Contacts of the strand formed by residues 1151 - 1154 (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 THR1151 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1149R PRO* 5.7 3.3 - - - +
1150R VAL* 1.3 75.7 + - - +
1152R VAL* 1.3 71.5 + - - +
1153R SER* 5.1 5.2 - - - +
1197R ASN 3.4 1.2 - - - +
1198R VAL* 3.4 5.7 - - - +
1199R ASN* 2.9 52.5 + - + +
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Residues in contact with VAL1152 (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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1142R VAL* 4.3 12.8 - - + -
1150R VAL* 4.2 8.2 + - + -
1151R THR* 1.3 85.4 - - - +
1153R SER* 1.3 70.7 + - - +
1154R TRP* 4.3 4.7 - - - +
1165R THR* 4.0 32.3 + - + +
1178R LEU* 4.1 17.9 - - + -
1180R SER* 3.4 28.3 - - - +
1196R CYS* 4.8 8.1 - - + -
1197R ASN 3.2 10.5 - - - +
1198R VAL* 4.5 6.1 - - + -
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Residues in contact with SER1153 (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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1151R THR* 5.1 6.0 - - - +
1152R VAL* 1.3 77.2 - - - +
1154R TRP* 1.3 63.6 + - - +
1156R SER* 4.0 2.6 - - - -
1157R GLY* 3.7 22.0 + - - -
1196R CYS* 3.5 3.3 - - - -
1197R ASN* 2.7 51.8 + - - +
1199R ASN* 5.3 2.1 + - - -
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Residues in contact with TRP1154 (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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1138R LEU* 4.6 3.4 - - + -
1139R GLY* 3.6 30.5 - - - -
1140R CYS* 4.0 2.5 - - - -
1152R VAL* 4.3 1.2 - - + +
1153R SER* 1.3 78.9 - - - +
1155R ASN* 1.3 72.5 + - - +
1156R SER 3.2 1.6 - - - -
1157R GLY* 2.8 12.2 + - - -
1158R ALA 3.3 7.1 + - - -
1159R LEU* 3.3 33.7 + - + +
1163R VAL* 3.8 20.9 - - + -
1165R THR* 5.6 0.2 - - - -
1180R SER* 3.0 49.9 + - - -
1181R VAL 4.5 1.2 + - - -
1182R VAL* 3.8 27.6 - - + +
1194R TYR* 4.6 9.4 - - + -
1195R ILE 3.4 22.0 - - - -
1196R CYS* 3.6 30.1 - - + -
1211R VAL* 4.1 15.7 - - + -
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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