Contacts of the strand formed by residues 1212 - 1219 (chain C) in PDB entry 1W1W
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 SER1212 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14C SER* 3.3 6.7 - - - -
16C ARG* 3.3 38.6 + - - +
1206C ARG* 3.5 10.6 - - - +
1207C GLN* 3.0 29.3 + - - +
1210C GLU* 3.4 17.2 - - - -
1211C ASN* 1.3 79.3 - - - +
1213C SER* 1.3 75.2 + - - +
1214C LYS* 4.4 9.1 + - - -
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Residues in contact with SER1213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C SER* 2.6 40.8 + - - -
15C TYR* 3.6 32.8 - - - -
19C THR* 4.6 3.8 + - - -
37C SER 2.5 27.3 + - - -
38C GLY* 3.8 0.2 - - - -
1204C VAL* 4.3 1.3 - - - -
1205C TYR 3.4 5.8 - - - -
1206C ARG* 3.7 4.0 - - - +
1212C SER* 1.3 84.6 + - - +
1214C LYS* 1.3 63.9 + - - +
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Residues in contact with LYS1214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C TYR* 4.9 0.4 - - - -
16C ARG 5.4 3.4 + - - -
19C THR* 5.7 2.7 - - - +
1203C GLY 3.6 0.2 - - - +
1204C VAL* 3.4 2.1 - - - +
1205C TYR* 2.8 66.9 + - + +
1207C GLN* 4.0 19.7 - - + -
1210C GLU* 2.8 44.4 + - - -
1212C SER* 4.4 10.1 + - - -
1213C SER* 1.3 79.2 - - - +
1215C ILE* 1.3 76.8 + - - +
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Residues in contact with ILE1215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C TYR* 3.7 16.4 - - + +
19C THR* 3.7 28.7 - - + +
20C LYS 4.3 14.8 - - - +
21C VAL* 4.0 13.0 - - + -
42C MET* 4.9 1.6 - - + -
1202C VAL* 3.8 26.7 - - + -
1203C GLY 3.4 4.0 - - - +
1204C VAL* 3.5 27.4 - - + -
1205C TYR* 4.6 1.4 + - - -
1214C LYS* 1.3 88.1 - - - +
1216C ILE* 1.3 77.4 + - - +
1217C THR* 4.5 7.4 - - + -
544G GLN* 4.3 4.3 + - - +
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Residues in contact with ILE1216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1203C GLY 3.1 26.3 + - - +
1205C TYR* 3.5 23.8 - - + +
1215C ILE* 1.3 79.5 - - - +
1217C THR* 1.3 66.4 + - - +
528G PHE* 3.2 33.4 - - + -
531G ILE* 5.0 4.0 - - + -
532G LEU* 3.7 25.8 - - + -
542G LEU* 4.0 21.1 - - + -
543G SER 5.2 2.0 - - - +
544G GLN* 2.9 26.2 - - + +
551G ILE* 3.8 17.0 - - + -
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Residues in contact with THR1217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C GLY 3.8 26.7 - - - +
1201C LEU 3.6 11.4 - - - +
1202C VAL* 4.1 13.2 - - + -
1215C ILE* 4.5 9.9 - - + -
1216C ILE* 1.3 79.9 - - - +
1218C LEU* 1.3 62.0 + - - +
528G PHE* 4.1 2.7 - - - -
544G GLN* 2.7 25.8 + - - +
547G ALA* 2.2 33.1 + - - +
548G PHE* 3.8 18.7 - - + -
549G GLY 4.4 2.4 - - - +
551G ILE* 4.2 6.6 - - - +
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Residues in contact with LEU1218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1200C ALA* 3.4 2.8 - - - +
1201C LEU* 2.8 38.7 + - + +
1217C THR* 1.3 76.7 - - - +
1219C ASP* 1.3 97.7 + - - +
1220C LEU* 3.7 19.8 + - + +
1223C TYR* 4.2 15.7 - - + +
504G PHE* 3.8 19.7 - - + -
524G ALA* 4.0 8.7 - - + +
528G PHE* 3.5 50.9 - - + -
548G PHE* 3.7 4.9 - - - -
551G ILE* 5.1 1.3 - - + -
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Residues in contact with ASP1219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1199C ASP 3.1 9.1 - - - +
1200C ALA* 4.3 3.9 - - - +
1218C LEU* 1.3 85.8 - - - +
1220C LEU* 1.3 58.5 + - - +
1221C SER* 2.6 35.8 + - - -
1222C ASN* 3.8 21.6 + - - +
1223C TYR* 3.5 11.4 - - - -
548G PHE* 3.6 26.3 - - + +
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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