Contacts of the helix formed by residues 176 - 188 (chain A) in PDB entry 2J7T
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 PHE 176 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A GLU* 3.9 20.0 + - + -
84A ILE* 3.8 27.1 - - + -
85A LEU* 4.0 18.8 - - + +
88A CYS* 4.6 2.5 - - - -
93A ILE* 3.9 24.9 - - + -
94A VAL* 4.5 2.2 - - + -
148A LEU* 3.8 31.2 - - + -
153A ILE* 4.4 3.6 - - + -
155A HIS* 3.6 27.1 - + + -
173A LEU* 3.8 22.4 - - + -
174A ALA* 4.2 2.2 - - - -
175A ASP* 1.3 78.1 - - - +
177A GLY* 1.3 57.8 + - - +
178A VAL 3.5 1.8 - - - -
179A SER* 3.9 21.8 - - - -
180A ALA* 2.8 31.5 + - - +
1324A 274 4.5 0.8 + - - -
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Residues in contact with GLY 177 (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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81A GLU* 3.6 18.7 + - - -
175A ASP* 3.2 16.1 + - - -
176A PHE* 1.3 73.2 - - - +
178A VAL* 1.3 60.6 + - - +
180A ALA* 3.2 2.5 + - - +
181A LYS* 2.9 39.3 + - - +
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Residues in contact with VAL 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PHE* 6.2 3.8 - - + -
155A HIS 4.4 0.2 - - - +
156A ARG* 3.8 28.7 - - + +
157A ASP* 3.6 33.4 - - + +
175A ASP* 4.6 3.4 + - - -
176A PHE* 3.5 0.4 - - - +
177A GLY* 1.3 73.0 - - - +
179A SER* 1.3 64.6 + - - +
181A LYS* 3.3 9.2 + - + +
182A ASN* 3.0 38.0 + - - +
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Residues in contact with SER 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ILE* 3.8 7.3 - - - +
153A ILE* 3.8 15.9 - - - +
154A ILE 2.6 28.1 + - - +
155A HIS 3.4 15.9 + - - -
156A ARG* 5.0 0.9 - - - -
176A PHE* 3.4 29.4 + - - +
178A VAL* 1.3 80.1 - - - +
180A ALA* 1.3 57.9 + - - +
182A ASN* 3.5 6.0 + - - +
183A LEU* 3.0 28.1 + - - +
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Residues in contact with ALA 180 (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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77A ASP* 3.7 8.9 - - - +
80A VAL* 3.7 7.2 - - - +
81A GLU* 3.6 39.3 - - + +
84A ILE* 3.6 11.4 - - + -
176A PHE 2.8 21.4 + - - +
177A GLY* 3.7 3.8 - - - +
179A SER* 1.3 71.4 - - - +
181A LYS* 1.3 62.3 + - + +
184A LYS* 2.9 30.8 + - - +
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Residues in contact with LYS 181 (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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47A PHE* 5.3 13.9 - - + -
77A ASP* 3.7 35.2 - - + +
177A GLY* 2.9 23.6 + - - +
178A VAL* 3.9 8.5 - - + +
180A ALA* 1.3 75.4 - - + +
182A ASN* 1.3 60.8 + - - +
184A LYS* 3.8 2.8 + - - +
185A THR* 3.0 25.8 + - - -
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Residues in contact with ASN 182 (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 ARG* 3.8 40.0 + - + +
178A VAL* 3.0 35.4 + - - +
179A SER* 3.6 6.3 - - - +
181A LYS* 1.3 78.3 - - - +
183A LEU* 1.3 60.6 + - - +
185A THR* 3.4 9.6 + - - -
186A LEU* 3.2 29.8 + - + +
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Residues in contact with LEU 183 (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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80A VAL* 3.9 11.0 - - + -
84A ILE* 3.8 28.5 - - + -
152A ARG 5.8 3.8 - - - +
153A ILE* 5.6 6.7 - - + -
179A SER 3.0 18.5 + - - +
180A ALA* 3.9 4.0 - - - +
182A ASN* 1.3 73.4 - - - +
184A LYS* 1.3 61.0 + - - +
186A LEU* 3.2 13.1 + - + +
187A GLN* 2.8 67.3 + - + +
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Residues in contact with LYS 184 (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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76A GLU* 5.0 5.2 - - + +
77A ASP* 4.0 17.9 - - - +
80A VAL* 4.1 22.8 - - + +
180A ALA 2.9 17.2 + - - +
181A LYS 3.9 5.6 - - - +
183A LEU* 1.3 75.3 - - - +
185A THR* 1.3 57.9 + - - +
187A GLN* 3.7 6.2 + - - +
188A LYS* 3.0 28.6 + - - +
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Residues in contact with THR 185 (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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181A LYS 3.0 14.9 + - - -
182A ASN* 3.4 12.1 + - - -
183A LEU 3.2 0.4 - - - -
184A LYS* 1.3 77.9 - - - +
186A LEU* 1.3 62.4 + - + +
188A LYS* 3.0 31.0 + - + +
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Residues in contact with LEU 186 (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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182A ASN* 3.2 18.2 + - + +
183A LEU* 3.2 15.5 + - + +
185A THR* 1.3 83.6 - - + +
187A GLN* 1.3 62.4 + - - +
188A LYS 3.4 4.9 + - - -
210A LYS* 3.7 43.3 - - + +
215A ASP* 5.9 0.4 - - - +
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Residues in contact with GLN 187 (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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80A VAL* 4.3 18.0 - - - +
183A LEU* 2.8 55.6 + - + +
184A LYS* 3.8 5.4 - - - +
186A LEU* 1.3 71.7 - - - +
188A LYS* 1.3 60.1 + - - +
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Residues in contact with LYS 188 (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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184A LYS 3.0 17.8 + - - +
185A THR* 3.0 19.5 + - + +
186A LEU 3.9 4.9 - - - -
187A GLN* 1.3 80.7 - - - +
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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