Contacts of the helix formed by residues 166 - 180 (chain B) in PDB entry 5ZCJ
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 VAL 166 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B HIS* 6.5 1.3 - - + -
55B ARG* 3.7 35.7 - - - +
59B LEU* 3.9 16.3 - - + +
60B LEU 3.1 18.0 + - - +
61B GLY* 4.1 1.8 - - - -
165B PHE* 1.3 70.5 - - - +
167B SER* 1.3 57.2 + - - +
168B THR* 3.7 16.6 - - - +
169B ALA* 2.7 43.5 + - + +
170B LYS 3.3 4.7 + - - -
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Residues in contact with SER 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU* 5.4 1.8 - - - +
103B GLU* 4.9 16.8 + - - +
165B PHE* 3.4 6.7 + - - -
166B VAL* 1.3 72.5 - - - +
168B THR* 1.3 66.2 + - - +
170B LYS* 3.4 8.5 + - - +
171B CYS* 3.3 28.8 + - - -
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Residues in contact with THR 168 (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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9B LEU* 4.0 17.5 - - + +
29B HIS* 5.9 3.6 - - + +
102B THR* 3.3 27.9 - - + +
103B GLU 5.0 0.7 + - - -
110B ALA* 3.6 27.4 - - + -
166B VAL* 3.1 11.5 - - + +
167B SER* 1.3 82.9 + - - +
169B ALA* 1.3 55.4 + - - +
171B CYS* 3.3 3.8 + - - +
172B GLN* 2.9 45.9 + - + +
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Residues in contact with ALA 169 (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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52B MET* 4.3 9.4 - - + +
60B LEU 4.1 4.3 - - - +
61B GLY* 3.8 28.7 - - - -
62B PHE* 3.6 12.4 - - + +
165B PHE* 4.9 0.4 - - + -
166B VAL* 2.7 24.6 + - + +
168B THR* 1.3 76.4 - - - +
170B LYS* 1.3 56.7 + - - +
172B GLN* 3.3 10.9 + - - +
173B LEU* 2.9 31.0 + - - +
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Residues in contact with LYS 170 (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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7B PRO* 4.8 12.7 - - + +
161B LEU* 3.2 48.2 + - + +
163B ASN 5.3 1.2 + - - -
165B PHE* 4.0 35.8 - - + +
166B VAL 3.3 3.8 + - - +
167B SER* 3.9 9.4 - - - +
168B THR 3.3 0.2 - - - -
169B ALA* 1.3 77.4 - - - +
171B CYS* 1.3 64.5 + - - +
173B LEU* 3.5 5.3 + - + +
174B LEU* 3.2 37.8 + - + +
192B LEU* 4.3 17.3 - - - +
195B ALA* 5.7 2.0 - - - +
199B GLN* 4.9 8.3 + - - +
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Residues in contact with CYS 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B PRO* 3.7 44.3 - - - +
9B LEU* 3.8 38.1 - - + +
100B HIS* 6.3 1.8 - - + -
167B SER* 3.3 15.7 + - - -
168B THR 3.3 6.4 + - - +
169B ALA 3.3 0.6 - - - -
170B LYS* 1.3 79.7 - - - +
172B GLN* 1.3 57.9 + - + +
174B LEU* 3.5 4.6 + - - +
175B PHE* 2.9 31.3 + - - +
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Residues in contact with GLN 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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9B LEU* 5.6 1.3 - - + -
29B HIS* 4.5 12.8 + - - +
62B PHE* 4.1 15.8 - - + -
100B HIS* 4.8 14.0 + - + +
110B ALA* 3.6 31.5 + - + +
111B HIS 4.1 4.6 + - - -
112B LEU* 3.7 42.0 - - + +
168B THR* 2.9 33.5 + - + +
169B ALA* 3.8 11.2 - - - +
171B CYS* 1.3 74.5 - - + +
173B LEU* 1.3 61.2 + - - +
175B PHE* 3.8 5.9 - - - +
176B ALA* 2.9 32.7 + - - +
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Residues in contact with LEU 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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31B MET* 4.6 2.7 - - - -
50B VAL* 4.3 18.6 - - + -
52B MET* 4.1 19.5 - - - -
62B PHE* 3.8 25.5 - - + -
145B VAL* 4.7 4.7 - - + -
157B PHE* 4.5 9.2 - - + -
