Contacts of the helix formed by residues 162 - 174 (chain B) in PDB entry 2J16
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 162 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156B MET* 4.1 0.9 - - - -
161B LEU* 1.3 75.7 - - - +
163B LEU* 1.3 62.1 + - - +
164B ARG* 3.7 8.0 + - - +
165B HIS* 3.3 33.0 + - - -
166B SER* 2.7 30.0 + - - -
191B GLU* 3.4 20.0 - - - -
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Residues in contact with LEU 163 (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* 3.8 11.4 - - + -
156B MET* 3.9 17.2 - - + +
162B SER* 1.3 73.4 - - - +
164B ARG* 1.3 55.6 + - - +
166B SER* 3.7 0.7 - - - -
167B TYR* 2.8 44.0 + - + +
184B ILE* 3.9 21.8 - - + +
187B LEU* 3.7 31.9 - - + -
188B MET* 3.7 38.8 - - + +
191B GLU* 3.5 21.1 + - - +
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Residues in contact with ARG 164 (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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162B SER* 3.3 8.6 + - - +
163B LEU* 1.3 81.1 - - - +
165B HIS* 1.3 66.1 + - + +
167B TYR* 3.6 4.8 - - - +
168B ASP* 2.8 48.8 + - - +
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Residues in contact with HIS 165 (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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62A LEU* 3.9 26.7 - - + +
69A TYR* 5.0 10.3 + + - -
135A LYS* 6.1 0.4 + - - -
173A ARG* 5.5 2.4 + - - -
161B LEU* 4.1 22.2 - - + -
162B SER* 3.3 23.2 + - - +
164B ARG* 1.3 87.2 - - + +
166B SER* 1.3 57.3 + - - +
168B ASP* 3.2 11.7 + - - +
169B LEU* 2.9 35.5 + - - +
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Residues in contact with SER 166 (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* 3.9 16.8 - - - -
155B ILE* 3.5 25.0 - - - +
156B MET* 3.3 23.2 - - - +
161B LEU* 3.5 15.0 - - - +
162B SER 2.7 22.8 + - - -
163B LEU 3.7 2.7 - - - -
165B HIS* 1.3 73.0 - - - +
167B TYR* 1.3 65.5 + - - +
169B LEU* 3.4 5.7 + - - +
170B LEU* 3.1 23.0 + - - +
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Residues in contact with TYR 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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152B ILE* 3.9 29.7 - - + +
163B LEU* 2.8 28.9 + - + +
164B ARG* 3.6 4.0 - - - +
166B SER* 1.3 72.7 - - - +
168B ASP* 1.3 72.8 + - - +
170B LEU* 3.3 1.6 + - - +
171B LYS* 2.8 70.4 + - + +
177B ILE* 3.7 22.1 + - + -
178B ASN* 5.7 0.3 - - - -
179B PRO* 4.4 17.4 - - + +
184B ILE* 5.5 7.6 - - + -
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Residues in contact with ASP 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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173A ARG* 3.4 19.3 + - - +
164B ARG* 2.8 39.2 + - - +
165B HIS* 3.5 12.7 + - - +
167B TYR* 1.3 90.4 - - - +
169B LEU* 1.3 61.7 + - - +
171B LYS* 3.4 4.6 + - - +
172B SER* 3.0 28.1 + - - -
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Residues in contact with LEU 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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62A LEU* 3.5 25.6 - - + +
63A VAL 4.3 10.3 - - - +
64A LEU* 4.6 0.7 - - - -
65A PRO* 3.7 36.1 - - + -
173A ARG* 3.4 34.5 - - - +
63B VAL 5.6 0.5 - - - +
64B LEU* 5.6 6.1 - - + -
155B ILE* 4.6 11.2 - - + -
161B LEU* 3.8 19.3 - - + -
165B HIS 2.9 17.8 + - - +
166B SER* 3.8 4.0 - - - +
167B TYR 3.3 0.2 - - - -
168B ASP* 1.3 77.3 - - - +
170B LEU* 1.3 64.0 + - - +
172B SER* 3.4 9.7 + - - -
173B ARG* 3.5 12.0 + - - +
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Residues in contact with LEU 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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63B VAL* 3.5 44.0 - - + +
64B LEU* 5.9 1.1 - - + -
70B LEU* 4.6 3.8 - - + -
148B ALA* 3.8 34.5 - - + +
151B ILE* 3.9 17.5 - - + -
152B ILE* 4.0 8.3 - - + -
155B ILE* 4.8 5.5 - - + +
166B SER 3.1 13.9 + - - +
167B TYR 3.8 2.7 - - - +
169B LEU* 1.3 78.4 - - - +
171B LYS* 1.3 53.4 + - - +
173B ARG* 3.2 3.3 + - + -
174B ALA* 2.7 38.8 + - + +
177B ILE* 3.7 26.2 - - + -
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Residues in contact with LYS 171 (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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167B TYR* 2.8 56.8 + - + +
168B ASP* 3.7 5.6 - - - +
170B LEU* 1.3 73.3 - - - +
172B SER* 1.3 62.1 + - - +
174B ALA 3.2 21.6 - - - +
175B ASP* 2.6 49.7 + - - +
177B ILE* 3.5 24.3 + - + +
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Residues in contact with SER 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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172A SER* 3.2 30.1 - - - +
173A ARG* 2.8 41.9 + - - -
168B ASP 3.0 10.8 + - - -
169B LEU 3.7 5.8 - - - -
170B LEU 3.2 0.4 - - - -
171B LYS* 1.3 76.8 - - - +
173B ARG* 1.3 60.7 + - - +
175B ASP* 5.1 3.6 + - - +
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Residues in contact with ARG 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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165A HIS* 5.5 3.2 + - - -
168A ASP* 3.4 26.2 + - - +
169A LEU* 3.6 22.1 - - - +
172A SER* 2.6 43.2 + - - -
61B LEU* 3.6 31.5 - - + +
62B LEU* 2.6 39.1 + - - +
63B VAL* 3.9 27.6 - - + +
169B LEU 3.5 8.0 + - - +
170B LEU* 3.2 7.6 + - - +
172B SER* 1.3 82.6 - - - +
174B ALA* 1.3 58.9 + - - +
175B ASP* 3.8 2.8 + - - +
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Residues in contact with ALA 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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56B TYR* 4.5 7.2 - - + +
61B LEU* 4.0 17.0 - - + -
63B VAL* 4.3 1.1 - - + -
70B LEU* 4.0 17.5 - - + -
170B LEU* 2.7 21.0 + - + +
171B LYS 3.2 8.0 - - - +
173B ARG* 1.3 70.9 - - - +
175B ASP* 1.3 63.5 + - - +
176B LYS 3.3 3.3 + - - -
177B ILE* 3.4 37.4 - - + +
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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