Contacts of the helix formed by residues 154 - 164 (chain A) in PDB entry 1QCF
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 SER 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A GLY 4.0 1.8 + - - -
153A ILE* 1.3 79.1 - - - +
155A ARG* 1.3 61.0 + - - +
156A LYS* 3.7 7.1 + - - +
157A ASP* 3.2 29.7 + - - +
158A ALA* 2.8 28.5 + - - +
175A ARG* 4.5 0.9 - - - -
178A GLU* 3.3 28.5 - - - -
372A GLU* 5.0 6.1 + - - -
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Residues in contact with ARG 155 (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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154A SER* 1.3 70.7 - - - +
156A LYS* 1.3 73.5 + - + +
158A ALA* 3.1 5.0 + - - +
159A GLU* 3.0 33.0 + - - +
175A ARG* 3.9 15.3 - - - +
178A GLU* 2.9 19.1 + - - +
179A THR* 5.2 0.2 + - - -
201A HIS* 2.8 41.1 - - + +
518A ASP* 5.5 0.2 - - - -
526A GLN* 2.3 71.7 + - - +
527A PTR 3.0 54.4 + - - +
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Residues in contact with LYS 156 (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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154A SER* 3.3 6.6 + - - +
155A ARG* 1.3 89.7 - - + +
157A ASP* 1.3 61.3 + - - +
159A GLU* 3.2 30.5 + - - +
160A ARG* 3.1 55.4 + - - +
178A GLU* 4.7 0.6 + - - +
365A ASP* 4.1 10.4 + - - -
372A GLU* 5.2 2.9 - - - +
517A ASP* 3.1 57.3 + - + +
518A ASP* 5.2 3.1 + - - +
526A GLN* 5.8 0.7 - - - +
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Residues in contact with ASP 157 (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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153A ILE* 3.6 19.0 - - + -
154A SER* 3.2 20.4 + - - +
156A LYS* 1.3 76.0 - - - +
158A ALA* 1.3 67.4 + - - +
160A ARG* 2.9 30.1 + - - +
161A GLN* 2.9 36.6 + - - +
320A ASP* 4.1 10.8 - - - +
321A LYS* 2.9 24.7 + - - -
372A GLU* 4.2 5.9 - - - +
399A VAL* 6.1 0.5 - - - +
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Residues in contact with ALA 158 (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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153A ILE* 3.5 12.3 - - + +
154A SER 2.8 14.2 + - - +
155A ARG 3.3 10.1 - - - +
157A ASP* 1.3 77.1 - - - +
159A GLU* 1.3 62.3 + - - +
161A GLN 4.0 0.2 - - - -
162A LEU* 3.1 31.5 + - - +
173A MET* 3.7 14.6 - - - +
175A ARG* 3.7 28.9 - - - +
187A SER* 4.0 8.5 - - - +
199A VAL* 5.1 0.2 - - - -
201A HIS* 4.5 0.9 - - + -
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Residues in contact with GLU 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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155A ARG* 3.0 26.6 + - - +
156A LYS* 3.3 35.9 + - - +
157A ASP 3.1 0.2 - - - -
158A ALA* 1.3 77.7 - - - +
160A ARG* 1.3 58.4 + - + +
162A LEU 3.4 0.7 + - - -
163A LEU* 2.9 43.6 + - + +
199A VAL* 3.8 23.9 - - + +
201A HIS* 2.9 30.6 + - + +
526A GLN* 5.4 1.7 + - - -
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Residues in contact with ARG 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* 3.1 39.4 + - - +
157A ASP* 2.9 32.0 + - - +
159A GLU* 1.3 76.4 - - + +
161A GLN* 1.3 64.6 + - + +
163A LEU* 3.5 6.7 + - - +
164A ALA* 3.1 21.3 + - - +
321A LYS* 3.8 5.4 - - - +
362A LYS* 5.4 4.7 - - - +
365A ASP* 3.0 43.6 + - - +
368A ALA* 4.3 0.4 - - - +
369A GLN* 3.4 33.5 - - - +
372A GLU* 3.6 18.0 + - - -
399A VAL* 5.7 9.6 - - + -
517A ASP* 4.2 8.9 + - - -
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Residues in contact with GLN 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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150A PHE* 4.4 16.3 - - - -
153A ILE* 3.3 31.3 - - - +
157A ASP* 2.9 23.6 + - - +
158A ALA 4.1 2.0 - - - +
160A ARG* 1.3 77.1 - - + +
162A LEU* 1.3 61.3 + - - +
164A ALA* 3.2 13.9 + - - +
167A ASN* 2.8 20.6 + - - -
173A MET* 4.6 2.2 - - + -
245A CYS* 3.5 15.4 - - - -
246A MET 5.0 5.4 - - - +
247A SER* 5.6 2.4 - - - -
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Residues in contact with LEU 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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158A ALA 3.1 18.8 + - - +
161A GLN* 1.3 77.1 - - - +
163A LEU* 1.3 58.2 + - - +
167A ASN* 3.2 11.9 + - - +
171A SER* 3.5 38.1 - - - +
172A PHE* 3.8 2.9 - - - +
173A MET* 4.2 6.5 - - + -
187A SER* 3.7 40.4 - - - +
188A VAL 4.2 0.2 - - - +
189A ARG* 3.0 28.5 + - + +
199A VAL* 3.7 26.7 - - + -
245A CYS* 3.4 31.0 - - + -
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Residues in contact with LEU 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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159A GLU* 2.9 32.2 + - + +
160A ARG* 3.9 5.4 - - - +
162A LEU* 1.3 73.6 - - - +
164A ALA* 1.3 67.3 + - - +
165A PRO* 3.6 2.9 - - - +
189A ARG* 3.9 17.6 + - - +
197A ASP* 4.0 40.6 - - + +
198A THR* 4.0 5.2 - - - +
199A VAL* 3.6 22.7 - - + +
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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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160A ARG 3.1 12.8 + - - +
161A GLN* 3.2 18.0 + - - +
163A LEU* 1.3 80.4 - - - +
165A PRO* 1.3 79.6 - - + +
166A GLY 3.4 0.9 + - - -
167A ASN* 3.0 20.5 + - - +
189A ARG* 3.6 4.2 + - - -
397A SER* 5.8 9.4 - - - +
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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