Contacts of the strand formed by residues 1003 - 1006 (chain R) in PDB entry 1YYL
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 GLN1003 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23H LYS* 3.3 31.0 + - - +
25H SER* 6.1 2.5 - - - -
1001R GLU* 3.3 23.6 + - - +
1002R VAL* 1.3 84.2 + - - +
1004R LEU* 1.3 64.5 + - - +
1005R VAL* 4.1 9.9 - - + +
1023R LYS 3.6 1.0 - - - +
1024R ALA* 3.1 5.9 - - - +
1025R SER* 2.8 46.7 + - - +
1102R HIS* 6.2 0.4 - - - -
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Residues in contact with LEU1004 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1002R VAL* 5.1 5.2 - - + -
1003R GLN* 1.3 77.4 + - - +
1005R VAL* 1.3 64.7 + - - +
1006R GLU 4.1 0.2 - - - -
1022R CYS* 4.0 13.9 - - - -
1023R LYS 3.5 1.8 - - - -
1024R ALA* 3.2 32.1 - - + -
1034R PHE* 3.7 14.1 - - + -
1092R CYS* 3.8 5.2 - - - +
1093R ALA* 3.8 15.7 - - - +
1094R GLY* 3.8 6.5 - - - +
1102R HIS* 3.4 42.0 - - + +
1103R TRP 3.8 18.2 + - - +
1104R GLY* 3.6 20.1 - - - -
1105R GLN* 3.9 3.3 + - - +
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Residues in contact with VAL1005 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5H VAL* 5.3 16.2 - - + -
23H LYS* 5.0 24.9 - - + +
1003R GLN* 4.8 11.0 - - + +
1004R LEU* 1.3 81.3 - - - +
1006R GLU* 1.3 69.9 + - - +
1021R SER* 4.5 0.7 + - - -
1022R CYS* 3.3 1.6 - - - -
1023R LYS* 2.8 47.5 + - + +
1025R SER* 5.5 3.1 - - - +
1105R GLN* 3.9 9.0 - - - +
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Residues in contact with GLU1006 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1005R VAL* 1.3 79.1 - - - +
1007R SER* 1.3 64.4 + - - +
1021R SER* 3.3 9.6 - - - +
1022R CYS* 3.9 8.3 - - + -
1036R TRP* 3.8 7.7 - - + -
1090R TYR 2.8 17.1 - - - +
1092R CYS* 3.1 41.2 + - + +
1104R GLY* 3.6 9.1 - - - -
1105R GLN* 3.0 33.5 + - - +
1106R GLY* 2.9 25.8 + - - -
1107R THR* 2.7 29.5 + - - +
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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