Contacts of the helix formed by residues 162 - 175 (chain M) in PDB entry 6NCA
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 GLY 162 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158M ALA 3.1 10.3 + - - -
160M LEU 3.3 0.4 - - - -
161M GLU* 1.3 80.4 - - - +
163M THR* 1.3 66.7 + - - +
164M CYS 3.4 1.3 - - - -
165M VAL* 3.5 1.4 + - - +
166M GLU* 3.1 39.3 + - - +
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Residues in contact with THR 163 (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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11 TYR* 3.4 38.8 - - + -
41 ASP* 4.8 5.9 + - - +
158M ALA 3.5 4.6 + - - -
159M TYR* 2.9 36.7 + - + -
162M GLY* 1.3 72.2 - - - +
164M CYS* 1.3 63.4 + - - +
166M GLU* 4.1 6.1 - - - +
167M TRP* 3.2 35.3 + - + +
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Residues in contact with CYS 164 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11 TYR* 6.2 0.9 - - - -
5M MET* 3.4 28.9 - - + -
101M CYS* 2.0 51.1 - - + -
159M TYR* 2.8 33.7 + - + +
160M LEU* 4.1 1.8 - - - +
163M THR* 1.3 73.1 - - - +
165M VAL* 1.3 56.6 + - - +
167M TRP* 3.0 4.5 + - - +
168M LEU* 2.6 39.0 + - - -
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Residues in contact with VAL 165 (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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101M CYS* 4.6 6.5 - - + -
103M VAL* 3.8 22.8 - - + +
107M TRP 3.9 0.7 - - - +
109M PHE* 3.6 31.9 - - + +
160M LEU 3.3 20.9 - - - +
161M GLU 3.8 13.2 - - - +
162M GLY 3.5 2.1 + - - +
163M THR 3.5 0.4 - - - -
164M CYS* 1.3 77.2 - - - +
166M GLU* 1.3 63.0 + - + +
168M LEU* 3.5 5.6 + - - +
169M ARG* 3.1 55.6 + - - +
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Residues in contact with GLU 166 (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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162M GLY* 3.1 25.6 + - - +
163M THR* 4.1 5.7 - - - +
165M VAL* 1.3 78.4 - - + +
167M TRP* 1.3 62.3 + - + +
169M ARG* 3.5 20.7 + - - +
170M ARG* 3.1 23.4 + - - +
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Residues in contact with TRP 167 (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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11 TYR* 3.9 50.2 - + + +
5M MET* 5.7 2.2 - - + -
55M GLU* 5.0 1.1 - - - -
59M TYR* 4.1 29.8 - + + -
163M THR* 3.2 29.0 + - + +
164M CYS* 3.0 5.1 + - - +
166M GLU* 1.3 81.0 - - + +
168M LEU* 1.3 61.5 + - - +
170M ARG* 3.2 48.6 + - - +
171M TYR* 2.9 59.7 + + + -
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Residues in contact with LEU 168 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3M HIS* 4.1 0.9 - - + -
4M SER* 3.9 25.6 - - - +
5M MET* 3.8 19.4 - - + +
28M VAL* 3.7 32.8 - - + -
101M CYS 4.7 2.7 - - - +
103M VAL* 3.8 35.7 - - + -
164M CYS* 2.6 30.7 + - - +
165M VAL* 3.9 4.7 - - - +
167M TRP* 1.3 72.2 - - - +
169M ARG* 1.3 57.5 + - + +
171M TYR* 3.1 8.0 + - + +
172M LEU* 2.9 43.3 + - + +
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Residues in contact with ARG 169 (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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103M VAL* 5.7 1.8 - - + -
107M TRP* 2.5 60.5 + - + +
108M ARG* 3.4 21.2 - - - +
109M PHE 4.4 0.4 - - - +
165M VAL* 3.1 41.1 + - + +
166M GLU* 3.6 28.5 - - - +
167M TRP 3.3 0.2 - - - -
168M LEU* 1.3 76.7 - - + +
170M ARG* 1.3 62.4 + - - +
172M LEU* 3.1 13.3 + - + +
173M GLU* 3.0 35.8 + - - +
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Residues in contact with ARG 170 (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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55M GLU* 2.8 39.0 + - - -
166M GLU 3.1 14.2 + - - +
167M TRP* 3.2 48.9 + - + +
169M ARG* 1.3 76.6 - - - +
171M TYR* 1.3 64.3 + - + +
173M GLU* 3.5 11.8 + - - +
174M ASN* 3.2 36.5 + - - +
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Residues in contact with TYR 171 (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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11 TYR 3.0 15.8 + - - -
5M MET* 3.7 28.0 - - - -
28M VAL* 4.1 16.6 - - + -
33M PHE* 3.6 18.6 - + - -
51M TRP* 3.6 26.9 - + + -
52M ILE* 3.6 22.4 - - + -
55M GLU* 4.7 8.1 - - - -
59M TYR* 2.5 33.3 + + - -
167M TRP* 2.9 44.1 + + + -
168M LEU* 3.1 10.3 + - + +
170M ARG* 1.3 78.4 - - + +
172M LEU* 1.3 62.7 + - - +
174M ASN* 3.4 3.2 + - + +
175M GLY* 3.0 19.8 + - - -
179M LEU* 4.3 3.0 - - - +
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Residues in contact with LEU 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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3M HIS* 4.0 27.1 - - + +
28M VAL* 4.5 2.0 - - + -
103M VAL* 5.0 2.5 - - + -
107M TRP* 3.4 54.1 - - + +
168M LEU* 2.9 44.3 + - + +
169M ARG* 3.1 15.0 + - + +
171M TYR* 1.3 77.1 - - - +
173M GLU* 1.3 61.0 + - - +
175M GLY 3.4 0.5 - - - -
176M LYS* 3.1 27.9 + - - +
179M LEU* 3.4 30.5 - - + +
180M GLN* 4.7 2.4 + - + -
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Residues in contact with GLU 173 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107M TRP* 4.4 16.0 - - + -
169M ARG* 3.0 25.0 + - - +
170M ARG* 3.9 11.8 - - - +
172M LEU* 1.3 77.2 - - - +
174M ASN* 1.3 68.3 + - - +
175M GLY 3.5 0.3 + - - -
176M LYS* 3.7 13.0 + - - +
180M GLN* 6.2 0.2 - - - +
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Residues in contact with ASN 174 (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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51M TRP* 3.9 23.3 + - + +
54M GLN* 3.5 38.9 + - - +
55M GLU* 3.7 21.4 + - - +
170M ARG* 3.2 28.8 + - - +
171M TYR* 4.0 5.8 - - + +
173M GLU* 1.3 83.7 - - - +
175M GLY* 1.3 58.0 + - - +
176M LYS 3.6 1.1 + - - -
177M GLU* 4.0 5.4 - - - +
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Residues in contact with GLY 175 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51M TRP* 3.6 26.9 - - - +
171M TYR 3.0 12.3 + - - -
172M LEU 3.4 4.0 - - - -
174M ASN* 1.3 78.2 - - - +
176M LYS* 1.3 62.5 + - - -
177M GLU* 3.2 8.5 - - - -
178M THR* 3.3 1.1 + - - -
179M LEU* 3.1 31.0 + - - +
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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