Contacts of the helix formed by residues 14 - 27 (chain A) in PDB entry 2NZ2
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 14 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A SER* 3.5 11.3 + - - -
13A GLY* 1.3 78.5 - - - +
15A LEU* 1.3 59.1 + - - -
16A ASP 3.4 2.2 + - - -
17A THR* 3.5 3.4 + - - -
18A SER* 2.7 35.4 + - - -
50A LYS* 5.0 1.1 - - - -
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Residues in contact with LEU 15 (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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14A GLY* 1.3 69.8 - - - +
16A ASP* 1.3 69.3 + - - +
18A SER* 3.7 3.4 - - - -
19A CYS* 3.0 38.4 + - - -
50A LYS* 5.9 0.7 - - - +
157A ARG* 4.0 9.2 - - + +
160A LEU* 4.1 13.9 - - + +
161A MET* 3.9 49.6 - - + +
164A ALA* 3.7 29.6 - - + -
169A ILE* 5.3 3.8 - - + -
170A PRO 5.6 1.8 - - - +
171A ILE* 5.0 6.5 - - + -
176A LYS* 6.5 1.8 - - - -
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Residues in contact with ASP 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLY 3.4 0.6 - - - -
15A LEU* 1.3 80.3 - - - +
17A THR* 1.3 56.6 + - + +
19A CYS* 3.1 3.3 + - - +
20A ILE* 2.9 40.0 + - + +
117A GLY 4.0 12.5 - - - +
119A THR* 5.0 6.2 - - - +
145A TRP* 3.1 31.1 + - - +
150A PHE* 5.4 0.4 - - - -
160A LEU* 3.6 23.9 - - - +
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Residues in contact with THR 17 (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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9A LEU* 3.5 6.5 - - + +
10A ALA 3.6 18.6 - - - +
11A TYR* 3.3 23.5 - - - -
12A SER* 3.1 34.7 + - - +
13A GLY 3.5 6.6 + - - -
14A GLY 3.5 3.6 + - - -
15A LEU 3.4 0.2 - - - -
16A ASP* 1.3 74.0 - - + +
18A SER* 1.3 61.6 + - - +
20A ILE* 3.9 7.9 - - + -
21A LEU* 3.2 19.8 + - - +
117A GLY* 4.1 25.4 - - - +
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Residues in contact with SER 18 (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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11A TYR* 3.7 10.9 + - - -
13A GLY 3.4 6.2 + - - -
14A GLY 2.7 23.7 + - - -
15A LEU* 3.7 4.9 - - - -
17A THR* 1.3 73.6 + - - +
19A CYS* 1.3 66.3 + - - +
21A LEU* 3.5 4.9 - - - +
22A VAL* 3.4 24.9 + - - +
50A LYS* 3.4 23.1 + - - -
54A LEU* 4.0 9.8 - - - +
169A ILE* 3.7 26.5 - - - +
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Residues in contact with CYS 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 3.0 36.2 + - - +
16A ASP 3.4 4.0 - - - +
18A SER* 1.3 75.1 - - - +
20A ILE* 1.3 54.4 + - + +
22A VAL* 3.0 5.9 + - - +
23A TRP* 2.8 35.4 + - - +
150A PHE* 5.3 3.1 - - + -
160A LEU* 3.8 38.4 - - + -
163A TYR* 3.7 28.6 - - + -
164A ALA* 4.2 1.8 - - - -
169A ILE* 3.8 16.8 - - - -
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Residues in contact with ILE 20 (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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9A LEU* 3.8 17.0 - - + -
16A ASP* 2.9 24.4 + - - +
17A THR* 4.2 6.3 - - - -
18A SER 3.4 0.2 - - - -
19A CYS* 1.3 72.9 - - - +
21A LEU* 1.3 65.4 + - - +
23A TRP* 3.7 6.9 - - + -
24A LEU* 2.8 44.5 + - + +
115A SER* 4.3 1.1 - - - +
117A GLY* 3.6 30.3 - - - -
144A PRO* 3.8 28.3 - - + -
145A TRP* 4.3 14.8 - - + +
150A PHE* 3.7 20.9 - - + -
