Contacts of the helix formed by residues 166 - 177 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B TYR* 4.1 15.3 - - - +
89B VAL* 3.3 39.3 - - + +
154B SER* 3.5 13.0 - - - +
155B GLU 4.3 0.4 - - - +
156B TRP* 3.6 34.4 + - + +
163B HIS 5.0 0.6 + - - -
164B GLU* 3.3 6.0 - - + +
165B SER* 1.3 76.2 - - - +
167B LEU* 1.3 67.2 + - - +
168B SER 3.2 0.9 - - - -
169B SER* 2.9 21.4 + - - -
170B VAL* 3.3 3.7 + - + +
351B ARG* 4.5 4.3 - - - +
401B SAH 3.4 59.5 - - + +
402B 49K 5.4 0.4 - - - -
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Residues in contact with LEU 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B TRP* 3.8 54.6 - - + -
162B LEU* 4.3 7.6 - - + -
165B SER* 3.4 2.3 - - - +
166B MET* 1.3 77.5 - - - +
168B SER* 1.3 56.4 + - - +
170B VAL* 2.9 11.7 + - + +
171B LEU* 2.8 49.6 + - + +
256B LEU* 4.2 14.4 - - + -
258B LEU* 4.0 11.0 - - + -
263B LEU* 4.7 6.3 - - + -
267B LEU* 3.7 36.6 - - + -
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Residues in contact with SER 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B GLU* 5.0 0.9 - - - -
165B SER* 4.0 13.0 + - - -
166B MET 3.2 0.4 - - - -
167B LEU* 1.3 76.5 - - - +
169B SER* 1.3 53.9 + - - +
171B LEU* 3.7 4.2 - - - +
172B HIS* 2.8 36.3 + - - +
264B GLU* 3.7 18.6 + - - +
267B LEU* 3.8 20.8 - - - +
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Residues in contact with SER 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B VAL* 4.7 2.9 - - - -
140B VAL* 3.7 9.4 - - - +
141B GLU* 2.5 30.4 + - - -
165B SER 4.7 1.8 + - - -
166B MET* 2.9 22.1 + - - -
168B SER* 1.3 77.9 - - - +
170B VAL* 1.3 61.6 + - - +
172B HIS* 3.3 4.6 + - - +
173B ALA* 3.0 23.4 + - - +
351B ARG* 4.8 6.9 + - - -
401B SAH 3.0 26.0 + - - -
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Residues in contact with VAL 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B VAL* 4.2 10.5 - - + -
152B ILE* 4.5 15.3 - - + +
154B SER* 3.3 36.1 - - - +
156B TRP* 3.7 28.7 - - + +
166B MET* 3.3 7.6 + - + +
167B LEU* 2.9 15.2 + - + +
169B SER* 1.3 77.6 - - - +
171B LEU* 1.3 60.1 + - + +
173B ALA* 3.1 8.7 + - - +
174B ARG* 3.0 26.5 + - + +
184B LEU* 4.5 14.1 - - + -
258B LEU* 5.5 3.1 - - + -
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Residues in contact with LEU 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B LEU* 2.8 36.9 + - + +
168B SER* 3.8 1.8 - - - +
170B VAL* 1.3 75.8 - - + +
172B HIS* 1.3 60.8 + - - +
174B ARG* 3.2 10.7 + - - +
175B THR* 3.0 28.1 + - - +
184B LEU* 5.8 0.7 - - + -
258B LEU* 3.4 32.1 - - + +
263B LEU* 4.0 18.4 - - + -
264B GLU* 3.7 41.3 - - + +
267B LEU* 3.9 26.5 - - + -
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Residues in contact with HIS 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B VAL* 4.9 1.4 + - - +
141B GLU* 3.6 52.1 - - + +
168B SER 2.8 21.7 + - - +
169B SER 3.5 5.6 - - - +
171B LEU* 1.3 72.6 - - - +
173B ALA* 1.3 63.7 + - - +
175B THR* 4.0 3.4 - - - -
176B LYS* 3.1 48.2 + - + +
264B GLU* 3.9 14.7 + - - +
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Residues in contact with ALA 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B LEU* 3.8 24.9 - - + -
89B VAL* 3.9 9.4 - - + -
140B VAL* 3.8 17.2 - - + +
152B ILE* 3.9 4.8 - - + +
169B SER 3.0 13.6 + - - +
170B VAL 3.1 8.5 + - - +
172B HIS* 1.3 79.5 + - - +
174B ARG* 1.3 58.5 + - - +
177B TRP* 2.9 41.3 + - - +
178B LEU 3.6 1.0 + - - -
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Residues in contact with ARG 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B ILE* 3.5 14.3 - - + +
170B VAL* 3.0 12.8 + - + +
171B LEU* 3.2 15.0 + - - +
173B ALA* 1.3 76.2 - - - +
175B THR* 1.3 74.3 + - - +
178B LEU* 3.0 53.8 + - + +
184B LEU* 3.9 26.7 - - + +
258B LEU 4.1 10.2 + - - -
259B SER* 3.3 45.2 + - - +
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Residues in contact with THR 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B LEU* 3.0 16.5 + - - +
172B HIS* 4.0 4.0 - - - -
174B ARG* 1.3 85.8 + - - +
176B LYS* 1.3 60.8 + - - +
178B LEU 5.1 2.3 + - - +
264B GLU* 3.7 14.0 + - - +
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Residues in contact with LYS 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B VAL 5.5 0.9 - - - +
141B GLU 3.3 24.6 + - - +
142B THR* 4.7 2.8 - - - +
143B VAL 4.5 6.9 + - - -
148B GLN* 4.3 13.0 + - - -
172B HIS* 3.1 36.9 + - + +
175B THR* 1.3 80.2 - - - +
177B TRP* 1.3 104.0 + - + +
178B LEU 5.5 0.2 - - - -
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Residues in contact with TRP 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LEU* 4.6 7.2 - - + -
140B VAL* 4.5 7.4 + - + -
143B VAL* 3.8 21.5 + - + +
144B GLU* 4.4 2.5 - - + -
145B LEU* 3.5 61.8 - - + +
147B GLU* 3.5 32.1 - - - -
148B GLN* 3.2 16.9 - - + +
149B VAL* 3.0 32.1 + - + -
173B ALA* 2.9 24.6 + - + +
176B LYS* 1.3 121.8 - - + +
178B LEU* 1.3 60.8 + - - +
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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