Contacts of the strand formed by residues 739 - 742 (chain A) in PDB entry 4QUM
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 739 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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737A LEU* 3.5 4.7 - - - +
738A SER* 1.3 87.3 + - - +
740A ILE* 1.3 80.6 + - - +
741A VAL* 4.3 3.6 - - + -
802A THR* 3.4 27.8 - - + +
804A LEU* 4.2 9.2 - - + -
828A VAL* 3.9 20.6 - - + +
831A LEU* 3.7 40.2 - - + +
832A ARG* 5.8 0.4 - - - -
833A VAL 6.2 0.2 - - - +
836A GLU* 4.1 2.2 + - - +
837A PRO 5.4 0.6 + - - -
838A VAL* 4.0 35.6 - - + -
839A LEU* 3.1 24.3 + - - +
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Residues in contact with ILE 740 (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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728A PHE* 4.1 20.2 - - + -
729A TRP* 4.2 13.7 - - + -
732A VAL* 4.0 24.9 - - + -
737A LEU* 5.6 1.1 - - + -
739A LEU* 1.3 80.5 - - - +
741A VAL* 1.3 72.0 + - - +
757A TYR* 3.9 8.5 - - - +
788A MET* 5.8 0.2 - - - -
801A VAL* 3.7 22.4 - - + -
802A THR 2.9 8.8 + - - +
803A HIS* 3.5 31.3 - - + +
804A LEU 2.8 27.2 + - - -
839A LEU* 3.4 17.7 - - + +
841A HIS* 4.4 5.2 - - + -
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Residues in contact with VAL 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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739A LEU* 4.3 10.5 - - + -
740A ILE* 1.3 78.6 - - - +
742A MET* 1.3 62.0 + - - +
743A LEU* 3.8 15.7 - - + -
804A LEU* 3.5 5.2 - - + -
824A PHE* 3.7 33.4 - - + -
828A VAL* 4.1 20.9 - - + -
838A VAL* 4.0 20.2 - - + -
839A LEU 2.7 12.7 + - - +
840A VAL* 3.3 9.5 - - + +
841A HIS* 2.8 29.6 + - - +
852A LEU* 4.2 9.6 - - + -
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Residues in contact with MET 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 ILE* 4.1 0.4 - - + -
741A VAL* 1.3 72.4 - - - +
743A LEU* 1.3 61.8 + - - +
744A THR* 3.3 38.1 + - + +
746A LEU* 3.6 30.5 - - + -
754A CYS* 3.9 10.3 - - - -
757A TYR* 3.8 9.0 - - - -
758A TRP* 3.5 25.6 - - + -
803A HIS* 3.9 11.9 - - + +
804A LEU 2.7 13.7 + - - +
805A GLN* 3.2 16.2 - - + +
806A TYR* 2.8 27.5 + - - +
841A HIS* 3.3 25.6 - - + +
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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