Contacts of the strand formed by residues 1200 - 1207 (chain B) 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 ALA1200 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B PHE 4.6 0.7 - - - +
26B SER* 3.6 22.7 - - - +
28B PHE 3.4 2.0 + - - -
29B THR* 3.6 7.6 - - + +
30B SER 3.3 19.8 + - - -
1198B SER* 3.4 10.6 - - - -
1199B ASP* 1.3 83.9 - - - +
1201B LEU* 1.3 65.9 + - - +
1218B LEU 3.4 12.6 - - - +
1219B ASP* 4.4 3.4 - - + +
1220B LEU* 4.0 2.7 - - - +
548F PHE* 3.9 20.0 - - + -
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Residues in contact with LEU1201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B SER* 3.4 23.8 - - - +
32B ILE* 3.6 24.9 - - + -
1195B PHE* 3.6 27.1 - - + +
1198B SER* 3.7 2.7 - - - +
1200B ALA* 1.3 84.3 - - - +
1202B VAL* 1.3 63.4 + - - +
1203B GLY 3.8 0.6 + - - -
1217B THR* 3.5 9.2 - - - +
1218B LEU* 2.8 35.4 + - + +
1220B LEU* 3.8 14.6 - - + -
525F SER* 3.8 26.0 - - - -
528F PHE* 3.6 23.7 - - + -
548F PHE* 4.8 1.0 - - - -
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Residues in contact with VAL1202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B VAL* 4.0 15.3 - - + -
22B GLY 4.7 2.2 - - - +
23B PHE* 4.0 18.4 - - + -
29B THR* 3.5 25.4 - - + -
30B SER 2.9 8.5 + - - -
31B ILE* 3.2 15.8 - - + +
32B ILE 3.0 21.6 + - - +
42B MET* 4.4 9.9 - - + -
1201B LEU* 1.3 74.3 - - - +
1203B GLY* 1.3 62.0 + - - +
1204B VAL* 3.7 1.9 + - + -
1215B ILE* 3.9 34.1 - - + -
1216B ILE 4.0 2.0 - - - -
1217B THR* 4.3 10.8 - - + -
528F PHE* 4.4 0.4 - - - -
548F PHE* 6.3 0.2 - - + -
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Residues in contact with GLY1203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B ILE* 3.3 7.9 - - - -
1202B VAL* 1.3 74.3 - - - +
1204B VAL* 1.3 60.9 + - - -
1205B TYR* 4.4 0.2 - - - -
1214B LYS 3.7 0.3 - - - +
1215B ILE* 3.5 8.1 - - - +
1216B ILE 3.0 33.8 + - - -
528F PHE* 3.5 14.0 - - - -
532F LEU* 3.4 24.8 - - - +
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Residues in contact with VAL1204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B TYR* 3.6 21.1 - - - +
31B ILE* 3.8 28.3 - - + -
32B ILE 2.8 6.9 + - - -
33B GLY* 3.4 13.5 - - - -
34B PRO* 3.7 2.8 - - - +
37B SER* 3.2 46.5 + - - +
38B GLY 4.0 2.7 - - - -
39B LYS* 4.1 8.3 - - + -
42B MET* 4.8 1.1 - - + -
1202B VAL* 4.1 2.5 - - + +
1203B GLY* 1.3 74.3 - - - -
1205B TYR* 1.3 65.1 + - - +
1213B SER* 4.2 4.0 - - - -
1214B LYS 3.4 8.1 - - - +
1215B ILE* 3.3 20.0 - - + -
532F LEU* 3.8 3.2 - - - +
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Residues in contact with TYR1205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B SER* 4.1 5.2 - - - -
1203B GLY 4.4 1.3 - - - -
1204B VAL* 1.3 76.2 - - - +
1206B ARG* 1.3 74.7 + - - +
1207B GLN* 4.7 7.2 - - + -
1213B SER* 3.4 3.4 - - - -
1214B LYS* 2.8 70.2 + - + +
1215B ILE 4.2 2.1 + - - -
1216B ILE* 3.5 28.6 - - + +
532F LEU* 3.6 33.2 - - + +
535F ALA* 3.8 13.7 - - + -
536F THR* 3.5 14.4 - - - +
542F LEU* 3.7 38.7 + - + +
543F SER* 5.0 0.9 - - - -
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Residues in contact with ARG1206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1120A LEU* 4.2 12.5 + - - +
1121A LYS* 3.2 43.6 - - - +
14B SER* 5.2 6.4 - - - -
36B GLY 4.2 2.0 + - - -
37B SER* 3.7 31.1 - - - -
1205B TYR* 1.3 89.4 - - - +
1207B GLN* 1.3 59.2 + - - +
1208B GLN* 3.7 23.6 - - - +
1211B ASN* 2.9 29.1 + - - +
1212B SER* 3.6 21.1 + - - +
1213B SER* 3.7 7.5 + - - -
2224B AGS 4.7 8.9 + - - -
535F ALA* 3.6 17.0 - - - +
536F THR* 3.2 28.6 + - + +
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Residues in contact with GLN1207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1205B TYR* 4.7 6.5 - - + -
1206B ARG* 1.3 74.6 - - - +
1208B GLN* 1.3 60.4 + - - +
1209B GLN* 3.1 29.0 + - - +
1210B GLU* 2.9 40.8 + - + +
1211B ASN* 2.9 23.5 + - - -
1212B SER 3.1 15.2 + - - +
1214B LYS* 4.0 22.4 - - + -
535F ALA 5.3 1.3 - - - -
556F LYS* 6.3 0.9 - - - -
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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