Contacts of the helix formed by residues 162 - 171 (chain A) in PDB entry 3SZQ
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 ASN 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A LYS* 1.3 82.9 - - - +
163A SER* 1.3 65.0 + - - +
164A ALA* 3.2 12.8 + - - +
165A HIS* 3.0 61.6 + - - +
166A TYR 3.4 3.3 + - - -
211A PHE* 3.4 15.1 - - - -
2B C 5.3 0.2 + - - -
9C T 6.0 5.8 - - + -
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Residues in contact with SER 163 (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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162A ASN* 1.3 74.2 - - - +
164A ALA* 1.3 58.2 + - - +
166A TYR* 3.1 3.7 + - - +
167A ILE* 2.8 34.9 + - - +
198A LEU* 3.5 37.1 - - - +
209A ARG* 3.9 29.7 + - - -
211A PHE* 3.6 19.5 - - - +
9C T 4.4 6.4 + - - -
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Residues in contact with ALA 164 (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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3A BME 4.0 8.9 - - - -
162A ASN* 3.2 10.4 + - - +
163A SER* 1.3 75.4 - - - +
165A HIS* 1.3 67.9 + - - +
167A ILE* 4.1 2.0 - - - +
168A SER* 2.9 27.9 + - - -
194A PHE* 3.7 39.9 + - + +
209A ARG* 5.6 0.2 - - - +
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Residues in contact with HIS 165 (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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3A BME 3.8 17.3 - - - -
67A LYS* 3.8 17.9 - - + -
159A SER 3.6 17.2 + - - -
160A LEU* 3.8 16.8 - - + -
161A LYS* 3.0 28.0 + - + -
162A ASN* 3.0 41.3 + - - +
164A ALA* 1.3 74.7 - - - +
166A TYR* 1.3 62.1 + - - +
168A SER* 2.7 23.7 + - - -
169A PHE* 3.3 13.9 - + - -
1B C 5.3 0.2 - - - -
2B C 2.8 31.1 + - - -
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Residues in contact with TYR 166 (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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155A HIS* 4.3 14.8 - + + -
160A LEU* 3.9 16.4 - - + -
162A ASN 3.4 5.3 + - - +
163A SER* 3.1 9.0 + - - +
165A HIS* 1.3 78.5 - - - +
167A ILE* 1.3 61.5 + - + +
169A PHE* 3.3 10.1 + - - +
170A THR* 2.7 52.9 + - + +
198A LEU* 4.4 10.1 - - + -
199A LYS 2.5 36.0 + - - -
200A CYS* 3.5 3.3 - - - -
201A TRP* 3.0 26.3 + + - +
211A PHE* 4.6 2.7 - - + -
214A LEU* 3.6 32.2 - - + +
218A LEU* 4.0 28.7 - - + +
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Residues in contact with ILE 167 (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 SER 2.8 25.0 + - - +
164A ALA 4.1 0.4 - - - +
166A TYR* 1.3 76.4 - - + +
168A SER* 1.3 60.2 + - - +
169A PHE 3.2 0.7 + - - -
170A THR* 3.6 6.5 - - - +
171A SER* 2.8 46.8 + - - +
193A LEU* 3.8 15.9 - - + +
194A PHE* 3.6 51.4 - - + +
196A GLU* 4.2 6.1 - - + +
197A ASP 5.2 3.4 - - - +
198A LEU* 4.1 19.1 - - + -
209A ARG* 3.9 12.8 - - - +
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Residues in contact with SER 168 (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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3A BME 3.8 12.2 - - - -
138A HIS* 3.2 31.8 + - - -
164A ALA 2.9 15.5 + - - -
165A HIS 2.7 19.8 + - - -
167A ILE* 1.3 77.3 - - - +
169A PHE* 1.3 61.2 + - - +
173A PHE* 3.6 21.6 - - - -
174A PHE* 3.3 23.0 + - - +
194A PHE* 3.8 11.8 - - - -
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Residues in contact with PHE 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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1A AMP 4.5 2.7 - - - -
3A BME 5.9 1.1 - - - -
67A LYS* 3.7 25.8 - - + -
71A HIS* 3.7 17.7 - + - -
134A LYS* 2.8 24.9 + - - +
138A HIS* 3.3 33.2 - + - -
149A HIS* 3.6 27.1 - + - -
151A MET* 3.4 26.0 - - + -
155A HIS* 3.3 27.1 - + + -
165A HIS* 3.3 20.4 - + - -
166A TYR 3.3 4.7 + - - +
167A ILE 3.1 0.8 - - - -
168A SER* 1.3 82.6 + - - +
170A THR* 1.3 59.6 + - - +
171A SER 3.7 1.1 - - - -
174A PHE* 3.7 26.9 - + - +
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Residues in contact with THR 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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134A LYS* 3.9 4.5 - - - +
155A HIS* 3.7 25.6 - - + +
166A TYR* 2.7 48.6 + - + +
167A ILE* 3.2 9.1 + - - -
169A PHE* 1.3 83.3 - - - +
171A SER* 1.3 60.1 + - - +
199A LYS 5.7 0.2 - - - -
201A TRP* 4.3 18.3 - - + +
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Residues in contact with SER 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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167A ILE* 2.8 29.3 + - - +
170A THR* 1.3 80.4 - - - +
172A PRO* 1.3 69.8 - - - +
173A PHE* 2.9 15.9 + - - +
174A PHE* 3.0 25.5 + - - +
193A LEU* 3.3 19.8 - - - +
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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