Contacts of the strand formed by residues 995 - 999 (chain B) 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 GLN 995 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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920B VAL* 3.5 12.8 - - - +
987B GLN* 2.4 32.8 + - + +
988B VAL 3.1 13.7 - - - +
989B GLU* 3.7 28.3 + - + +
993B GLY 3.9 10.3 + - - -
994B SER* 1.3 79.1 - - - +
996B LEU* 1.3 69.3 + - - +
964C GLN* 4.3 12.1 + - - +
971C GLN* 3.6 4.2 - - - +
972C VAL* 2.9 45.6 + - + +
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Residues in contact with LEU 996 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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907B SER* 5.6 0.2 - - - +
908B LYS 3.3 26.9 - - - +
909B HIS 4.5 0.4 - - - -
910B LYS* 4.4 22.7 - - + +
986B TYR 3.6 0.5 - - - +
987B GLN* 3.2 6.1 - - - +
988B VAL* 2.9 39.4 + - + +
990B PHE* 3.5 21.7 - - + -
994B SER* 5.6 2.2 - - - +
995B GLN* 1.3 84.3 - - - +
997B VAL* 1.3 63.9 + - - +
998B VAL* 4.0 16.4 - - + -
969C ASP 4.8 3.4 - - - +
970C GLY* 3.4 7.2 - - - +
971C GLN* 3.8 26.9 - - + +
972C VAL* 4.1 0.7 - - - -
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Residues in contact with VAL 997 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
923B THR* 5.0 2.7 - - - +
925B GLU* 4.8 1.3 - - - +
985B MET* 3.8 36.8 - - + +
986B TYR 3.5 6.3 - - - +
987B GLN* 4.1 13.0 - - + -
996B LEU* 1.3 75.2 - - - +
998B VAL* 1.3 62.4 - - - +
947C VAL* 4.1 16.2 - - + -
966C ARG* 4.0 31.3 + - + +
970C GLY* 2.9 20.9 + - - +
972C VAL* 3.5 24.2 - - + -
19b GLN* 4.7 7.4 + - - +
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Residues in contact with VAL 998 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
907B SER* 4.1 13.7 - - - +
908B LYS 5.8 0.2 - - - +
985B MET* 3.5 9.1 - - - -
986B TYR* 2.7 49.6 + - - +
988B VAL* 4.3 9.2 - - + -
996B LEU* 4.0 23.8 - - + -
997B VAL* 1.3 80.0 - - - +
999B LYS* 1.3 60.8 + - - +
1002B ASP* 4.2 16.8 - - + +
1003B VAL* 3.6 29.8 - - + -
970C GLY* 6.5 0.4 - - - -
19b GLN* 6.3 0.9 - - - +
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Residues in contact with LYS 999 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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927B PHE* 4.0 27.2 - - - -
940B ASN* 4.3 15.6 - - - +
983B ILE* 3.9 30.8 - - + +
984B GLN 4.0 6.5 - - - +
985B MET* 3.6 26.0 - - + -
986B TYR* 4.2 3.8 - - - -
998B VAL* 1.3 77.9 - - - +
1000B ARG* 1.3 67.7 + - - +
1001B ASP* 3.4 3.4 - - + +
1002B ASP* 3.0 25.6 + - - +
1003B VAL* 3.7 4.3 + - - +
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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