Contacts of the helix formed by residues 162 - 176 (chain A) in PDB entry 3J2I
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 GLN 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A GLY 3.8 8.8 - - - +
161A ASN* 1.3 74.6 - - - +
163A ASN* 1.3 67.6 + - - +
164A THR* 4.1 11.9 - - - +
165A GLN* 2.8 38.5 + - + +
166A VAL* 3.9 1.6 + - - +
215A LYS* 5.3 4.8 - - + +
216A ALA* 3.3 26.3 + - - +
217A GLU* 3.5 28.6 - - - +
218A PHE* 3.7 8.9 - - - -
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Residues in contact with ASN 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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162A GLN* 1.3 71.9 - - - +
164A THR* 1.3 77.2 + - - +
166A VAL* 2.9 17.8 + - - +
167A THR* 3.2 14.2 + - - +
200A THR 2.8 29.3 + - - +
201A ILE* 3.9 10.3 - - + +
213A HIS* 3.3 8.8 - - - -
214A GLU 3.1 23.0 + - - -
215A LYS* 3.6 1.7 - - - +
216A ALA* 2.8 38.2 + - + +
218A PHE* 3.6 25.5 - - + -
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Residues in contact with THR 164 (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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162A GLN* 3.1 8.3 - - - +
163A ASN* 1.3 83.1 + - - +
165A GLN* 1.3 55.7 + - - +
167A THR* 3.3 10.8 + - + -
168A GLU* 2.9 52.3 + - + +
213A HIS* 6.1 0.5 - - - -
215A LYS* 3.5 36.1 - - - +
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Residues in contact with GLN 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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156A LEU* 4.1 19.6 - - + +
161A ASN* 3.3 28.8 + - + +
162A GLN* 2.8 44.2 + - + +
164A THR* 1.3 78.7 - - - +
166A VAL* 1.3 60.8 + - + +
168A GLU* 3.5 11.3 + - - +
169A ALA* 3.0 28.6 + - - +
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Residues in contact with VAL 166 (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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153A ALA* 4.1 12.3 - - + -
156A LEU* 4.0 24.0 - - + +
157A VAL* 3.9 21.8 - - + -
162A GLN 4.2 1.6 - - - +
163A ASN 2.9 10.7 + - - +
165A GLN* 1.3 74.5 - - + +
167A THR* 1.3 66.4 + - - +
169A ALA* 3.2 2.8 + - - +
170A TRP* 2.9 58.4 + - + +
201A ILE* 3.8 14.1 - - + -
218A PHE* 4.0 17.0 - - + -
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Residues in contact with THR 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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163A ASN 3.2 10.0 + - - -
164A THR* 3.5 15.7 - - + -
166A VAL* 1.3 77.7 - - - +
168A GLU* 1.3 67.3 + - + +
170A TRP* 3.4 9.3 + - - +
171A ASN* 3.2 25.0 + - - +
201A ILE* 3.9 1.1 - - - +
202A ILE* 2.6 41.8 + - + +
204A ASN* 4.1 4.3 + - - +
205A PRO* 3.6 28.9 - - + -
210A LYS* 6.3 0.4 - - - -
213A HIS* 5.8 0.3 - - - -
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Residues in contact with GLU 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 THR* 2.9 39.8 + - + +
165A GLN* 3.9 10.3 - - - +
167A THR* 1.3 76.0 - - + +
169A ALA* 1.3 64.6 + - - +
171A ASN* 3.3 7.4 + - - +
172A LYS* 3.2 30.7 + - + +
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Residues in contact with ALA 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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152A ALA* 4.7 9.6 - - + -
156A LEU* 3.7 21.8 - - + -
165A GLN 3.0 18.7 + - - +
166A VAL 3.6 3.8 - - - +
168A GLU* 1.3 76.2 - - - +
170A TRP* 1.3 59.8 + - + +
172A LYS* 3.2 10.1 + - - +
173A VAL* 2.9 33.2 + - - +
354A LEU* 4.4 16.6 - - + -
