Contacts of the helix formed by residues 170 - 185 (chain M) in PDB entry 6N1H
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 ASN 170 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125I ARG* 4.4 0.2 - - - +
187I TYR* 3.3 34.5 + - - +
190I GLU* 5.1 5.1 - - - +
191I ASP* 3.1 40.1 + - + +
169M TRP* 1.3 73.9 - - - +
171M TRP* 1.3 65.1 + - - +
172M THR* 3.7 17.7 + - - +
173M CYS* 3.2 19.5 + - - +
174M LYS* 3.3 31.3 + - - +
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Residues in contact with TRP 171 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191I ASP* 4.5 2.3 + - - +
112M LEU* 3.6 35.0 - - + +
113M HIS* 3.2 45.1 - + + -
170M ASN* 1.3 79.3 - - - +
172M THR* 1.3 59.3 + - - +
173M CYS 3.1 1.5 + - - -
174M LYS* 4.4 16.7 - - - +
175M ASP* 2.9 34.2 + - - +
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Residues in contact with THR 172 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170M ASN* 3.3 14.8 + - - -
171M TRP* 1.3 77.5 - - - +
173M CYS* 1.3 58.3 + - - +
175M ASP* 3.1 16.8 - - - +
176M LEU* 4.4 9.4 - - - +
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Residues in contact with CYS 173 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187I TYR* 4.4 10.3 - - + -
136M LEU* 4.6 6.1 - - - +
140M VAL* 3.9 21.7 - - + +
169M TRP* 3.6 22.5 - - - -
170M ASN* 3.2 34.3 - - - +
171M TRP 3.1 0.2 - - - -
172M THR* 1.3 82.4 - - - +
174M LYS* 1.3 67.5 + - - +
175M ASP 3.2 1.1 - - - -
176M LEU* 3.3 24.7 + - + +
177M LEU* 3.4 8.1 + - - +
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Residues in contact with LYS 174 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112M LEU 3.2 23.6 + - - +
115M ILE* 3.5 18.5 - - + +
116M ASP* 3.0 33.6 + - - +
166M THR* 4.5 9.6 + - - +
169M TRP* 3.7 39.8 + - + -
170M ASN 3.3 27.0 + - - +
171M TRP* 3.8 18.6 + - - +
173M CYS* 1.3 77.9 - - - +
175M ASP* 1.3 57.1 + - - +
177M LEU* 3.3 5.9 + - - +
178M LEU 3.3 16.8 + - - -
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Residues in contact with ASP 175 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112M LEU* 3.1 33.4 - - + +
171M TRP* 2.9 29.9 + - - +
172M THR* 3.1 18.1 - - - +
174M LYS* 1.3 73.7 - - - +
176M LEU* 1.3 67.3 + - - +
177M LEU 3.2 0.7 - - - -
178M LEU* 3.3 12.9 - - + +
179M GLN* 3.1 35.8 + - - +
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Residues in contact with LEU 176 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135M ALA* 4.4 7.2 - - + +
136M LEU* 3.8 23.6 - - + -
139M LYS* 3.8 45.3 - - + +
140M VAL* 5.3 1.6 - - + -
172M THR 4.4 9.6 - - - +
173M CYS* 3.3 19.5 + - + +
174M LYS 3.2 0.6 - - - -
175M ASP* 1.3 82.4 + - - +
177M LEU* 1.3 56.8 + - - +
178M LEU 3.3 0.2 - - - -
179M GLN* 3.5 20.3 + - - +
180M ALA* 3.2 21.3 + - - +
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Residues in contact with LEU 177 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115M ILE* 3.7 27.1 - - + -
122M LEU* 5.6 1.3 - - + -
132M LEU* 4.2 7.6 - - + -
136M LEU* 3.8 33.0 - - + -
159M MET* 5.5 5.2 - - + -
162M LEU* 3.7 25.6 - - + -
163M PHE* 5.9 1.1 - - + -
169M TRP* 3.6 33.4 - - + -
173M CYS 3.4 5.3 + - - +
174M LYS 3.3 9.7 + - - +
175M ASP 3.2 0.2 - - - -
176M LEU* 1.3 75.7 - - - +
178M LEU* 1.3 59.8 + - - +
179M GLN 3.3 0.4 - - - -
180M ALA* 3.3 1.8 + - - +
181M LEU* 3.0 38.5 + - + +
