Contacts of the helix formed by residues 158 - 174 (chain A) in PDB entry 1Q2L
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 TYR 158 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A MET* 4.1 4.9 - - + -
96A MET* 3.8 37.9 - - + -
104A ALA* 3.5 30.3 + - + +
155A ASP* 4.4 3.5 + - + -
156A LYS 3.3 0.6 - - - -
157A LYS* 1.3 119.6 + - + +
159A ALA* 1.3 64.2 + - - +
160A GLU 3.3 2.9 - - - -
161A ARG* 3.3 43.6 + - + -
162A GLU* 3.0 24.5 + - + +
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Residues in contact with ALA 159 (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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89A TYR* 2.6 30.1 + - - +
93A MET* 3.8 16.1 - - + +
156A LYS* 2.9 27.5 + - + +
158A TYR* 1.3 76.9 - - - +
160A GLU* 1.3 57.6 + - - +
162A GLU 3.6 0.2 + - - -
163A ARG* 3.0 19.5 + - - +
214A VAL* 5.3 9.4 - - + -
215A GLN* 6.5 0.9 - - + -
218A LEU* 6.1 1.1 - - + -
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Residues in contact with GLU 160 (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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156A LYS 4.5 0.8 + - - -
157A LYS 4.7 3.9 + - - +
158A TYR 3.3 0.8 - - - -
159A ALA* 1.3 75.7 - - - +
161A ARG* 1.3 69.0 + - - +
163A ARG* 3.2 26.7 + - - +
164A ASN* 3.0 36.4 + - - +
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Residues in contact with ARG 161 (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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96A MET* 3.2 15.5 - - - +
105A ASP* 3.1 40.2 + - - -
157A LYS 5.4 0.6 + - - +
158A TYR* 3.3 40.2 + - + +
160A GLU* 1.3 79.3 + - - +
162A GLU* 1.3 83.7 + - - +
164A ASN* 3.3 8.8 + - - +
165A ALA* 2.9 25.9 + - + +
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Residues in contact with GLU 162 (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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89A TYR* 3.9 7.6 - - + -
92A HIS* 3.0 40.6 + - + +
93A MET* 3.7 15.7 - - - -
96A MET* 3.7 33.5 - - + +
158A TYR* 3.0 17.4 + - + +
161A ARG* 1.3 110.3 + - - +
163A ARG* 1.3 60.4 + - - +
165A ALA* 3.6 8.3 - - - +
166A VAL* 2.8 35.0 + - - +
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Residues in contact with ARG 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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89A TYR* 3.7 15.2 - - + +
159A ALA 3.0 19.2 + - - +
160A GLU* 3.2 27.3 + - - +
162A GLU* 1.3 75.2 - - - +
164A ASN* 1.3 82.0 + - - +
166A VAL* 3.2 6.8 + - - +
167A ASN* 2.9 26.7 + - - +
202A ASN 4.7 0.6 - - - +
203A LEU* 3.9 24.5 + - + +
206A LEU* 4.0 21.7 - - + +
207A SER* 2.9 41.6 + - - +
208A ASP 5.5 0.2 - - - +
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Residues in contact with ASN 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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160A GLU* 3.0 24.7 + - - +
161A ARG* 3.5 9.8 - - - +
163A ARG* 1.3 106.7 + - - +
165A ALA* 1.3 59.4 + - - +
167A ASN* 3.3 6.3 + - - +
168A ALA* 2.8 30.1 + - - +
203A LEU* 3.5 11.7 - - - +
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Residues in contact with ALA 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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92A HIS* 4.2 9.6 - - + +
161A ARG* 2.9 17.1 + - + +
162A GLU* 3.3 23.5 + - - +
164A ASN* 1.3 76.3 - - - +
166A VAL* 1.3 63.8 + - - +
168A ALA* 3.2 7.3 + - - +
169A GLU* 3.0 28.4 + - + +
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Residues in contact with VAL 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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88A HIS* 3.7 14.6 - - + +