357A LEU* 4.9 0.4 - - + -
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Residues in contact with TRP 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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149A CYS* 2.9 51.2 + - + +
152A ALA* 4.8 5.2 - - + -
153A ALA* 3.7 15.6 - - + +
166A VAL* 2.9 37.9 + - + +
167A THR* 3.7 9.2 - - - +
169A ALA* 1.3 78.8 - - + +
171A ASN* 1.3 59.1 + - - +
173A VAL* 4.7 0.2 - - - -
174A ALA* 2.9 33.1 + - - +
181A PRO* 4.0 10.0 - - + +
185A MET 5.6 0.2 - - - -
187A SER* 3.9 20.9 - - - -
201A ILE* 3.8 20.9 - - + -
202A ILE 4.5 2.5 - - - -
203A GLN* 3.6 40.4 - - + -
204A ASN 6.2 0.4 - - - +
226A VAL* 3.8 7.0 - - + -
227A ASP 4.1 6.7 - - - -
228A VAL* 3.7 19.5 - - + -
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Residues in contact with ASN 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 THR* 3.2 12.6 + - - +
168A GLU* 3.8 9.2 - - - +
169A ALA 3.3 0.2 - - - -
170A TRP* 1.3 80.2 - - - +
172A LYS* 1.3 57.3 + - + +
175A HIS* 2.9 62.0 + - + -
181A PRO* 3.4 21.2 - - - +
204A ASN* 3.2 38.3 + - - +
205A PRO* 5.6 1.0 - - - +
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Residues in contact with LYS 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 GLU* 3.2 17.4 + - + +
169A ALA* 3.2 8.8 + - - +
171A ASN* 1.3 75.4 - - + +
173A VAL* 1.3 62.3 + - - +
175A HIS* 3.7 5.4 + - - +
176A SER* 2.9 26.2 + - - -
351A ASP* 4.3 23.1 + - + +
353A GLU* 4.8 9.3 + - - -
354A LEU* 3.4 24.2 - - + +
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Residues in contact with VAL 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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145A ALA* 3.8 13.2 - - - +
148A LEU* 3.6 31.0 - - + +
149A CYS* 3.9 12.1 - - - +
152A ALA* 4.6 17.3 - - + -
169A ALA 2.9 23.3 + - - +
172A LYS* 1.3 76.2 - - - +
174A ALA* 1.3 65.1 + - - +
176A SER* 3.1 21.9 + - - -
177A PHE* 3.4 13.7 - - + -
349A VAL* 4.6 4.5 - - + -
354A LEU* 3.7 26.2 - - + -
358A LEU* 4.8 6.5 - - + -
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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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145A ALA* 4.2 11.0 - - - -
149A CYS* 4.2 4.7 - - - -
170A TRP 2.9 17.7 + - - +
171A ASN 4.1 0.4 - - - +
173A VAL* 1.3 77.2 - - - +
175A HIS* 1.3 64.3 + - - +
177A PHE* 3.0 10.2 + - - +
179A CYS* 2.9 36.9 + - - +
181A PRO* 3.7 23.1 - - + -
230A VAL* 4.1 13.9 - - + -
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Residues in contact with HIS 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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171A ASN* 2.9 53.4 + - + +
172A LYS* 4.0 5.0 - - - +
174A ALA* 1.3 77.8 - - + +
176A SER* 1.3 56.8 + - - +
177A PHE 3.0 0.4 - - - -
178A ASN* 2.9 26.7 + - - +
179A CYS 3.3 17.7 - - - +
180A THR* 4.7 11.3 + - - +
181A PRO* 4.7 4.0 - - - +
204A ASN* 5.5 0.8 + - - -
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Residues in contact with SER 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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172A LYS 2.9 19.3 + - - -
173A VAL* 3.1 14.7 + - - -
175A HIS* 1.3 78.2 - - - +
177A PHE* 1.3 63.2 - - - +
178A ASN 3.5 0.7 - - - -
347A MET* 3.4 23.1 - - - +
348A GLU 4.0 7.4 - - - +
349A VAL* 4.0 32.3 - - - +
350A GLN 4.6 2.9 + - - -
351A ASP* 5.5 1.9 + - - +
354A LEU* 4.8 1.6 - - - +
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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