Contacts of the helix formed by residues 181 - 192 (chain A) in PDB entry 6MOL
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 HIS 181 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A ALA 3.9 9.2 - - - -
145A ARG 4.2 0.8 + - - -
146A ALA 3.6 11.0 + - - -
147A GLY* 3.5 36.7 + - - -
176A ALA 3.4 7.2 + - - +
179A ALA* 3.5 29.2 - - + +
180A GLY* 1.3 79.4 + - - +
182A LEU* 1.3 64.0 + - - +
183A GLU* 3.2 7.6 - - + +
184A ILE* 3.2 26.7 - - + +
185A VAL* 3.2 17.3 - - - +
217A ILE* 3.7 2.8 - - - +
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Residues in contact with LEU 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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180A GLY 3.9 2.8 + - - -
181A HIS* 1.3 71.7 - - - +
183A GLU* 1.3 85.8 + - + +
185A VAL* 3.6 9.8 - - + +
186A GLU* 3.1 52.0 + - + +
216A GLU* 3.6 37.0 - - + +
217A ILE* 3.8 21.8 - - + +
220A VAL* 5.5 4.5 - - + -
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Residues in contact with GLU 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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149A LEU* 3.5 29.3 - - + +
181A HIS* 3.2 6.5 - - + +
182A LEU* 1.3 102.2 + - + +
184A ILE* 1.3 58.4 + - + +
186A GLU* 4.1 6.6 + - - +
187A VAL* 3.2 26.9 + - - +
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Residues in contact with ILE 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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143A ALA 4.7 0.4 - - - +
144A ALA* 3.8 29.8 - - + +
147A GLY* 4.3 6.7 - - - -
148A HIS 4.2 2.7 - - - +
149A LEU* 3.7 35.7 - - + +
152A VAL* 4.0 20.9 - - + -
176A ALA* 3.7 22.2 - - + -
181A HIS* 3.2 33.6 - - + +
183A GLU* 1.3 77.0 - - + +
185A VAL* 1.3 60.4 + - - +
186A GLU 3.3 0.7 - - - -
187A VAL* 3.7 6.2 - - - +
188A LEU* 2.8 36.2 + - + +
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Residues in contact with VAL 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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173A LEU* 3.8 17.7 - - + +
176A ALA* 3.6 25.4 - - + -
177A ALA* 4.2 2.0 - - + +
181A HIS 3.2 18.0 + - - +
182A LEU* 3.2 11.5 + - - +
184A ILE* 1.3 76.0 - - - +
186A GLU* 1.3 58.4 + - + +
188A LEU* 3.3 3.0 + - - +
189A LEU* 2.9 47.5 + - + +
217A ILE* 4.1 24.5 - - + -
220A VAL* 4.3 9.6 - - + -
221A LEU* 4.1 11.2 - - + -
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Residues in contact with GLU 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 LEU* 3.1 36.0 + - - +
183A GLU* 4.4 6.9 - - - +
185A VAL* 1.3 77.0 - - + +
187A VAL* 1.3 54.2 + - + +
189A LEU* 3.4 7.0 + - - +
190A LYS* 2.7 35.9 + - - +
220A VAL* 3.8 33.5 - - + +
224A TYR* 4.3 9.4 + - + +
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Residues in contact with VAL 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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149A LEU* 4.1 13.0 - - + -
152A VAL* 4.3 9.4 - - + -
153A GLU* 4.3 21.8 - - + +
156A LEU* 3.8 21.1 - - + -
183A GLU 3.2 20.4 + - - +
184A ILE* 3.4 7.1 + - - +
185A VAL 3.3 0.6 - - - -
186A GLU* 1.3 77.1 - - + +
188A LEU* 1.3 61.3 + - - +
190A LYS* 3.1 5.9 + - - +
191A TYR* 2.9 42.3 + - + -
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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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140A LEU* 3.8 30.7 - - + -
144A ALA* 4.9 5.4 - - + -
152A VAL* 4.6 7.6 - - + -
156A LEU* 4.2 12.1 - - + -
162A VAL* 3.5 20.8 - - + +
172A PRO* 3.7 35.4 - - + +
173A LEU* 4.0 18.4 - - + +
176A ALA* 4.3 10.1 - - + -
184A ILE* 2.8 27.0 + - + +
185A VAL 3.7 3.8 - - - +
187A VAL* 1.3 72.8 - - - +
189A LEU* 1.3 57.8 + - - +
191A TYR 3.4 0.5 + - - -
192A GLY 3.0 21.1 + - - -
193A ALA* 3.2 15.2 + - + +
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Residues in contact with LEU 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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173A LEU* 3.9 24.2 - - + -
185A VAL* 2.9 37.9 + - + +
186A GLU* 3.8 1.8 - - - +
188A LEU* 1.3 73.3 - - - +
190A LYS* 1.3 65.8 + - - +
192A GLY* 3.3 11.3 + - - -
193A ALA* 3.8 22.1 + - + +
195A VAL* 4.1 14.4 - - + -
220A VAL* 3.9 9.9 - - + +
221A LEU* 4.2 9.4 - - + -
224A TYR* 3.5 58.2 - - + -
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Residues in contact with LYS 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 GLU 2.7 22.3 + - - +
187A VAL* 3.1 9.8 + - - +
189A LEU* 1.3 74.6 - - - +
191A TYR* 1.3 65.7 - - + +
192A GLY* 3.4 0.5 + - - -
224A TYR* 4.4 9.1 + - - +
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Residues in contact with TYR 191 (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 GLU* 4.2 10.4 + - + +
156A LEU* 3.5 53.4 - - + -
157A LYS* 4.0 17.2 + - - +
162A VAL* 4.1 19.6 - - + +
187A VAL* 2.9 33.9 + - + +
188A LEU 4.0 4.0 - - - +
190A LYS* 1.3 79.7 - - + +
192A GLY* 1.3 57.9 + - - +
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Residues in contact with GLY 192 (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 VAL* 3.4 19.2 - - - +
163A ASN* 3.8 11.6 + - - -
188A LEU 3.0 7.1 + - - -
189A LEU 3.3 6.4 + - - -
190A LYS 3.2 4.4 - - - -
191A TYR* 1.3 79.3 - - - +
193A ALA* 1.3 59.6 + - - -
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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