Contacts of the strand formed by residues 929 - 933 (chain A) in PDB entry 4E5Z
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 929 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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923A VAL 4.0 0.9 - - - +
925A ASP* 3.2 30.1 + - - +
927A MET 3.0 8.5 + - - -
928A ARG* 1.3 79.5 - - - +
930A VAL* 1.3 79.1 + - - +
931A LEU* 5.1 0.2 - - - +
947A ARG* 3.4 3.1 + - - -
948A ASP* 3.4 19.7 + - - +
950A ASN 3.1 29.6 + - - -
951A PRO* 4.3 1.1 - - - -
952A ASN* 4.1 11.0 + - - +
954A MET* 3.7 17.5 - - - -
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Residues in contact with VAL 930 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
922A LEU* 3.5 30.3 - - + -
923A VAL 3.4 11.4 - - - +
924A GLY* 4.9 0.7 - - - -
929A SER* 1.3 92.6 + - - +
931A LEU* 1.3 65.7 + - - +
947A ARG* 3.6 10.4 + - - -
948A ASP* 3.4 26.3 + - + -
954A MET* 4.2 6.1 - - + -
957A VAL* 4.3 15.0 - - + -
965A PHE* 5.4 3.6 - - + -
975A PHE* 3.9 31.4 - - + -
977A CYS* 4.3 11.7 - - - -
992A LEU* 5.0 5.6 - - + -
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Residues in contact with LEU 931 (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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905A HIS* 3.4 31.4 - - + +
907A ASN 4.2 2.5 - - - +
908A ASN* 3.9 14.4 - - - +
921A ILE 3.5 1.4 - - - +
922A LEU* 3.5 5.9 - - - +
923A VAL* 2.7 50.9 + - + +
930A VAL* 1.3 75.6 - - - +
932A LEU* 1.3 62.1 + - - +
933A LEU* 3.9 10.0 + - + -
944A GLU* 3.6 26.0 - - + +
946A ALA 3.3 21.5 - - - +
947A ARG* 3.2 36.3 - - + +
992A LEU* 5.1 1.1 - - - -
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Residues in contact with LEU 932 (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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920A PHE* 3.9 20.9 - - + -
921A ILE 3.2 16.6 - - - +
922A LEU* 4.8 3.8 - - + +
931A LEU* 1.3 72.4 - - - +
933A LEU* 1.3 73.4 - - - +
944A GLU* 4.2 0.9 - - - -
945A ILE* 3.3 41.9 + - + +
946A ALA 3.2 19.2 + - - +
965A PHE* 3.7 29.8 - - + -
979A LYS* 3.6 32.3 - - + +
992A LEU* 4.4 18.3 - - + +
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Residues in contact with LEU 933 (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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888A VAL* 4.3 16.2 - - + -
905A HIS* 3.4 54.5 - - + +
920A PHE* 3.4 3.1 - - - -
921A ILE* 2.5 49.5 + - + +
923A VAL* 4.4 14.6 - - + -
931A LEU* 3.9 5.3 + - + -
932A LEU* 1.3 82.1 - - - +
934A ALA* 1.3 63.5 + - - +
942A PHE* 4.3 15.5 - - + -
943A GLU 3.2 20.6 - - - +
944A GLU* 4.0 10.1 - - + -
945A ILE* 4.6 1.1 - - - +
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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