Contacts of the strand formed by residues 1145 - 1150 (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 LYS1145 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1144Q ALA* 1.3 73.2 - - - +
1146Q VAL* 1.3 72.6 + - - +
1147Q GLN* 3.0 36.6 + - + +
1195Q GLU 3.7 0.6 - - - +
1196Q VAL* 3.3 7.4 - - - +
1197Q THR* 3.1 55.6 + - + +
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Residues in contact with VAL1146 (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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1134Q CYS* 4.8 0.9 - - - -
1136Q LEU* 3.7 28.0 - - + -
1144Q ALA 4.2 1.1 + - - +
1145Q LYS* 1.3 82.6 - - - +
1147Q GLN* 1.3 69.7 + - - +
1148Q TRP* 4.7 4.8 - - - +
1161Q GLU* 3.2 25.5 + - - +
1175Q LEU* 3.8 11.7 - - + -
1177Q SER* 3.5 27.8 + - - +
1194Q CYS* 3.9 24.7 - - - -
1195Q GLU 3.3 3.6 - - - +
1196Q VAL* 4.3 2.7 - - + -
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Residues in contact with GLN1147 (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* 3.0 40.3 + - + +
1146Q VAL* 1.3 78.4 - - - +
1148Q TRP* 1.3 64.3 + - - +
1149Q LYS* 5.5 2.5 - - + +
1154Q LEU* 4.3 31.8 - - + +
1155Q GLN 5.9 0.7 - - - -
1194Q CYS* 3.7 1.4 - - - -
1195Q GLU* 2.8 65.5 + - + +
1197Q THR* 5.9 2.2 - - - +
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Residues in contact with TRP1148 (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* 4.2 14.8 - - + -
1132Q VAL* 3.3 46.9 - - + -
1133Q VAL 4.1 1.3 - - - -
1134Q CYS* 3.7 22.4 - - + -
1146Q VAL* 4.7 3.3 - - + +
1147Q GLN* 1.3 77.2 - - - +
1149Q LYS* 1.3 63.9 + - - +
1150Q VAL* 5.9 0.2 - - + -
1154Q LEU* 3.7 2.8 - - - +
1155Q GLN* 2.8 52.3 + - + +
1159Q SER* 3.9 20.7 - - - -
1177Q SER* 2.8 50.7 + - - -
1179Q LEU* 3.8 24.6 - - + +
1192Q TYR* 5.0 3.8 - + + -
1193Q ALA 3.3 26.0 - - - -
1194Q CYS* 4.4 4.3 - - + -
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Residues in contact with LYS1149 (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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1147Q GLN* 5.0 3.4 - - + +
1148Q TRP* 1.3 77.9 - - - +
1150Q VAL* 1.3 62.1 + - - +
1151Q ASP 3.4 4.9 + - - -
1152Q ASN* 3.8 37.2 + - - +
1153Q ALA 3.5 5.4 - - - -
1154Q LEU* 4.7 14.4 - - + -
1191Q VAL* 3.7 0.9 - - - +
1193Q ALA* 3.0 50.4 + - + +
1195Q GLU* 3.0 42.2 + - + +
1206Q THR* 3.7 13.7 + - - +
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Residues in contact with VAL1150 (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* 5.6 0.7 - - + -
1149Q LYS* 1.3 68.8 - - - +
1151Q ASP* 1.3 69.8 + - - +
1152Q ASN 3.2 0.2 - - - -
1153Q ALA* 3.1 21.9 + - - +
1155Q GLN* 3.1 36.1 - - + +
1179Q LEU* 4.1 10.8 - - + -
1181Q LEU* 5.0 4.7 - - + -
1189Q HIS* 3.4 42.3 + - + +
1191Q VAL 3.6 3.6 - - - +
1192Q TYR* 3.4 36.1 - - + -
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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