
758A LEU* 2.8 38.0 + - + +
760A VAL* 4.2 18.2 - - + -
783A ILE* 4.7 0.9 - - - -
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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