Contacts of the strand formed by residues 793 - 797 (chain A) in PDB entry 2R4B
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 GLN 793 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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715A GLU* 4.8 4.0 - - - +
718A LEU* 4.1 10.0 - - - +
720A ARG* 2.9 37.8 + - - +
750A ILE* 3.6 16.5 - - + +
751A LYS 3.4 4.3 - - - +
752A ILE* 3.9 17.2 - - + +
786A VAL* 3.4 8.5 - - - +
787A CYS* 2.6 47.7 + - + +
789A SER 2.8 27.8 + - - -
790A PRO* 3.4 15.2 - - - +
791A THR* 3.4 8.9 + - - +
792A ILE* 1.3 74.8 - - - +
794A LEU* 1.3 63.6 + - - +
795A VAL* 4.0 1.6 + - + +
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Residues in contact with LEU 794 (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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1A GW7 3.2 37.9 - - + +
750A ILE* 3.2 6.4 - - - -
751A LYS* 2.8 46.8 + - + +
753A LEU* 4.8 6.1 - - + -
765A PHE* 3.2 36.3 - - + -
769A ALA* 5.2 0.4 - - + -
772A MET* 4.3 11.0 - - - -
783A LEU* 3.9 28.7 - - + -
785A GLY 4.1 1.3 - - - -
786A VAL* 4.1 7.4 - - + -
792A ILE* 5.4 0.2 - - + -
793A GLN* 1.3 73.3 - - - +
795A VAL* 1.3 59.7 + - - +
864A LEU* 4.1 22.7 - - + -
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Residues in contact with VAL 795 (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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713A LEU* 3.8 20.4 - - + -
718A LEU* 3.8 39.9 - - + -
737A TRP* 4.9 3.4 - - + -
748A VAL* 3.9 29.6 - - + -
749A ALA 3.5 2.9 - - - +
750A ILE* 4.4 7.9 - - + -
783A LEU* 3.4 5.7 - - - +
784A LEU* 2.9 27.5 + - + +
785A GLY 3.0 20.6 + - - +
787A CYS 4.9 1.6 - - - +
793A GLN 4.4 7.0 - - - +
794A LEU* 1.3 77.7 - - - +
796A THR* 1.3 63.4 + - - +
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Residues in contact with THR 796 (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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1A GW7 3.4 68.3 - - + +
748A VAL* 3.3 6.1 - - - +
749A ALA 2.8 34.9 + - - +
781A VAL* 4.3 10.8 - - + +
782A ARG 2.9 21.0 + - - -
784A LEU* 4.2 10.1 - - - +
795A VAL* 1.3 76.9 - - - +
797A GLN* 1.3 62.2 + - - +
860A THR* 5.6 1.6 - - - +
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Residues in contact with GLN 797 (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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1A GW7 3.3 13.9 - - - -
746A ILE* 5.2 5.6 - - + -
747A PRO* 3.9 14.2 - - + +
781A VAL* 6.0 1.2 - - - +
782A ARG 4.7 1.1 + - - +
784A LEU* 3.7 23.4 - - + +
796A THR* 1.3 79.8 + - - +
798A LEU* 1.3 71.4 + - - +
799A MET* 3.6 29.0 + - + +
800A PRO* 5.7 2.2 - - - +
852A LYS* 5.2 14.8 + - - +
858A LYS* 5.5 3.3 + - - -
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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