Contacts of the strand formed by residues 962 - 966 (chain A) in PDB entry 5D6Y
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 VAL 962 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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948A SER* 4.7 1.6 + - - -
949A GLN* 4.9 0.5 - - - +
960A GLY 5.0 1.1 - - - +
961A GLU* 1.3 83.9 - - + +
963A VAL* 1.3 70.2 + - - +
964A GLN* 6.0 1.8 - - + -
974A GLY* 6.2 0.4 - - - -
975A ALA 3.4 11.0 - - - +
976A LYS* 4.1 29.4 - - + +
898B SER* 5.7 4.7 - - - +
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Residues in contact with VAL 963 (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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930A VAL* 4.6 4.0 - - + -
946A ILE* 4.3 15.9 - - + -
948A SER* 3.5 10.8 - - - +
949A GLN* 4.1 6.7 - - - +
957A PRO* 3.7 36.6 - - + -
961A GLU* 3.9 5.8 - - + +
962A VAL* 1.3 81.9 - - - +
964A GLN* 1.3 64.7 + - - +
965A VAL* 4.2 11.2 - - + -
974A GLY* 3.6 2.8 - - - -
975A ALA* 2.9 56.2 + - + +
976A LYS 4.3 0.4 - - - -
977A PHE* 4.1 10.5 - - + +
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Residues in contact with GLN 964 (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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946A ILE* 3.9 5.2 - - - +
947A VAL* 3.1 30.5 + - + +
948A SER* 2.9 26.0 + - - -
962A VAL* 6.0 2.2 - - + -
963A VAL* 1.3 76.9 - - - +
965A VAL* 1.3 59.9 + - - +
972A VAL* 3.7 15.5 - - + -
973A TYR 3.4 5.2 - - - +
974A GLY* 4.9 5.6 - - - -
920D VAL* 5.5 0.5 - - - +
921D ARG* 5.0 5.2 + - - +
987D GLN* 3.1 29.0 + - - +
995D GLN* 4.2 3.5 - - - +
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Residues in contact with VAL 965 (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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930A VAL* 4.3 7.6 - - + -
932A PHE* 3.8 29.8 - - + -
941A LEU* 3.8 25.4 - - + -
945A ASP 3.4 11.7 - - - +
946A ILE* 4.2 10.3 - - + -
963A VAL* 4.2 9.4 - - + -
964A GLN* 1.3 76.3 - - - +
966A ARG* 1.3 73.0 + - - +
967A TRP* 3.4 3.5 + - + +
972A VAL* 3.4 3.7 - - - +
973A TYR* 2.8 33.1 + - - +
975A ALA* 4.0 19.3 - - + -
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Residues in contact with ARG 966 (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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944A GLU 3.1 17.6 + - - -
945A ASP* 2.8 39.8 + - - +
947A VAL* 3.7 26.0 - - + +
965A VAL* 1.3 72.5 - - - +
967A TRP* 1.3 72.9 + - - +
970A GLY* 3.9 20.9 - - - +
971A GLN 3.8 3.8 - - - -
972A VAL* 4.3 9.2 - - + +
925D GLU* 2.9 48.8 + - - +
927D PHE* 4.6 4.3 - - - -
942D TYR* 3.5 17.6 + - - -
985D MET* 4.2 8.1 - - - +
997D VAL* 3.6 26.6 + - + +
20d LEU 5.3 6.5 - - - +
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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