Contacts of the strand formed by residues 1205 - 1211 (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 THR1205 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13H LYS* 4.3 3.4 - - - +
115H SER* 4.9 6.0 + - - -
1118R GLY* 3.7 8.3 - - - -
1119R PRO* 4.2 22.7 - - + +
1198R VAL* 5.2 2.5 - - + +
1199R ASN* 3.6 3.6 + - - +
1200R HIS* 3.0 35.2 + - + +
1203R SER* 2.6 32.0 + - - -
1204R ASN* 1.3 76.3 - - - +
1206R LYS* 1.3 64.6 + - - +
1207R VAL* 3.8 22.9 - - + +
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Residues in contact with LYS1206 (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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12H LYS* 6.0 1.6 - - - +
13H LYS* 4.1 44.2 + - + +
16H SER* 3.7 23.4 - - - -
1197R ASN* 6.6 0.2 - - + -
1198R VAL 3.6 6.3 - - - +
1199R ASN* 3.4 26.6 - - - +
1204R ASN 4.0 1.4 + - - -
1205R THR* 1.3 75.7 - - - +
1207R VAL* 1.3 65.0 + - - +
1208R ASP* 5.5 10.0 - - - +
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Residues in contact with VAL1207 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1119R PRO* 5.4 5.6 - - + +
1121R VAL* 4.6 24.7 - - + +
1196R CYS 4.0 0.9 - - - +
1197R ASN* 3.9 0.3 - - - -
1198R VAL* 3.0 36.5 + - + +
1205R THR* 3.8 21.0 - - + +
1206R LYS* 1.3 79.3 - - - +
1208R ASP* 1.3 77.5 + - - +
1209R LYS* 5.0 6.1 - - + -
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Residues in contact with ASP1208 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1195R ILE* 3.7 16.2 - - + -
1196R CYS 3.4 3.1 - - - -
1197R ASN* 2.5 40.9 + - - +
1206R LYS* 5.5 10.3 - - - +
1207R VAL* 1.3 84.1 + - - +
1209R LYS* 1.3 64.2 + - - +
1210R LYS 4.3 0.4 + - - -
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Residues in contact with LYS1209 (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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1123Q GLU* 3.9 26.6 + - - +
1121R VAL* 3.6 48.7 - - + +
1123R PRO* 4.1 18.5 - - + +
1140R CYS* 4.1 2.0 - - - -
1195R ILE* 3.5 3.7 - - - -
1196R CYS* 3.1 35.6 + - - -
1207R VAL* 4.3 6.0 + - + -
1208R ASP* 1.3 80.4 - - - +
1210R LYS* 1.3 71.9 + - - +
1211R VAL* 3.7 5.0 + - - +
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Residues in contact with LYS1210 (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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1123R PRO* 4.4 9.2 - - - +
1193R THR* 3.5 38.2 - - - +
1194R TYR 3.5 10.1 - - - +
1195R ILE* 4.1 17.2 - - + +
1208R ASP 4.3 0.8 + - - -
1209R LYS* 1.3 80.4 + - - +
1211R VAL* 1.3 66.1 + - - +
1212R GLU* 3.3 35.1 + - + +
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Residues in contact with VAL1211 (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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1123R PRO* 4.2 11.4 - - + -
1124R LEU 3.9 27.1 - - - +
1125R ALA* 4.2 6.7 - - - +
1126R PRO* 4.2 0.7 - - + -
1138R LEU* 4.0 28.5 - - + +
1139R GLY 3.6 20.0 - - - +
1140R CYS* 4.1 7.2 - - - -
1154R TRP* 4.1 15.7 - - + -
1189R LEU* 5.7 0.5 - - - +
1194R TYR* 2.8 33.5 + - - +
1209R LYS 3.9 10.5 - - - +
1210R LYS* 1.3 78.5 - - - +
1212R GLU* 1.3 67.6 + - - +
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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