Contacts of the helix formed by residues 166 - 177 (chain A) in PDB entry 4Y2H
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 MET 166 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A TYR* 4.4 13.0 - - - +
89A VAL* 3.3 40.4 - - + +
154A SER* 3.8 11.4 - - - +
155A GLU 4.6 0.2 - - - +
156A TRP* 3.5 34.1 + - + +
162A LEU 5.6 0.2 - - - -
163A HIS 4.8 0.8 + - - -
164A GLU* 3.0 8.7 + - + +
165A SER* 1.3 76.4 - - - +
167A LEU* 1.3 65.1 + - - +
168A SER 3.2 0.2 - - - -
169A SER* 2.9 23.8 + - - -
170A VAL* 3.4 3.8 + - + +
351A ARG* 5.8 2.7 - - - +
401A SAH 3.4 59.5 - - + +
402A 49K 5.3 0.4 - - - -
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Residues in contact with LEU 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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156A TRP* 3.6 52.4 - - + +
162A LEU* 4.1 8.3 - - + -
165A SER* 3.3 2.5 - - - -
166A MET* 1.3 76.0 - - - +
168A SER* 1.3 62.7 + - - +
170A VAL* 3.1 10.5 + - + +
171A LEU* 3.0 46.0 + - + +
256A LEU* 3.7 21.3 - - + -
258A LEU* 4.3 11.9 - - + -
263A LEU* 5.2 2.2 - - + -
267A LEU* 3.7 34.8 - - + -
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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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141A GLU* 4.8 2.0 - - - -
165A SER* 3.8 15.4 + - - -
167A LEU* 1.3 75.1 - - - +
169A SER* 1.3 55.7 + - - +
171A LEU* 3.7 4.8 - - - +
172A HIS* 2.7 36.1 + - - +
264A GLU* 6.4 1.6 - - - +
267A LEU* 3.9 19.0 - - - +
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Residues in contact with SER 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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89A VAL* 4.6 3.6 - - - -
140A VAL* 3.6 13.1 - - - +
141A GLU* 2.4 29.2 + - - -
165A SER 5.1 0.5 + - - -
166A MET* 2.9 21.3 + - - -
168A SER* 1.3 75.7 - - - +
170A VAL* 1.3 61.1 + - - +
172A HIS* 3.4 3.5 + - - +
173A ALA* 2.8 30.3 + - - +
351A ARG* 5.1 4.2 + - - -
401A SAH 3.1 24.0 + - - -
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Residues in contact with VAL 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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89A VAL* 4.3 10.8 - - + -
152A ILE* 4.5 20.6 - - + +
154A SER* 3.6 28.3 - - - +
156A TRP* 3.7 31.9 - - + +
166A MET* 3.9 7.4 - - + +
167A LEU* 3.1 14.9 + - + +
169A SER* 1.3 76.6 - - - +
171A LEU* 1.3 60.9 + - + +
173A ALA* 3.2 6.2 + - - +
174A ARG* 2.8 28.1 + - - +
184A LEU* 4.5 15.0 - - + -
258A LEU* 5.2 2.5 - - + -
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Residues in contact with LEU 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 LEU* 3.0 40.9 + - + +
168A SER* 3.9 3.8 - - - +
170A VAL* 1.3 76.8 - - + +
172A HIS* 1.3 66.7 + - - +
174A ARG* 3.1 18.6 + - + +
175A THR* 2.9 23.2 + - - -
184A LEU* 6.1 0.9 - - + -
258A LEU* 3.9 32.8 - - + +
263A LEU* 3.8 20.6 - - + +
264A GLU* 3.7 49.8 - - + +
267A LEU* 4.5 6.3 - - + -
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Residues in contact with HIS 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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140A VAL* 4.6 2.7 + - + -
141A GLU* 3.5 50.2 + - + +
168A SER 2.7 22.7 + - - +
169A SER* 3.5 8.3 - - - +
171A LEU* 1.3 73.1 - - - +
173A ALA* 1.3 58.6 + - - +
175A THR* 3.4 3.2 + - - -
176A LYS* 3.0 46.8 + - + +
264A GLU* 3.9 9.5 + - - +
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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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87A LEU* 3.9 16.2 - - + -
89A VAL* 3.9 9.0 - - + -
140A VAL* 3.8 27.3 - - + +
152A ILE* 3.8 4.1 - - + +
169A SER 2.8 19.5 + - - +
170A VAL 3.6 4.3 - - - +
171A LEU 3.2 0.2 - - - -
172A HIS* 1.3 73.2 + - - +
174A ARG* 1.3 61.0 + - - +
177A TRP* 2.8 41.8 + - + +
178A LEU 3.6 1.2 + - - -
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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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152A ILE* 3.5 16.5 - - + +
170A VAL 2.8 18.4 + - - +
171A LEU* 3.1 22.8 + - + +
173A ALA* 1.3 74.5 - - - +
175A THR* 1.3 90.8 + - - +
178A LEU* 3.1 38.1 + - + +
184A LEU* 3.8 22.0 - - + -
258A LEU 2.8 25.5 + - - -
259A SER* 3.9 13.2 + - - +
260A ARG 3.2 27.5 + - - -
261A ALA* 4.0 9.1 - - - +
264A GLU* 4.4 11.9 - - - +
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Residues in contact with THR 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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148A GLN* 5.0 2.3 - - - +
171A LEU 2.9 7.7 + - - -
172A HIS* 3.9 3.8 - - - -
174A ARG* 1.3 99.4 + - - +
176A LYS* 1.3 61.6 + - - +
178A LEU 4.9 2.6 + - - +
264A GLU* 3.2 24.8 + - - +
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Residues in contact with LYS 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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140A VAL 5.7 0.2 - - - +
141A GLU 3.6 18.8 + - - +
142A THR* 5.0 2.0 - - - +
143A VAL 4.1 14.3 + - - -
144A GLU* 4.5 11.9 + - - -
148A GLN* 3.3 14.4 - - - +
172A HIS* 3.0 36.7 + - + +
175A THR* 1.3 80.1 - - + +
177A TRP* 1.3 95.3 + - + +
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Residues in contact with TRP 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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87A LEU* 4.3 12.8 - - + -
140A VAL* 4.5 7.2 + - + -
143A VAL* 3.6 32.7 + - + +
144A GLU* 3.6 20.4 - - + -
145A LEU* 3.4 58.8 - - + -
147A GLU* 3.7 24.0 - - - -
148A GLN* 3.3 16.1 - - + +
149A VAL* 2.8 30.3 + - + -
172A HIS* 6.0 0.2 - - - -
173A ALA* 2.8 28.5 + - + +
176A LYS* 1.3 112.3 - - + +
178A LEU* 1.3 60.0 + - - +
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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