89A TYR* 4.3 20.4 - - + -
92A HIS* 4.0 29.6 - - + +
162A GLU 2.8 19.8 + - - +
163A ARG 3.5 6.5 - - - +
165A ALA* 1.3 76.1 - - - +
167A ASN* 1.3 63.6 + - - +
169A GLU* 3.2 2.8 + - - +
170A LEU* 3.0 24.2 + - + +
200A GLY 3.1 27.8 - - - +
201A GLY 3.7 9.0 - - - +
202A ASN 4.7 0.2 - - - +
206A LEU* 3.8 15.0 - - + -
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Residues in contact with ASN 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 ARG 2.9 11.1 + - - +
164A ASN 3.7 4.6 + - - +
166A VAL* 1.3 78.2 - - - +
168A ALA* 1.3 56.3 + - - +
170A LEU* 3.5 1.5 + - - +
171A THR* 2.7 48.2 + - - -
201A GLY 4.7 1.1 - - - -
202A ASN* 3.4 17.4 - - - +
203A LEU* 3.3 60.2 + - + +
471A PHE* 4.2 6.6 - - - -
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Residues in contact with ALA 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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164A ASN 2.8 18.5 + - - +
165A ALA* 3.2 8.3 + - - +
167A ASN* 1.3 75.4 - - - +
169A GLU* 1.3 66.3 + - + +
171A THR* 3.3 6.4 + - - -
172A MET* 3.0 43.7 + - + +
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Residues in contact with GLU 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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88A HIS* 3.1 6.5 + - - -
92A HIS* 3.0 17.9 - - - -
165A ALA* 3.0 14.6 + - - +
166A VAL* 3.7 5.2 - - - +
168A ALA* 1.3 78.9 - - + +
170A LEU* 1.3 67.2 + - + +
172A MET* 3.2 12.4 + - + +
173A ALA* 3.1 23.3 + - - +
963A ZN 1.9 38.3 - - - -
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Residues in contact with LEU 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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88A HIS* 3.7 26.0 - - + -
166A VAL 3.0 21.3 + - - +
167A ASN 4.0 2.7 - - - +
169A GLU* 1.3 80.4 - - + +
171A THR* 1.3 57.2 - - - +
173A ALA* 3.2 3.6 + - + +
174A ARG* 2.9 30.5 + - - +
179A MET* 3.7 28.5 - - + -
198A PHE* 4.8 7.2 - - + -
199A SER 4.5 4.9 - - - +
200A GLY* 3.8 24.9 - - - +
201A GLY 3.5 17.9 - - - +
471A PHE* 3.6 18.8 - - + -
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Residues in contact with THR 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 ASN* 2.7 34.7 + - - -
168A ALA* 3.6 7.4 - - - -
169A GLU 3.3 0.2 - - - -
170A LEU* 1.3 75.2 - - - +
172A MET* 1.3 62.8 + - + +
174A ARG* 2.9 34.4 + - - +
175A THR* 4.7 3.5 + - - +
471A PHE* 3.7 17.1 - - + -
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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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168A ALA* 3.0 43.4 + - + +
169A GLU* 3.2 10.3 + - + +
171A THR* 1.3 79.0 - - + +
173A ALA* 1.3 59.9 + - - +
174A ARG 3.5 0.2 - - - -
175A THR* 3.7 14.1 + - - +
176A ARG* 4.3 6.1 + - - +
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Residues in contact with ALA 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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169A GLU 3.1 14.8 + - - +
170A LEU* 3.2 5.3 + - + +
172A MET* 1.3 76.9 - - - +
174A ARG* 1.3 60.5 + - - +
175A THR 3.0 7.4 + - - -
176A ARG* 3.1 48.8 + - - +
179A MET* 3.2 32.2 - - + +
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Residues in contact with ARG 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 LEU 2.9 11.1 + - - +
171A THR* 2.9 35.5 + - - +
173A ALA* 1.3 76.3 - - - +
175A THR* 1.3 75.1 + - + +
176A ARG 3.3 0.9 - - - -
179A MET* 4.5 3.1 - - - -
180A ARG* 3.3 26.8 + - - +
471A PHE* 3.0 41.7 + - + -
472A VAL* 3.5 37.5 + - + +
473A ASP* 2.9 26.0 + - - +
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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