Contacts of the helix formed by residues 1193 - 1198 (chain A) in PDB entry 1SIW
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 LYS1193 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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548A TYR* 3.4 40.4 + - + +
549A HIS* 2.8 41.2 + - - +
551A ASP* 4.9 7.3 - - - +
552A MET* 5.3 0.2 - - - +
628A LEU* 4.9 4.9 - - + -
1054A PHE* 6.5 0.2 - - - -
1056A GLU* 3.2 24.8 + - - -
1062A ARG* 5.0 4.3 - - - +
1192A PRO* 1.3 74.6 - - - +
1194A PRO* 1.3 73.4 - - + +
1195A THR* 3.7 22.7 - - - +
1196A HIS* 2.9 45.0 + - + +
1197A MET* 4.0 6.6 + - - +
1213A THR* 4.2 3.7 - - - +
1214A VAL 5.8 0.8 + - - +
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Residues in contact with PRO1194 (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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625A ALA* 4.5 1.3 - - + -
628A LEU* 4.2 10.1 - - + -
642A LEU* 3.8 28.9 - - + -
645A PHE* 4.4 13.9 - - + -
1050A TRP* 3.7 10.0 - - + -
1054A PHE* 3.5 42.2 - - + -
1192A PRO 4.1 0.4 - - - +
1193A LYS* 1.3 89.7 - - + +
1195A THR* 1.3 56.6 + - - +
1197A MET* 2.9 39.3 + - + +
1198A ILE* 3.5 6.6 - - - +
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Residues in contact with THR1195 (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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229A GLN* 5.3 1.6 - - - -
551A ASP* 5.1 0.3 + - - -
1050A TRP* 4.3 5.6 - - - +
1051A MET* 3.7 28.0 - - - +
1054A PHE* 3.8 30.3 - - + -
1056A GLU* 4.2 17.4 + - + -
1193A LYS* 3.7 26.0 - - + +
1194A PRO* 1.3 76.0 - - - +
1196A HIS* 1.3 60.2 + - - +
1197A MET 3.0 2.1 + - - -
1198A ILE* 3.0 23.1 - - + +
1211A TYR* 2.7 24.7 + - - -
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Residues in contact with HIS1196 (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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225A PRO* 3.4 27.3 - - + +
229A GLN* 4.4 0.2 - - - -
548A TYR 4.7 0.7 - - - -
550A LEU* 3.9 18.6 - - + -
551A ASP* 2.7 32.5 + - - -
655A LEU* 4.4 0.3 - - - +
1193A LYS* 2.9 40.1 + - + +
1195A THR* 1.3 86.1 + - - +
1197A MET* 1.3 59.9 + - - +
1211A TYR* 3.7 14.3 - - + -
1212A GLY* 3.2 42.2 + - - +
1213A THR* 3.4 7.3 + - - -
1214A VAL* 3.9 18.5 + - + +
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Residues in contact with MET1197 (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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642A LEU* 3.8 19.5 - - + +
645A PHE* 3.7 13.7 - - + +
646A ASN* 3.6 38.1 - - + +
649A ALA* 3.9 5.9 - - + +
654A TRP* 3.5 20.2 - - - +
655A LEU* 3.9 25.2 - - + +
1050A TRP* 4.4 4.9 - - + -
1192A PRO* 3.8 29.8 - - + -
1193A LYS 4.1 0.9 - - - +
1194A PRO* 2.9 29.1 + - + +
1196A HIS* 1.3 80.4 - - - +
1198A ILE* 1.3 68.0 + - - +
1199A GLY 3.3 1.9 + - - -
1213A THR* 3.8 17.0 - - + -
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Residues in contact with ILE1198 (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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654A TRP* 3.8 7.6 - - - +
655A LEU* 5.2 0.7 - - - +
1048A HIS* 3.5 48.9 - - + +
1050A TRP* 3.7 19.3 - - + -
1051A MET* 4.5 6.7 - - + -
1194A PRO 3.5 4.5 - - - +
1195A THR* 3.0 45.4 + - - +
1196A HIS 3.7 0.4 - - - -
1197A MET* 1.3 78.4 - - - +
1199A GLY* 1.3 64.3 + - - +
1201A TYR* 4.3 0.2 - - + -
1204A LEU* 3.4 41.4 - - + +
1205A ALA* 4.8 0.7 - - - -
1211A TYR* 3.6 19.6 - - + -
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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