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Residues in contact with LEU 21 (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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9A LEU* 3.7 9.4 - - + +
11A TYR* 3.9 25.1 - - + -
17A THR 3.2 17.6 + - - +
18A SER 3.5 6.3 - - - +
20A ILE* 1.3 76.6 - - - +
22A VAL* 1.3 62.2 + - + +
24A LEU* 4.7 0.4 - - - -
25A LYS* 3.1 25.2 + - + +
31A VAL* 3.8 31.8 - - + +
33A ALA* 4.4 7.0 - - + -
51A ALA* 4.0 29.4 - - + +
54A LEU* 4.1 20.6 - - + +
55A GLY 4.3 1.3 - - - -
56A ALA* 3.9 21.3 - - - +
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Residues in contact with VAL 22 (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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18A SER 3.4 13.2 + - - +
19A CYS 3.0 7.9 + - - +
21A LEU* 1.3 75.7 - - - +
23A TRP* 1.3 52.3 + - - +
25A LYS* 3.3 19.0 + - - +
26A GLU* 2.8 36.7 + - + +
54A LEU* 3.8 32.5 - - + +
163A TYR* 3.6 13.9 - - + +
167A HIS* 3.7 31.0 - - + +
169A ILE* 3.7 18.2 - - + -
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Residues in contact with TRP 23 (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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19A CYS 2.8 16.2 + - - +
20A ILE 3.7 3.1 - - - +
22A VAL* 1.3 77.2 - - - +
24A LEU* 1.3 77.8 + - + +
26A GLU* 3.2 7.2 + - - +
27A GLN* 2.9 70.8 + - + +
29A TYR* 6.1 0.9 - + - -
142A ILE* 4.5 0.2 - - + -
144A PRO* 4.2 19.3 - - + -
147A MET* 3.6 35.2 - - + -
149A GLU* 3.9 16.7 + - + -
150A PHE* 3.3 52.4 - + + +
153A ARG* 3.8 25.7 - - - +
154A PHE* 4.7 1.1 - + - -
163A TYR* 3.3 19.4 + + + +
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Residues in contact with LEU 24 (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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7A VAL* 4.1 17.7 - - + -
9A LEU* 4.3 10.3 - - + -
20A ILE* 2.8 45.1 + - + +
23A TRP* 1.3 83.6 - - + +
25A LYS* 1.3 59.5 + - - +
27A GLN* 3.3 7.2 + - - -
29A TYR* 3.0 42.8 + - + -
31A VAL* 3.7 15.9 - - + -
115A SER* 3.8 14.6 - - - +
142A ILE* 3.7 43.5 - - + -
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Residues in contact with LYS 25 (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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21A LEU* 3.1 15.6 + - + +
22A VAL* 3.3 26.7 - - - +
24A LEU* 1.3 74.4 - - - +
26A GLU* 1.3 68.2 + - - +
27A GLN 3.1 1.4 + - - -
28A GLY* 3.1 13.2 + - - -
29A TYR 3.6 16.1 - - - +
31A VAL* 3.9 6.0 - - + +
54A LEU 2.7 32.0 + - - +
55A GLY* 3.8 23.9 - - - +
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Residues in contact with GLU 26 (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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22A VAL* 2.8 25.4 + - + +
23A TRP* 3.4 12.8 - - - +
25A LYS* 1.3 74.7 - - - +
27A GLN* 1.3 68.7 + - - +
28A GLY 3.5 0.5 + - - -
153A ARG* 4.7 4.5 + - - -
163A TYR* 2.9 24.9 + - - -
167A HIS* 2.8 32.4 + - + -
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Residues in contact with GLN 27 (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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4A LYS 4.4 7.4 + - - -
23A TRP* 2.9 78.0 + - + +
24A LEU 3.7 6.1 - - - +
25A LYS 3.1 1.4 + - - -
26A GLU* 1.3 84.0 + - - +
28A GLY* 1.3 58.0 + - - +
29A TYR* 3.7 17.7 + - + -
149A GLU* 5.4 3.6 - - - +
153A ARG* 5.3 2.6 - - - +
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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