Contacts of the strand formed by residues 1191 - 1197 (chain Q) 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 VAL1191 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1149Q LYS 3.7 0.9 - - - +
1150Q VAL* 3.5 3.3 - - - +
1151Q ASP* 2.8 73.7 + - - +
1152Q ASN* 5.4 4.0 - - - +
1190Q LYS* 1.3 76.6 - - + +
1192Q TYR* 1.3 62.2 + - - +
1193Q ALA* 5.1 3.8 - - + +
1208Q SER* 4.4 16.6 - - - +
1209Q PHE 3.2 6.7 - - - +
1210Q ASN* 3.0 26.0 - - - +
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Residues in contact with TYR1192 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1117Q ILE* 3.6 5.2 - - - +
1132Q VAL* 4.7 8.7 - - + -
1148Q TRP* 5.0 3.4 - + + -
1149Q LYS 3.9 2.0 - - - -
1150Q VAL* 3.4 32.8 - - + -
1179Q LEU* 4.3 11.0 - - + -
1181Q LEU* 4.0 11.9 - - + -
1185Q ASP 3.8 1.2 + - - -
1186Q TYR* 2.6 69.8 + + - -
1189Q HIS* 3.3 17.8 - - + +
1190Q LYS 4.0 14.4 - - - -
1191Q VAL* 1.3 72.7 - - - +
1193Q ALA* 1.3 60.4 + - - +
1208Q SER* 2.9 18.2 - - - -
1209Q PHE* 2.8 44.0 + + + -
1211Q ARG* 4.0 10.1 - - + -
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Residues in contact with ALA1193 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1148Q TRP* 3.3 14.8 - - - -
1149Q LYS* 3.0 52.8 + - + +
1191Q VAL* 5.2 5.2 - - + -
1192Q TYR* 1.3 72.8 - - - +
1194Q CYS* 1.3 60.1 + - - +
1195Q GLU 4.1 0.2 - - - -
1206Q THR* 4.1 14.8 - - + -
1207Q LYS 3.5 0.9 - - - +
1208Q SER* 3.3 20.9 - - - +
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Residues in contact with CYS1194 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1115Q VAL* 4.8 0.6 - - - +
1117Q ILE* 4.3 10.3 - - + +
1134Q CYS* 2.0 53.4 - - + -
1146Q VAL* 3.9 12.3 - - - -
1147Q GLN 3.8 2.5 - - - -
1148Q TRP* 4.4 8.1 - - + -
1193Q ALA* 1.3 73.1 - - - +
1195Q GLU* 1.3 59.5 + - - +
1196Q VAL* 3.9 15.4 + - - +
1205Q VAL 3.7 1.9 - - - +
1206Q THR* 3.1 23.6 - - - -
1207Q LYS* 2.8 20.2 + - + +
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Residues in contact with GLU1195 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1145Q LYS 3.7 0.7 - - - +
1146Q VAL* 3.3 4.3 - - - +
1147Q GLN* 2.8 69.8 + - + +
1149Q LYS* 3.0 29.7 + - + +
1193Q ALA 4.1 0.6 - - - -
1194Q CYS* 1.3 71.3 - - - +
1196Q VAL* 1.3 60.0 + - - +
1197Q THR* 4.4 6.9 - - + +
1204Q PRO* 2.8 36.7 - - + +
1205Q VAL 4.3 0.2 - - - +
1206Q THR* 2.6 28.2 + - - +
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Residues in contact with VAL1196 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1113Q PRO* 4.5 8.3 - - + -
1115Q VAL* 4.1 16.8 - - + -
1136Q LEU* 3.6 47.3 - - + -
1145Q LYS 3.3 7.9 - - - +
1146Q VAL* 4.3 5.2 - - + -
1194Q CYS* 3.9 17.7 - - - +
1195Q GLU* 1.3 79.1 - - - +
1197Q THR* 1.3 74.0 + - - +
1198Q HIS* 4.8 1.6 - - + -
1201Q LEU* 3.5 14.4 - - + +
1204Q PRO* 3.5 1.0 - - - +
1205Q VAL 2.9 38.8 + - - +
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Residues in contact with THR1197 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1144Q ALA* 4.1 0.5 - - - -
1145Q LYS* 3.1 54.2 + - + +
1147Q GLN* 5.9 1.8 - - - +
1195Q GLU* 4.4 8.7 - - + +
1196Q VAL* 1.3 78.0 - - - +
1198Q HIS* 1.3 62.7 + - - +
1201Q LEU* 4.4 1.3 - - - -
1204Q PRO* 3.5 35.2 - - + -
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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