Contacts of the strand formed by residues 952 - 961 (chain A) in PDB entry 2VZ9
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 952 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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921A GLN* 4.3 23.0 + - - -
947A SER* 3.4 6.6 - - - -
948A ASP* 3.3 42.2 + - - -
950A ASN* 3.4 16.1 + - - +
951A GLY* 1.3 80.0 - - - +
953A LEU* 1.3 63.7 + - - +
954A ILE* 3.7 1.0 + - - +
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Residues in contact with LEU 953 (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 HIS* 3.9 43.5 - - + +
921A GLN* 3.9 10.4 + - - +
945A GLU* 3.9 35.4 - - + +
946A VAL 4.0 2.0 - - - +
947A SER* 5.1 0.4 - - - +
951A GLY 3.9 0.2 + - - -
952A SER* 1.3 73.2 - - - +
954A ILE* 1.3 78.7 + - - +
955A ALA 3.7 15.7 - - - +
956A SER* 4.6 6.7 - - - +
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Residues in contact with ILE 954 (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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891A TYR* 3.3 46.2 - - + +
919A LEU* 3.5 2.8 - - - +
920A HIS* 2.9 26.1 + - - -
921A GLN* 3.7 34.3 - - + +
922A ALA 5.0 0.7 - - - +
923A THR* 3.9 15.0 - - - +
933A LEU* 4.6 2.5 - - + -
946A VAL* 2.9 28.0 + - + +
947A SER 4.3 2.5 - - - +
948A ASP* 4.0 24.9 - - + +
952A SER* 4.1 6.5 - - - +
953A LEU* 1.3 81.7 - - - +
955A ALA* 1.3 59.6 + - - +
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Residues in contact with ALA 955 (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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891A TYR* 4.2 20.9 - - + -
917A VAL* 5.2 0.9 - - + -
918A THR 3.3 5.8 - - - -
919A LEU* 3.7 26.0 - - + -
920A HIS* 4.0 0.9 - - - -
944A PHE* 4.0 8.7 - - + -
945A GLU* 3.3 4.2 - - - -
946A VAL* 2.7 41.0 + - + +
953A LEU* 3.7 3.1 - - - +
954A ILE* 1.3 83.4 - - - +
956A SER* 1.3 61.7 + - - +
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Residues in contact with SER 956 (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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916A ASP 3.6 2.6 - - - +
917A VAL* 3.3 0.9 - - - +
918A THR* 2.8 33.5 + - - +
920A HIS* 2.8 29.7 + - - -
944A PHE* 3.4 14.6 - - - -
945A GLU* 4.8 3.8 - - - -
953A LEU* 4.6 11.8 - - - +
955A ALA* 1.3 76.4 - - - +
957A GLY* 1.3 58.8 + - - +
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Residues in contact with GLY 957 (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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915A GLU 3.8 9.0 - - - -
916A ASP* 4.0 7.2 - - - -
917A VAL* 4.0 1.8 - - - -
943A ALA* 3.4 4.0 - - - +
944A PHE* 3.1 41.9 + - - +
956A SER* 1.3 76.0 - - - +
958A LYS* 1.3 69.3 + - - +
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Residues in contact with LYS 958 (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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913A VAL 3.5 0.5 - - - +
914A PHE* 3.2 6.2 - - - -
915A GLU* 2.9 56.4 + - + +
916A ASP* 5.5 7.5 + - + +
941A SER* 4.1 19.6 + - - +
942A HIS* 3.1 18.6 - - + +
943A ALA* 4.2 8.3 - - + -
944A PHE* 3.3 4.6 - - - -
957A GLY* 1.3 79.5 - - - +
959A VAL* 1.3 61.3 + - - +
960A TYR* 4.9 4.5 - - + -
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Residues in contact with VAL 959 (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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895A THR* 3.9 10.5 - - + -
896A TRP* 5.6 0.4 - - - +
899A LEU* 4.1 15.9 - - + +
912A VAL* 3.9 4.3 - - + -
913A VAL 3.1 6.1 - - - +
914A PHE* 3.2 52.5 - - + -
937A LEU* 4.0 13.6 - - + +
942A HIS* 2.9 20.6 + - - +
944A PHE* 3.1 31.2 - - + -
958A LYS* 1.3 70.5 - - - +
960A TYR* 1.3 71.5 + - - +
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Residues in contact with TYR 960 (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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899A LEU* 3.7 14.7 - - - +
912A VAL* 3.5 2.3 - - - +
913A VAL* 3.0 56.5 + - + +
915A GLU* 3.1 40.4 + - + -
942A HIS* 3.9 38.4 - + + +
958A LYS* 4.9 3.4 - - + -
959A VAL* 1.3 83.6 - - - +
961A GLN* 1.3 89.1 + - - +
962A TRP* 3.4 3.3 + + - -
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Residues in contact with GLN 961 (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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899A LEU* 4.1 7.1 - - - +
903A LEU* 3.6 17.8 - - + +
905A GLN* 3.1 39.8 + - - +
909A GLU 3.8 11.9 + - - -
910A THR* 3.8 14.5 - - + +
911A PRO* 3.7 15.3 - - + +
912A VAL* 4.8 0.4 - - - +
960A TYR* 1.3 88.2 - - - +
962A TRP* 1.3 64.1 + - - +
963A GLU* 3.5 26.5 + - - +
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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