Contacts of the helix formed by residues 168 - 173 (chain A) in PDB entry 1F89
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 168 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A GLU* 3.3 23.3 - - - +
98A THR* 2.8 29.2 - - - +
111A ASN* 3.5 29.6 - - - +
113A SER* 3.7 14.8 - - - +
126A HIS* 3.5 24.9 - - + +
128A LYS* 4.1 16.1 - - + +
166A VAL* 5.1 0.2 - - + -
167A GLY* 1.3 78.9 - - - +
169A CYS* 1.3 60.9 + - + +
170A TYR 2.9 2.1 + - - -
171A ASP* 2.6 51.3 + - - +
191A TYR* 4.9 1.1 - - - -
192A PRO* 3.7 11.4 - - + +
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Residues in contact with CYS 169 (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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53A GLU* 3.6 25.8 - - - +
59A TYR* 4.2 6.7 - - - -
128A LYS* 4.0 10.3 - - - +
167A GLY 4.3 0.2 + - - -
168A ILE* 1.3 70.5 - - - +
170A TYR* 1.3 63.1 + - - +
171A ASP 2.9 5.9 + - - -
172A MET* 3.1 27.4 + - - +
191A TYR* 5.0 1.6 - - - -
192A PRO 3.3 7.7 + - - -
193A SER* 3.4 15.8 + - - -
194A ALA 3.9 25.8 - - - -
195A PHE* 4.1 19.5 - - - -
232A TYR* 5.3 1.8 - - - -
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Residues in contact with TYR 170 (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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128A LYS* 3.9 10.7 - - - +
130A HIS* 3.2 42.0 - - + +
131A LEU* 3.7 20.0 - - - -
168A ILE 2.9 1.8 + - - -
169A CYS* 1.3 81.7 - - - +
171A ASP* 1.3 60.8 + - - +
172A MET 3.2 0.4 - - - -
173A ARG* 3.2 44.6 + - - +
174A PHE* 3.3 33.6 - + - -
195A PHE* 5.5 1.6 - - - -
574B VAL* 4.2 7.5 - - + +
575B PRO* 3.4 43.5 + - + +
577B THR 5.4 2.8 + - - -
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Residues in contact with ASP 171 (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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126A HIS* 3.2 13.1 + - - -
128A LYS* 3.7 3.1 - - - -
129A VAL* 3.5 10.5 + - - +
130A HIS* 2.9 40.6 + - - +
167A GLY* 4.2 3.1 - - - -
168A ILE* 2.6 49.4 + - - +
170A TYR* 1.3 72.5 - - - +
172A MET* 1.3 60.5 + - - +
173A ARG 3.1 1.8 + - - -
174A PHE* 3.3 18.8 + - - +
177A LEU* 3.3 26.1 - - + +
191A TYR* 3.8 3.8 + - + -
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Residues in contact with MET 172 (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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169A CYS 3.1 14.6 + - - +
171A ASP* 1.3 77.5 - - - +
173A ARG* 1.3 58.8 + - + +
174A PHE 3.1 1.6 - - - -
191A TYR* 3.3 31.2 - - + -
193A SER* 4.1 9.6 - - - -
195A PHE* 4.0 27.6 - - + -
204A TRP* 4.3 5.2 - - - +
207A LEU* 3.3 39.2 - - + +
208A ALA* 3.8 5.4 - - - +
211A ARG* 3.2 31.3 + - + +
221A LEU* 3.4 43.1 - - + -
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Residues in contact with ARG 173 (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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170A TYR* 3.2 34.1 + - + +
171A ASP 3.1 1.4 - - - -
172A MET* 1.3 80.2 - - + +
174A PHE* 1.3 69.2 - - + +
175A PRO* 3.7 7.3 - - - +
195A PHE* 3.4 20.4 - - + -
199A THR* 2.9 26.9 + - - +
203A HIS* 3.2 38.6 + - - +
207A LEU* 4.0 19.3 - - + +
211A ARG* 3.8 7.1 + - - +
513B VAL* 5.4 4.5 - - + +
514B ASP* 4.2 9.2 - - - +
574B VAL* 3.6 36.5 - - + +
578B LYS* 5.1 2.4 + - - -
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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