Contacts of the helix formed by residues 191 - 194 (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 ILE 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A VAL* 3.4 13.3 - - + +
190A PRO* 1.3 71.8 - - + +
192A PRO* 1.3 66.9 - - + +
193A ALA 3.9 4.9 - - - +
194A MET* 3.5 23.9 + - + -
216A PHE* 3.3 33.1 - - + -
220A TYR* 3.4 32.1 - - + -
222A ASP* 5.3 2.0 - - - +
579A GLY* 5.2 3.6 - - - -
580A GLN* 3.4 37.5 - - + +
581A GLU* 5.1 0.7 - - - +
713A ARG* 2.7 17.8 + - - -
1098A HIS* 5.7 0.2 - - + -
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Residues in contact with PRO 192 (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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190A PRO 3.1 4.2 - - - +
191A ILE* 1.3 84.4 - - + +
193A ALA* 1.3 62.2 + - + +
194A MET 3.0 1.0 + - - -
195A SER 3.1 1.6 + - - -
196A MET* 2.9 31.7 + - - -
199A TYR* 3.5 20.9 - - + -
216A PHE* 3.5 26.9 - - + -
581A GLU* 5.9 1.8 - - - +
583A LEU* 3.8 13.7 - - + -
589A TRP* 3.3 42.2 - - + -
713A ARG* 3.8 8.1 - - - +
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Residues in contact with ALA 193 (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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191A ILE* 3.2 1.7 - - + -
192A PRO* 1.3 82.3 - - + +
194A MET* 1.3 61.3 + - + +
195A SER 3.4 0.4 + - - -
196A MET* 4.2 2.9 - - - +
580A GLN 3.3 25.6 - - - +
581A GLU 4.6 1.3 - - - +
582A LYS 3.6 20.9 - - - +
583A LEU* 3.7 23.8 - - + +
797A MET 4.0 1.0 - - - +
798A ASN* 3.3 4.3 - - - -
799A THR* 3.1 33.7 + - - +
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Residues in contact with MET 194 (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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49A HIS 3.6 3.7 - - - +
50A GLY* 3.5 8.1 - - - -
51A VAL* 3.1 44.4 - - + +
55A GLY 5.1 1.1 - - - -
56A SER 4.6 6.3 - - - -
191A ILE* 3.5 16.8 + - + -
192A PRO 3.1 1.2 - - - -
193A ALA* 1.3 79.8 - - + +
195A SER* 1.3 63.5 + - - +
580A GLN* 3.3 46.4 - - + +
797A MET 3.9 1.6 - - - -
798A ASN* 3.1 36.8 + - - +
799A THR 3.2 26.7 - - - +
809A LEU* 3.6 4.9 - - - +
1248A SF4 5.8 2.5 - - - -
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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