160B PHE* 4.3 15.3 - - + -
161B LEU* 4.4 20.4 - - + -
165B PHE* 4.7 4.3 - - + -
169B ALA 2.9 17.4 + - - +
170B LYS* 3.8 5.8 - - - +
172B GLN* 1.3 77.4 - - - +
174B LEU* 1.3 58.7 - - + +
176B ALA* 3.2 2.5 + - - +
177B LEU* 2.9 56.7 + - + +
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Residues in contact with LEU 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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6B VAL* 4.1 11.7 - - + -
7B PRO* 3.8 24.7 - - + +
157B PHE* 4.4 6.3 - - + -
161B LEU* 4.2 23.6 - - + -
170B LYS* 3.2 23.5 + - + +
171B CYS* 4.0 4.0 - - - +
173B LEU* 1.3 76.9 - - + +
175B PHE* 1.3 63.4 + - - +
177B LEU* 3.6 3.3 + - - -
178B LYS* 3.3 21.1 + - - +
188B LEU* 3.8 33.5 - - + +
192B LEU* 3.6 36.6 - - + -
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Residues in contact with PHE 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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11B GLN* 3.9 34.1 - - - -
97B LEU* 4.2 10.3 - - + -
98B SER* 3.5 28.5 - - - -
100B HIS* 4.0 19.3 - + - +
112B LEU* 4.6 2.9 - - + -
171B CYS 2.9 18.8 + - - +
172B GLN* 3.8 6.7 - - - +
174B LEU* 1.3 77.6 - - - +
176B ALA* 1.3 65.7 + - - +
178B LYS* 3.3 7.0 + - + +
179B VAL* 3.2 54.5 + - + +
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Residues in contact with ALA 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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31B MET* 3.5 27.4 - - + -
97B LEU* 4.1 8.5 - - + -
112B LEU* 4.0 15.9 - - + -
114B ALA* 5.8 0.2 - - + -
172B GLN 2.9 18.8 + - - +
173B LEU 3.9 0.4 - - - +
175B PHE* 1.3 75.9 - - - +
177B LEU* 1.3 65.5 + - - +
179B VAL* 4.0 8.7 - - - -
180B LEU* 2.9 35.7 + - + +
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Residues in contact with LEU 177 (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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31B MET* 4.0 8.5 - - + -
50B VAL* 4.4 3.4 - - + -
147B LEU* 3.8 23.1 - - + -
157B PHE* 3.7 29.8 - - + -
173B LEU* 2.9 37.6 + - + +
174B LEU* 4.0 4.3 - - - +
175B PHE 3.4 0.2 - - - -
176B ALA* 1.3 77.0 - - - +
178B LYS* 1.3 57.2 + - - +
182B MET* 3.0 65.7 + - + -
183B MET* 3.1 21.2 + - + -
188B LEU* 4.0 11.4 - - + -
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Residues in contact with LYS 178 (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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8B GLU* 5.4 5.5 + - - -
174B LEU 3.3 10.3 + - - +
175B PHE* 3.3 11.8 + - + +
176B ALA 3.1 0.8 - - - -
177B LEU* 1.3 76.9 - - - +
179B VAL* 1.3 70.4 + - + +
181B ASN* 3.1 24.9 + - - +
183B MET 4.0 11.0 - - - +
185B GLU* 3.3 48.3 + - + +
188B LEU* 4.1 12.7 - - + +
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Residues in contact with VAL 179 (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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97B LEU* 4.0 22.4 - - + -
175B PHE* 3.2 43.0 + - + +
176B ALA* 3.7 10.8 - - - +
178B LYS* 1.3 85.9 - - + +
180B LEU* 1.3 67.0 + - + +
181B ASN* 3.2 10.4 + - - +
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Residues in contact with LEU 180 (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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31B MET* 4.2 8.1 - - + -
33B TYR* 3.6 43.3 + - + +
48B PHE* 5.6 0.5 - - - -
97B LEU* 4.4 21.3 - - + -
114B ALA* 4.1 15.7 - - + -
176B ALA* 2.9 27.8 + - + +
179B VAL* 1.3 82.3 - - + +
181B ASN* 1.3 71.1 + - - +
182B MET* 3.3 23.4 + - + +
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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