Contacts of the helix formed by residues 162 - 175 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158P ALA 3.1 11.4 + - - -
160P LEU 3.2 0.4 - - - -
161P GLU* 1.3 80.7 - - - +
163P THR* 1.3 65.9 + - - +
164P CYS 3.4 1.3 - - - -
165P VAL* 3.5 2.7 + - - +
166P GLU* 3.2 36.7 + - - +
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Residues in contact with THR 163 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14 TYR* 3.6 36.8 - - + +
44 ASP* 4.2 6.2 + - - +
158P ALA 3.7 3.8 + - - -
159P TYR* 2.8 47.1 + - + -
162P GLY* 1.3 72.7 - - - +
164P CYS* 1.3 61.7 + - - +
166P GLU* 3.6 6.4 + - - +
167P TRP* 3.2 26.6 + - + -
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Residues in contact with CYS 164 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14 TYR 5.3 0.7 - - - +
5P MET* 3.5 28.0 - - + +
101P CYS* 2.0 53.2 - - + -
159P TYR* 2.9 20.4 + - + +
160P LEU* 4.0 9.0 - - - +
163P THR* 1.3 78.8 - - - +
165P VAL* 1.3 54.6 + - - +
167P TRP* 3.0 3.2 + - - +
168P LEU* 2.7 39.2 + - - -
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Residues in contact with VAL 165 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101P CYS* 5.0 3.8 - - + -
103P VAL* 3.9 22.7 - - + -
107P TRP 3.7 6.7 - - - +
109P PHE* 4.0 22.7 - - + +
160P LEU 3.5 19.5 - - - +
161P GLU 3.7 17.5 - - - +
162P GLY 3.5 2.8 + - - +
163P THR 3.4 0.6 - - - -
164P CYS* 1.3 78.0 - - + +
166P GLU* 1.3 62.4 + - + +
168P LEU* 4.0 4.3 - - - +
169P ARG* 3.1 58.9 + - - +
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Residues in contact with GLU 166 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162P GLY* 3.2 22.9 + - - +
163P THR* 3.9 7.9 - - - +
164P CYS 3.2 0.6 - - - -
165P VAL* 1.3 78.3 - - + +
167P TRP* 1.3 67.8 + - + +
169P ARG* 3.6 20.2 + - - +
170P ARG* 3.2 21.9 + - - +
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Residues in contact with TRP 167 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14 TYR* 3.1 51.5 - + - +
5P MET* 4.9 0.9 - - + -
55P GLU* 4.2 6.1 - - - -
59P TYR* 3.5 37.2 - + - -
163P THR* 3.2 26.1 + - + +
164P CYS* 3.0 4.1 + - - +
166P GLU* 1.3 85.1 + - + +
168P LEU* 1.3 61.4 + - - +
170P ARG* 3.3 32.3 + - - +
171P TYR* 2.9 67.4 + + + -
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Residues in contact with LEU 168 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3P HIS* 4.1 3.4 - - + +
4P SER* 4.1 26.5 - - - +
5P MET* 4.2 12.7 - - + +
28P VAL* 3.7 32.3 - - + -
101P CYS 4.8 2.0 - - - +
103P VAL* 3.5 36.6 - - + -
164P CYS* 2.7 33.3 + - - +
165P VAL* 4.0 3.8 - - - +
167P TRP* 1.3 72.9 - - - +
169P ARG* 1.3 58.2 + - + +
171P TYR* 3.1 7.7 + - + +
172P LEU* 2.8 46.9 + - + +
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Residues in contact with ARG 169 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103P VAL* 5.9 2.5 - - + -
107P TRP* 2.3 74.4 + - + +
108P ARG* 3.8 11.1 - - - +
165P VAL* 3.1 38.7 + - - +
166P GLU* 3.9 21.6 - - - +
168P LEU* 1.3 76.9 - - + +
170P ARG* 1.3 64.6 + - - +
172P LEU* 3.1 12.6 + - + +
173P GLU* 3.1 32.3 + - - +
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Residues in contact with ARG 170 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55P GLU* 2.6 36.6 + - - -
166P GLU 3.2 13.5 + - - +
167P TRP* 3.5 39.4 - - - +
168P LEU 3.3 0.2 - - - -
169P ARG* 1.3 78.5 - - - +
171P TYR* 1.3 59.5 + - + +
173P GLU* 3.5 6.1 + - - +
174P ASN* 3.0 50.0 + - - +
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Residues in contact with TYR 171 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14 TYR* 4.3 6.7 - - - +
5P MET* 3.6 26.7 - - - -
7P TYR* 5.1 0.2 - - - -
28P VAL* 4.1 15.9 - - + -
33P PHE* 3.5 20.0 - + - -
51P TRP* 3.6 28.1 - + + -
52P ILE* 3.6 15.9 - - + -
55P GLU* 5.0 4.3 - - - -
59P TYR* 2.6 31.5 + + - -
167P TRP* 2.9 50.5 + + + -
168P LEU* 3.1 10.5 + - + +
170P ARG* 1.3 77.7 - - + +
172P LEU* 1.3 58.9 + - - +
174P ASN* 3.2 8.9 + - - +
175P GLY* 2.9 27.5 + - - -
179P LEU* 4.0 5.3 - - + +
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Residues in contact with LEU 172 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3P HIS* 3.5 32.8 - - + +
28P VAL* 4.6 2.5 - - + -
103P VAL* 5.5 2.0 - - + -
107P TRP* 3.6 50.0 - - + +
168P LEU* 2.8 43.6 + - + +
169P ARG* 3.1 13.0 + - + +
171P TYR* 1.3 76.1 - - - +
173P GLU* 1.3 57.1 + - - +
175P GLY 3.3 2.6 - - - +
176P LYS* 3.0 28.6 + - - -
179P LEU* 3.5 28.9 - - + +
180P GLN* 3.8 8.3 - - + +
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Residues in contact with GLU 173 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107P TRP* 4.2 23.2 - - + -
169P ARG* 3.1 20.3 + - - +
170P ARG* 3.9 6.1 - - - +
172P LEU* 1.3 77.0 - - - +
174P ASN* 1.3 65.7 + - - +
175P GLY 3.4 0.3 + - - -
176P LYS* 3.6 16.2 + - - +
180P GLN* 5.1 1.8 - - - -
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Residues in contact with ASN 174 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51P TRP* 3.6 22.1 + - + +
52P ILE* 5.9 0.4 - - - +
54P GLN* 3.5 33.2 + - - +
55P GLU* 3.8 22.0 + - - +
170P ARG* 3.0 40.1 + - - +
171P TYR* 3.2 11.0 + - - +
173P GLU* 1.3 80.5 - - - +
175P GLY* 1.3 57.0 + - - +
176P LYS 3.6 0.8 + - - -
177P GLU* 3.9 8.7 - - - +
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Residues in contact with GLY 175 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51P TRP* 3.8 24.0 - - - +
171P TYR 2.9 13.1 + - - -
172P LEU 3.3 4.9 - - - -
174P ASN* 1.3 77.0 - - - +
176P LYS* 1.3 64.9 + - - -
177P GLU* 3.2 7.2 - - - -
178P THR 3.7 1.3 - - - -
179P LEU* 3.0 33.1 + - - +
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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