Contacts of the helix formed by residues 172 - 181 (chain A) in PDB entry 5A0Q
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 GLN 172 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A ILE* 6.1 1.1 - - - +
33A ASN* 3.5 29.8 + - - +
38A THR* 4.9 1.8 - - - -
167A ALA* 3.9 10.0 - - - +
168A ALA* 3.8 21.1 - - - +
169A GLY 3.3 29.7 + - - +
170A VAL 3.1 4.8 - - - +
171A LYS* 1.4 77.0 - - - +
173A THR* 1.3 59.8 + - + +
175A SER* 2.8 18.8 + - - -
176A THR* 2.7 27.9 + - - -
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Residues in contact with THR 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 VAL 5.4 1.6 - - - +
172A GLN* 1.3 83.2 - - + +
174A GLU* 1.3 87.0 + - + +
176A THR* 3.2 17.5 + - - -
177A SER* 3.4 15.6 + - - -
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Residues in contact with GLU 174 (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 VAL 4.1 3.3 - - - +
171A LYS* 3.3 54.1 + - + +
173A THR* 1.3 95.1 - - + +
175A SER* 1.4 59.1 + - - +
177A SER* 3.9 14.4 + - - -
178A PHE* 4.0 3.8 + - - +
205A VAL* 3.7 23.3 - - + +
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Residues in contact with SER 175 (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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38A THR* 4.9 2.7 - - - +
40A VAL* 4.4 5.6 - - - +
167A ALA* 3.2 22.5 - - - +
171A LYS 3.0 14.6 + - - -
172A GLN* 2.8 21.5 + - - -
174A GLU* 1.4 72.9 - - - +
176A THR* 1.4 61.6 + - - +
177A SER 3.2 2.2 - - - -
178A PHE* 3.0 6.6 + - - +
179A LEU* 3.0 23.9 + - - +
201A CYS* 3.4 21.8 - - - -
205A VAL* 3.3 16.5 - - - +
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Residues in contact with THR 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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163A PHE* 6.3 2.0 - - + -
167A ALA* 4.6 10.6 + - - +
172A GLN 2.7 22.6 + - - -
173A THR* 3.2 11.3 + - - -
175A SER* 1.4 74.9 + - - +
177A SER* 1.3 56.3 + - - +
179A LEU* 3.4 11.9 + - + +
180A GLU* 3.0 28.2 + - + +
53B SER* 4.1 26.2 - - - +
55B LEU* 4.3 8.7 - - + -
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Residues in contact with SER 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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173A THR 3.4 10.9 + - - -
174A GLU* 4.0 10.0 + - - -
175A SER 3.2 0.6 - - - -
176A THR* 1.3 77.8 - - - +
178A PHE* 1.3 56.6 + - - +
180A GLU* 3.2 13.1 + - - +
181A LYS* 3.0 40.7 + - - +
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Residues in contact with PHE 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 GLU 4.4 2.0 - - - +
175A SER 3.0 10.3 + - - +
177A SER* 1.3 80.0 - - - +
179A LEU* 1.3 58.5 + - - +
181A LYS* 3.5 18.7 + - + +
182A LYS* 3.4 58.8 + - + +
197A THR* 4.7 3.8 - - + -
200A THR* 3.9 21.5 - - - -
201A CYS* 3.6 37.0 - - + -
204A THR* 4.5 19.1 - - + -
205A VAL* 4.3 16.4 - - + -
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Residues in contact with LEU 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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40A VAL* 4.0 20.2 - - + -
42A VAL* 4.6 8.5 - - + -
165A ALA* 2.6 39.9 - - + +
166A THR* 3.6 17.3 - - - +
167A ALA* 3.9 14.6 - - + +
175A SER 3.0 13.3 + - - +
176A THR* 3.5 19.5 - - + +
177A SER 3.3 0.2 - - - -
178A PHE* 1.3 75.4 - - - +
180A GLU* 1.4 62.9 + - - +
182A LYS* 3.2 23.5 + - - +
197A THR* 5.0 7.6 - - + -
201A CYS* 4.2 11.0 - - + -
55B LEU* 3.5 21.6 - - + +
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Residues in contact with GLU 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 THR* 3.0 17.4 + - + +
177A SER* 3.2 10.8 + - - +
179A LEU* 1.4 72.2 - - - +
181A LYS* 1.4 65.0 + - - +
182A LYS 4.1 4.0 - - - -
52B LYS 5.3 0.7 - - - +
53B SER* 3.2 19.7 - - - +
54B ILE* 2.7 45.2 - - + +
55B LEU* 3.6 11.4 - - + +
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Residues in contact with LYS 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 SER* 3.0 26.6 + - - +
178A PHE* 3.6 21.8 - - + +
179A LEU 3.3 0.4 - - - -
180A GLU* 1.4 77.1 - - + +
182A LYS* 1.3 76.6 + - - +
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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