Contacts of the helix formed by residues 162 - 175 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158N ALA 3.1 10.5 + - - -
161N GLU* 1.3 80.9 - - - +
163N THR* 1.3 67.0 + - - +
164N CYS 3.4 1.1 - - - -
165N VAL* 3.9 1.8 - - - +
166N GLU* 3.0 38.7 + - - +
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Residues in contact with THR 163 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12 TYR* 3.6 32.8 - - + -
42 ASP* 5.4 5.2 + - - +
158N ALA 3.5 4.1 + - - -
159N TYR* 2.9 40.1 + - + -
162N GLY* 1.3 72.8 - - - +
164N CYS* 1.3 64.6 + - - +
166N GLU* 3.9 6.7 - - - +
167N TRP* 3.1 28.5 + - + +
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Residues in contact with CYS 164 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5N MET* 3.4 26.5 - - + -
101N CYS* 2.0 51.8 - - + -
159N TYR* 2.7 32.8 + - + +
160N LEU* 3.8 5.4 - - - +
163N THR* 1.3 72.6 - - - +
165N VAL* 1.3 53.7 + - - +
167N TRP* 3.0 2.8 + - - +
168N LEU* 2.5 44.9 + - - +
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Residues in contact with VAL 165 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101N CYS* 4.9 4.9 - - + -
103N VAL* 4.1 17.5 - - + -
107N TRP 4.0 5.8 - - - +
109N PHE* 4.0 25.4 - - + +
160N LEU 3.3 19.1 - - - +
161N GLU 3.5 19.1 - - - +
162N GLY 3.4 3.2 + - - +
163N THR 3.4 0.2 - - - -
164N CYS* 1.3 75.4 - - - +
166N GLU* 1.3 62.8 + - + +
168N LEU* 3.9 5.9 - - - +
169N ARG* 3.0 65.7 + - + +
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Residues in contact with GLU 166 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162N GLY* 3.0 26.6 + - - +
163N THR* 3.9 7.8 - - - +
165N VAL* 1.3 78.8 - - + +
167N TRP* 1.3 64.2 + - + +
169N ARG* 3.5 16.2 + - - +
170N ARG* 3.1 23.9 + - - +
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Residues in contact with TRP 167 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12 TYR* 3.6 52.1 - + + -
5N MET* 4.8 4.3 - - + -
55N GLU* 5.0 0.7 - - - -
59N TYR* 3.8 32.8 - + - -
163N THR* 3.1 27.5 + - + +
164N CYS* 3.0 4.7 + - - +
166N GLU* 1.3 83.2 + - + +
168N LEU* 1.3 61.9 + - - +
170N ARG* 3.2 41.8 + - - +
171N TYR* 2.8 60.8 + + + -
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Residues in contact with LEU 168 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3N HIS 4.2 0.2 - - - +
4N SER* 3.9 11.9 - - - +
5N MET* 3.7 34.9 - - + +
28N VAL* 3.8 26.2 - - + -
101N CYS* 4.6 3.4 - - + +
103N VAL* 3.6 38.4 - - + -
164N CYS* 2.5 35.5 + - - +
165N VAL* 3.9 4.0 - - - +
167N TRP* 1.3 71.8 - - - +
169N ARG* 1.3 62.0 + - + +
171N TYR* 3.2 5.8 + - + +
172N LEU* 3.0 39.7 + - + +
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Residues in contact with ARG 169 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103N VAL* 6.1 1.3 - - + -
106N ASP 4.8 0.4 + - - -
107N TRP* 2.0 68.7 + - + +
108N ARG* 3.7 13.5 - - - +
109N PHE 5.6 0.2 - - - +
165N VAL* 3.0 45.8 + - + +
166N GLU* 3.7 15.6 - - - +
168N LEU* 1.3 78.1 - - + +
170N ARG* 1.3 62.3 + - - +
172N LEU* 3.2 12.9 + - + +
173N GLU* 3.0 30.2 + - + +
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Residues in contact with ARG 170 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54N GLN 5.6 1.0 + - - -
55N GLU* 2.1 46.5 + - - +
166N GLU 3.1 13.8 + - - +
167N TRP* 3.2 44.2 + - + +
169N ARG* 1.3 76.3 - - - +
171N TYR* 1.3 59.6 + - - +
173N GLU* 3.3 7.3 + - + +
174N ASN* 2.9 51.7 + - - +
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Residues in contact with TYR 171 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12 TYR* 3.0 16.5 + - - -
5N MET* 3.4 35.7 - - + -
28N VAL* 4.0 14.4 - - + -
33N PHE* 3.4 21.5 - + - -
51N TRP* 3.5 31.0 - + + -
52N ILE* 3.6 15.3 - - + -
55N GLU* 4.5 3.6 - - - -
59N TYR* 2.5 32.3 + - - -
167N TRP* 2.8 42.7 + + + +
168N LEU* 3.2 5.8 + - - +
170N ARG* 1.3 78.3 - - + +
172N LEU* 1.3 63.1 + - - +
174N ASN* 3.3 4.9 + - - -
175N GLY* 2.9 21.7 + - - -
179N LEU* 4.0 4.0 - - - +
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Residues in contact with LEU 172 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3N HIS* 3.9 37.2 - - + +
28N VAL* 4.3 14.4 - - + -
103N VAL* 5.4 2.7 - - + -
107N TRP* 3.6 49.4 - - + +
168N LEU* 3.0 31.3 + - + +
169N ARG* 3.2 9.6 + - + +
171N TYR* 1.3 76.4 - - - +
173N GLU* 1.3 57.2 + - - +
175N GLY 3.4 0.7 - - - -
176N LYS* 3.0 32.2 + - - +
179N LEU* 3.5 27.2 - - + +
180N GLN* 4.1 5.9 - - + +
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Residues in contact with GLU 173 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107N TRP* 4.0 23.4 - - + -
169N ARG* 3.0 19.8 + - + +
170N ARG* 3.7 6.7 - - + +
172N LEU* 1.3 78.3 - - - +
174N ASN* 1.3 64.1 + - - +
176N LYS* 3.6 19.6 + - - +
177N GLU* 5.3 0.2 - - - +
180N GLN* 5.2 2.4 - - - +
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Residues in contact with ASN 174 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51N TRP* 3.7 31.3 + - + +
52N ILE* 5.7 0.8 - - - +
54N GLN* 4.5 14.2 + - - +
55N GLU* 3.7 5.9 + - - -
170N ARG* 2.9 65.7 + - - +
171N TYR* 3.9 7.1 - - - +
173N GLU* 1.3 79.8 - - - +
175N GLY* 1.3 58.6 + - - +
176N LYS 3.6 0.6 + - - -
177N GLU* 3.9 9.7 - - - +
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Residues in contact with GLY 175 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51N TRP* 3.5 28.2 - - - -
171N TYR 2.9 12.4 + - - -
172N LEU 3.4 4.0 - - - -
174N ASN* 1.3 77.0 - - - +
176N LYS* 1.3 63.9 + - - -
177N GLU* 3.2 6.3 - - - -
178N THR* 3.0 2.7 + - - -
179N LEU* 3.0 30.5 + - - +
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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