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Residues in contact with LEU 178 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112M LEU* 3.7 34.1 - - + -
114M PHE* 3.6 35.9 - - + -
115M ILE* 4.4 8.5 - - + +
174M LYS 3.3 7.0 + - - +
175M ASP* 3.3 19.1 - - + +
176M LEU 3.3 0.4 - - - -
177M LEU* 1.3 77.7 - - - +
179M GLN* 1.3 57.9 + - + +
181M LEU* 3.4 3.0 + - + +
182M ARG* 3.0 70.7 + - - +
189M VAL* 4.2 7.4 - - + -
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Residues in contact with GLN 179 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175M ASP* 3.1 21.6 + - - +
176M LEU* 3.6 20.6 - - - +
177M LEU 3.3 0.4 - - - -
178M LEU* 1.3 77.1 - - + +
180M ALA* 1.3 58.2 + - - +
182M ARG* 3.3 12.7 + - - +
183M GLU* 3.0 40.0 + - + +
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Residues in contact with ALA 180 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131M TRP* 3.3 10.6 - - + -
132M LEU* 3.7 21.3 - - + +
135M ALA* 3.9 27.1 - - + -
136M LEU* 3.9 7.0 - - + -
176M LEU* 3.2 14.4 + - + +
177M LEU 3.8 4.3 - - - +
178M LEU 3.2 0.4 - - - -
179M GLN* 1.3 74.1 - - - +
181M LEU* 1.3 61.3 + - - +
183M GLU* 4.6 4.3 - - - -
184M SER* 3.1 28.6 + - - -
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Residues in contact with LEU 181 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114M PHE* 5.0 3.4 - - + -
115M ILE* 4.1 13.2 - - + -
122M LEU* 4.0 24.7 - - + -
126M VAL* 4.2 23.6 - - + -
132M LEU* 3.8 28.5 - - + -
159M MET* 5.6 2.7 - - + -
177M LEU* 3.0 36.2 + - + +
178M LEU* 3.8 5.4 - - - +
179M GLN 3.3 0.2 - - - -
180M ALA* 1.3 77.7 - - - +
182M ARG* 1.3 57.4 + - - +
184M SER* 4.5 2.0 - - - +
185M GLN* 2.8 42.3 + - + +
186M SER 3.5 1.2 + - - -
188M LEU* 5.4 1.1 - - + -
189M VAL* 3.8 20.8 - - + +
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Residues in contact with ARG 182 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114M PHE* 6.0 0.6 - - - -
178M LEU* 3.0 56.8 + - - +
179M GLN* 3.3 11.3 + - - +
181M LEU* 1.3 74.8 - - - +
183M GLU* 1.3 61.6 + - + +
186M SER* 2.3 37.5 + - - +
189M VAL* 3.7 21.8 - - + +
193M GLU* 3.3 23.2 + - - -
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Residues in contact with GLU 183 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131M TRP* 3.4 28.8 - - + -
179M GLN* 3.0 25.9 + - + +
180M ALA* 4.1 2.7 - - - +
182M ARG* 1.3 80.7 - - + +
184M SER* 1.3 62.4 + - - +
186M SER* 4.6 1.9 + - - -
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Residues in contact with SER 184 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128M ASN* 2.5 38.6 + - - +
131M TRP* 3.5 19.5 - - - -
132M LEU* 3.7 9.1 - - - +
180M ALA 3.1 19.4 + - - -
181M LEU* 4.1 1.1 - - - -
183M GLU* 1.3 81.1 - - - +
185M GLN* 1.3 75.6 + - - +
187M TYR* 5.3 1.0 - - - -
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Residues in contact with GLN 185 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125M ARG 4.8 3.6 + - - -
126M VAL* 5.5 2.5 - - + -
127M THR* 4.4 15.4 + - - +
128M ASN* 3.3 19.1 + - - +
132M LEU* 5.5 0.6 - - + +
181M LEU* 2.8 30.3 + - + +
184M SER* 1.3 97.4 + - - +
186M SER* 1.3 64.1 + - - +
187M TYR* 3.1 56.9 + - + -
188M LEU* 3.8 41.4 - - + +
189M VAL 4.9 1.3 - - - +
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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