Contacts of the helix formed by residues 181 - 190 (chain A) in PDB entry 7NG0
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 THR 181 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A PRO* 6.2 0.7 - - - -
175A LEU* 3.7 7.1 - - - +
180A ILE* 1.3 76.2 - - - +
182A GLU* 1.3 64.9 + - - +
183A ARG* 3.2 5.3 + - - +
184A HIS* 3.0 50.1 + - + +
185A ALA* 3.4 8.7 + - - +
211A VAL* 3.6 12.6 - - + +
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Residues in contact with GLU 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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126A PRO* 4.2 25.8 - - + +
161A LYS* 3.2 31.8 + - - +
164A LEU* 4.2 15.7 - - + +
175A LEU* 4.3 8.7 - - - +
181A THR* 1.3 75.0 - - - +
183A ARG* 1.3 62.8 + - + +
185A ALA* 3.3 5.3 + - - +
186A ARG* 2.8 66.6 + - - +
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Residues in contact with ARG 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A THR* 3.2 3.9 + - - +
182A GLU* 1.3 83.7 - - + +
184A HIS* 1.3 66.5 + - - +
186A ARG* 3.3 20.3 + - - +
187A ALA* 3.4 11.8 + - - +
211A VAL* 3.6 37.5 - - + +
215A GLU* 4.4 4.3 - - - +
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Residues in contact with HIS 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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179A ALA 5.6 1.1 - - - -
180A ILE* 4.0 15.3 - - + -
181A THR* 3.0 53.5 + - + +
183A ARG* 1.3 77.4 - - - +
185A ALA* 1.3 62.6 + - - +
187A ALA* 3.5 9.7 + - - +
188A LEU* 3.4 19.0 + - - +
204A ILE* 3.6 19.5 - - + +
209A LEU 3.0 17.6 + - - -
210A ASN* 2.9 38.1 + - - -
211A VAL* 3.9 7.3 - - + +
214A THR* 3.1 22.7 - - + +
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Residues in contact with ALA 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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164A LEU* 4.2 2.5 - - + -
167A LEU* 3.6 23.3 - - + +
171A VAL* 4.3 1.1 - - + -
175A LEU* 4.2 13.9 - - + -
180A ILE* 4.0 15.9 - - + +
181A THR 3.4 7.5 + - - +
182A GLU 3.3 8.7 + - - +
183A ARG 3.2 0.2 - - - -
184A HIS* 1.3 79.5 - - - +
186A ARG* 1.3 66.1 + - - +
188A LEU* 2.9 27.9 + - - +
189A ILE* 3.3 10.6 + - - +
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Residues in contact with ARG 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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157A THR* 6.1 0.4 - - - +
160A ASN* 3.3 66.7 + - - +
161A LYS* 4.0 6.3 - - - +
164A LEU* 4.5 4.7 - - - +
182A GLU* 2.8 58.3 + - - +
183A ARG* 3.3 14.0 + - - +
185A ALA* 1.3 76.2 - - - +
187A ALA* 1.3 64.1 - - - +
189A ILE* 3.1 34.8 + - + +
190A ALA* 4.0 2.3 + - - +
215A GLU* 6.1 0.2 - - - +
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Residues in contact with ALA 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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183A ARG 3.4 4.9 + - - +
184A HIS 3.6 10.1 - - - +
185A ALA 3.1 0.2 - - - -
186A ARG* 1.3 80.2 - - - +
188A LEU* 1.3 63.3 + - - +
190A ALA* 3.1 23.2 + - - +
214A THR* 4.4 4.0 - - + -
215A GLU* 3.8 30.7 - - + +
218A VAL* 3.5 29.1 - - + +
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Residues in contact with LEU 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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167A LEU* 4.1 10.1 - - + -
171A VAL* 4.5 19.5 - - + -
180A ILE* 4.9 1.6 - - + -
184A HIS 3.4 16.4 - - - +
185A ALA* 2.9 17.8 + - - +
187A ALA* 1.3 73.5 - - - +
189A ILE* 1.3 56.5 + - - +
190A ALA 3.1 0.4 + - - -
191A LEU* 3.3 18.9 + - + -
197A GLN* 2.8 51.0 + - + +
200A LEU* 3.9 37.2 - - + -
201A LEU* 4.8 6.3 - - + -
204A ILE* 4.0 19.1 - - + -
214A THR* 4.4 0.9 - - + -
218A VAL* 4.1 6.1 - - + -
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Residues in contact with ILE 189 (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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160A ASN 5.1 0.2 - - - +
163A ARG* 3.9 36.8 - - + +
164A LEU* 3.9 15.7 - - + -
166A LYS* 5.5 6.5 - - + -
167A LEU* 3.8 18.6 - - + -
185A ALA 3.4 9.4 - - - +
186A ARG* 3.2 33.9 - - + +
187A ALA 3.1 0.2 - - - -
188A LEU* 1.3 76.8 - - - +
190A ALA* 1.3 59.6 + - - +
191A LEU 3.5 0.3 + - - -
192A LYS* 3.6 30.6 + - - +
197A GLN* 4.1 3.9 + - - +
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Residues in contact with ALA 190 (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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186A ARG 4.0 1.9 + - - +
187A ALA* 3.1 14.6 + - - +
189A ILE* 1.3 77.3 - - - +
191A LEU* 1.3 65.6 + - - +
192A LYS* 3.2 15.1 + - - +
218A VAL* 4.4 3.8 - - + -
222A LEU* 3.9 26.9 - - + +
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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