Contacts of the helix formed by residues 174 - 181 (chain A) in PDB entry 1PTH
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 ALA 174 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A PRO 2.9 10.2 + - - -
173A ASP* 1.3 70.6 + - - +
175A GLU* 1.3 54.0 + - - +
177A LEU* 3.6 8.2 - - - +
178A SER* 2.7 39.5 + - - -
449A VAL* 3.9 18.6 - - + +
452A ILE* 3.7 33.2 - - + -
453A LYS* 4.2 9.0 - - + -
456A ARG* 3.8 9.2 - - - +
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Residues in contact with GLU 175 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A ASP* 2.9 18.6 + - - +
174A ALA* 1.3 75.5 - - - +
176A PHE* 1.3 58.9 + - - +
178A SER* 3.5 2.9 - - - -
179A ARG* 2.9 60.5 + - - +
446A HIS* 5.8 1.6 - - - +
449A VAL* 3.7 28.5 - - - +
453A LYS* 5.1 5.7 + - - -
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Residues in contact with PHE 176 (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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173A ASP* 2.7 29.7 + - + +
175A GLU* 1.3 71.5 - - - +
177A LEU* 1.3 63.8 + - + +
178A SER 3.0 1.3 - - - -
179A ARG* 2.8 8.3 + - + +
180A ARG* 2.7 69.2 + - + +
490A GLU* 3.5 14.8 - - - -
494A LEU* 3.5 40.6 - - + -
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Residues in contact with LEU 177 (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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172A PRO* 3.3 29.2 - - + +
173A ASP 2.9 14.5 + - - +
174A ALA* 3.6 8.1 - - - +
176A PHE* 1.3 76.7 - - - +
178A SER* 1.3 58.1 + - - +
181A PHE* 3.1 59.5 + - + +
182A LEU* 4.1 2.6 + - - +
452A ILE* 4.7 11.4 - - + -
456A ARG* 4.0 12.6 - - - +
491A LEU* 4.6 1.8 - - + -
494A LEU* 4.0 10.8 - - + -
495A TYR* 2.8 37.5 - - + +
502A GLU* 4.0 1.1 - - - +
505A PRO* 4.7 9.0 - - + -
509A LEU* 6.0 0.9 - - + -
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Residues in contact with SER 178 (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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174A ALA 2.7 26.5 + - - -
175A GLU 3.5 4.0 - - - -
177A LEU* 1.3 74.8 - - - +
179A ARG* 1.3 56.8 + - - +
182A LEU* 3.1 21.2 + - - +
183A LEU* 3.0 27.7 + - - +
445A LEU* 3.8 13.8 - - - +
448A ALA 4.0 5.4 + - - -
449A VAL* 3.5 34.9 + - - +
452A ILE* 4.1 7.4 - - - +
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Residues in contact with ARG 179 (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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175A GLU* 2.9 53.5 + - - +
176A PHE* 2.8 15.1 + - + +
178A SER* 1.3 73.4 - - - +
180A ARG* 1.3 58.8 + - + +
183A LEU* 3.4 35.4 - - + +
185A ARG* 3.2 18.9 + - - -
445A LEU* 3.9 22.1 - - - +
449A VAL* 5.2 0.2 - - - +
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Residues in contact with ARG 180 (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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176A PHE* 2.7 55.0 + - + +
179A ARG* 1.3 75.3 - - + +
181A PHE* 1.3 84.3 + - + +
185A ARG* 3.2 22.1 + - - +
438A ARG* 3.4 39.8 + - - +
486A GLU* 6.1 3.0 - - - +
487A MET* 5.5 0.8 - - - +
490A GLU* 2.5 36.8 + - - -
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Residues in contact with PHE 181 (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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177A LEU* 3.1 26.6 + - + +
180A ARG* 1.3 96.4 - - + +
182A LEU* 1.3 62.3 + - + +
183A LEU 3.6 1.1 - - - -
437A GLY 3.6 0.2 - - - -
438A ARG* 2.7 30.5 + - - +
487A MET* 3.5 43.1 - - + -
490A GLU* 3.7 37.0 - - + -
491A LEU* 3.5 29.4 - - + -
494A LEU* 3.7 15.7 - - + -
509A LEU* 3.4 34.8 - - + +
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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