Contacts of the helix formed by residues 162 - 174 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A MET* 4.3 0.4 - - - -
161A LEU* 1.3 77.2 - - - +
163A LEU* 1.3 63.8 + - - +
164A ARG* 3.7 8.2 + - - +
165A HIS* 3.3 32.7 + - - -
166A SER* 2.9 27.4 + - - -
191A GLU* 3.2 12.3 - - - -
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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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152A ILE* 3.9 6.1 - - + -
156A MET* 3.9 20.3 - - + +
162A SER* 1.3 72.8 - - - +
164A ARG* 1.3 58.1 + - - +
166A SER* 3.8 0.2 - - - -
167A TYR* 2.9 35.4 + - + +
184A ILE* 4.0 17.0 - - + +
187A LEU* 3.7 33.4 - - + -
188A MET* 3.7 44.2 - - + +
191A GLU* 3.0 22.0 + - - +
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Residues in contact with ARG 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A SER* 3.3 8.6 + - - +
163A LEU* 1.3 79.6 - - - +
165A HIS* 1.3 63.4 + - + +
167A TYR* 3.8 5.0 - - + +
168A ASP* 2.9 48.1 + - - +
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Residues in contact with HIS 165 (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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161A LEU* 3.9 22.2 - - + -
162A SER* 3.3 23.9 + - - +
164A ARG* 1.3 83.6 - - + +
166A SER* 1.3 57.5 + - - +
168A ASP* 3.3 10.5 + - - +
169A LEU* 2.8 36.9 + - - +
62B LEU* 3.6 34.2 - - + +
69B TYR* 4.9 10.6 + + - -
173B ARG* 5.5 3.1 + - - -
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Residues in contact with SER 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A ILE* 3.8 11.9 - - - -
155A ILE* 3.3 37.5 - - - +
156A MET* 3.3 27.9 + - - +
161A LEU* 3.8 3.8 - - - +
162A SER 2.9 18.6 + - - -
163A LEU 3.8 2.2 - - - -
165A HIS* 1.3 73.6 - - - +
167A TYR* 1.3 65.8 + - - +
169A LEU* 3.3 5.1 + - - +
170A LEU* 3.1 23.7 + - - +
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Residues in contact with TYR 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A ILE* 4.0 27.4 - - + +
163A LEU* 2.9 26.2 + - + +
164A ARG* 3.8 4.3 - - + +
166A SER* 1.3 75.1 - - - +
168A ASP* 1.3 66.5 + - - +
170A LEU* 3.3 1.7 + - - +
171A LYS* 2.8 75.9 + - + +
177A ILE* 4.1 19.0 + - + -
178A ASN* 5.6 1.4 - - - +
179A PRO* 4.4 15.7 - - + +
184A ILE* 4.7 13.9 - - + -
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Residues in contact with ASP 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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164A ARG* 2.9 36.9 + - - +
165A HIS* 3.3 11.2 + - - +
167A TYR* 1.3 90.2 - - - +
169A LEU* 1.3 64.0 + - - +
171A LYS* 3.7 5.9 - - - +
172A SER* 3.0 30.0 + - - -
173B ARG* 3.9 20.2 + - - +
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Residues in contact with LEU 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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63A VAL 5.3 2.0 - - - +
64A LEU* 5.4 4.9 - - + -
155A ILE* 4.8 10.5 - - + -
161A LEU* 4.0 16.2 - - + -
165A HIS 2.8 18.9 + - - +
166A SER* 3.7 4.7 - - - +
167A TYR 3.3 0.2 - - - -
168A ASP* 1.3 78.0 - - - +
170A LEU* 1.3 62.7 + - - +
172A SER* 3.5 9.1 + - - -
173A ARG* 3.6 12.5 + - - +
62B LEU* 4.0 22.0 - - + +
63B VAL 4.4 10.3 - - - +
64B LEU 4.2 0.9 - - - -
65B PRO* 3.6 42.8 - - + -
173B ARG* 3.6 32.9 - - - +
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Residues in contact with LEU 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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63A VAL* 3.6 43.3 - - + +
64A LEU* 5.4 2.5 - - + -
70A LEU* 4.8 3.6 - - + -
148A ALA* 3.6 42.4 - - + +
151A ILE* 4.0 18.8 - - + -
152A ILE* 3.8 12.6 - - + -
155A ILE* 4.9 5.5 - - + +
166A SER 3.1 14.3 + - - +
167A TYR 3.9 2.0 - - - +
169A LEU* 1.3 75.7 - - - +
171A LYS* 1.3 56.5 + - - +
173A ARG* 3.1 4.3 + - + -
174A ALA* 2.7 36.0 + - + -
177A ILE* 4.0 14.8 - - + -
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Residues in contact with LYS 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 TYR* 2.8 59.0 + - + +
168A ASP* 3.7 7.4 - - - +
170A LEU* 1.3 72.6 - - - +
172A SER* 1.3 62.4 + - - +
173A ARG 3.1 1.4 + - - -
174A ALA 3.9 3.4 - - - -
175A ASP* 2.8 71.4 + - - +
177A ILE* 3.8 25.9 - - + +
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Residues in contact with SER 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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168A ASP 3.0 12.3 + - - -
169A LEU 3.7 5.8 - - - -
171A LYS* 1.3 75.9 - - - +
173A ARG* 1.3 57.9 + - - +
175A ASP* 5.2 1.7 + - - +
172B SER* 3.2 28.7 - - - +
173B ARG* 2.6 47.5 + - - -
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Residues in contact with ARG 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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61A LEU* 3.7 31.8 - - + +
62A LEU* 2.7 30.7 + - - +
63A VAL* 3.6 35.9 - - + +
169A LEU 3.6 8.7 + - - +
170A LEU* 3.1 7.9 + - - +
172A SER* 1.3 82.2 - - - +
174A ALA* 1.3 56.0 + - - +
175A ASP 3.8 2.4 + - - -
165B HIS* 5.7 2.2 + - - -
168B ASP* 3.4 28.0 + - - +
169B LEU* 3.4 22.1 - - - +
172B SER* 2.8 40.1 + - - -
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Residues in contact with ALA 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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61A LEU* 3.8 20.0 - - + -
63A VAL* 4.3 5.4 - - + -
70A LEU* 4.2 13.7 - - + -
144A LEU* 5.3 1.8 - - + -
170A LEU* 2.7 16.0 + - + +
171A LYS 3.2 6.4 - - - +
173A ARG* 1.3 72.9 - - - +
175A ASP* 1.3 64.3 + - - +
176A LYS 3.1 4.3 + - - -
177A ILE* 3.3 36.3 + - + +
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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