Contacts of the strand formed by residues 1200 - 1207 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A PHE 4.6 0.4 - - - +
26A SER* 3.4 25.3 + - - -
29A THR* 3.5 8.3 - - + +
30A SER 3.3 10.9 + - - -
1198A SER* 3.2 18.5 - - - -
1199A ASP* 1.3 80.3 - - - +
1201A LEU* 1.3 65.2 + - - +
1218A LEU 3.4 13.2 - - - +
1219A ASP* 4.4 4.7 - - + +
1220A LEU 4.1 1.3 - - - +
548E PHE* 3.9 20.0 - - + -
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Residues in contact with LEU1201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A THR* 4.4 0.2 - - - -
30A SER* 3.4 18.2 - - - +
32A ILE* 3.9 12.3 - - + -
1195A PHE* 3.6 15.3 - - + +
1198A SER* 3.5 20.4 - - - +
1200A ALA* 1.3 83.8 - - - +
1202A VAL* 1.3 65.8 + - - +
1203A GLY 3.9 0.2 - - - -
1217A THR* 3.5 9.0 - - - +
1218A LEU* 2.8 32.5 + - + +
1220A LEU* 3.8 17.3 - - + -
525E SER* 3.8 30.1 - - - -
528E PHE* 3.6 32.3 - - + -
548E PHE* 4.8 1.2 - - - -
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Residues in contact with VAL1202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A VAL* 3.8 24.9 - - + -
22A GLY 4.6 2.7 - - - +
23A PHE* 4.1 16.8 - - + -
29A THR* 3.4 24.9 - - + -
30A SER 2.9 5.5 + - - -
31A ILE* 3.3 15.9 - - + +
32A ILE* 2.9 24.1 + - - +
42A MET* 4.6 8.3 - - + -
1201A LEU* 1.3 74.5 - - - +
1203A GLY* 1.3 60.3 + - - +
1204A VAL* 3.8 2.5 + - + -
1215A ILE* 4.0 28.3 - - + -
1216A ILE 4.0 2.7 - - - -
1217A THR* 4.3 8.5 - - + -
528E PHE* 4.4 0.4 - - - -
548E PHE* 6.5 0.2 - - + -
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Residues in contact with GLY1203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ILE* 3.3 7.9 - - - -
1202A VAL* 1.3 71.6 - - - +
1204A VAL* 1.3 61.4 + - - -
1205A TYR* 4.5 0.2 - - - -
1214A LYS 3.6 0.2 - - - +
1215A ILE* 3.5 8.5 - - - +
1216A ILE 3.0 33.0 + - - +
528E PHE* 3.5 12.9 - - - -
532E LEU* 3.4 26.3 - - - +
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Residues in contact with VAL1204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A TYR* 3.6 21.3 - - - +
31A ILE* 3.8 27.8 - - + -
32A ILE 2.8 9.4 + - - +
33A GLY* 3.5 19.2 - - - -
34A PRO* 3.7 4.9 - - - +
37A SER* 3.3 38.0 - - - +
38A GLY 3.9 2.7 - - - -
39A LYS* 4.1 4.5 - - + -
42A MET* 4.8 1.3 - - + -
1202A VAL* 4.3 2.7 - - + +
1203A GLY* 1.3 74.4 - - - -
1205A TYR* 1.3 65.7 + - - +
1213A SER* 4.3 3.4 - - - -
1214A LYS 3.3 8.7 - - - +
1215A ILE* 3.5 20.0 - - + -
532E LEU* 3.7 4.4 - - - +
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Residues in contact with TYR1205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A SER* 4.1 7.0 - - - -
1203A GLY 4.5 0.9 - - - -
1204A VAL* 1.3 74.6 - - - +
1206A ARG* 1.3 84.1 + - - +
1207A GLN* 4.6 7.6 - - + -
1213A SER* 3.4 4.2 - - - -
1214A LYS* 2.8 70.5 + - + +
1215A ILE 4.5 1.4 + - - -
1216A ILE* 3.5 28.2 - - + +
532E LEU* 3.5 33.4 - - + +
535E ALA* 3.9 16.6 - - + -
536E THR* 3.5 15.0 - - - +
542E LEU* 3.7 34.4 + - + +
543E SER* 5.2 0.5 - - - -
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Residues in contact with ARG1206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A SER* 5.1 6.6 - - - -
36A GLY 3.9 2.2 + - - -
37A SER* 3.6 30.9 - - - -
1205A TYR* 1.3 88.2 - - - +
1207A GLN* 1.3 57.5 + - - +
1208A GLN* 3.7 21.7 - - + +
1211A ASN* 2.9 30.3 + - - +
1212A SER* 3.5 22.1 + - - +
1213A SER* 3.7 5.7 + - - -
2224A AGS 4.6 7.3 + - - -
1120B LEU* 4.1 14.1 + - - +
1121B LYS* 3.0 45.6 - - - +
535E ALA 3.5 17.2 - - - +
536E THR* 3.2 29.4 + - + +
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Residues in contact with GLN1207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1205A TYR* 4.6 5.8 - - + -
1206A ARG* 1.3 73.4 - - - +
1208A GLN* 1.3 63.8 + - - +
1209A GLN* 3.1 28.5 + - - +
1210A GLU* 2.8 39.4 + - + +
1211A ASN 2.9 16.8 + - - -
1212A SER 3.0 10.6 + - - +
1214A LYS* 4.0 28.5 - - + -
535E ALA 5.2 1.6 - - - -
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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