Contacts of the helix formed by residues 15 - 25 (chain L) in PDB entry 2NZV
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 HIS 15 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291G VAL* 6.1 2.9 - - + +
293G PRO* 5.2 9.0 - - + -
296G ASP* 3.0 26.9 + - - +
324G ARG* 4.3 18.9 + - - -
12L SER* 3.0 31.9 + - - +
13L GLY 3.6 4.2 + - - -
14L ILE* 1.3 82.2 + - - +
16L ALA* 1.3 77.5 + - + +
18L PRO* 3.3 10.2 - - - +
19L ALA* 3.0 15.5 + - - -
50L VAL 5.6 1.5 + - - -
51L MET* 3.8 5.9 + - - +
54L GLY* 3.8 28.6 - - - -
55L ILE 4.0 15.1 + - - -
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Residues in contact with ALA 16 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77G GLU* 5.8 1.1 - - - +
295G TYR* 3.1 40.7 - - + -
296G ASP* 3.1 8.8 + - - +
12L SER* 6.5 0.9 - - - -
15L HIS* 1.3 88.9 - - + +
17L ARG* 1.3 63.2 + - + +
18L PRO* 3.8 7.2 - - + -
19L ALA* 2.9 10.6 + - - +
20L THR* 2.9 13.2 + - - -
51L MET* 4.0 2.8 - - - +
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Residues in contact with ARG 17 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80G ARG* 3.5 35.7 - - - +
84G ASP* 3.0 27.6 - - - +
295G TYR* 3.3 13.5 - - + +
16L ALA* 1.3 74.2 - - - +
18L PRO* 1.3 57.8 - - + +
19L ALA 2.9 5.2 - - - -
20L THR* 3.4 8.6 - - - -
21L THR* 2.7 41.7 + - - +
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Residues in contact with PRO 18 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L SER* 5.6 10.5 - - - -
13L GLY 5.3 2.2 - - - +
15L HIS 3.3 12.3 - - - +
16L ALA* 3.3 7.4 - - + -
17L ARG* 1.3 94.3 - - + +
19L ALA* 1.3 56.8 + - - +
21L THR* 3.9 8.5 - - - -
22L LEU* 3.6 11.3 + - - +
84L GLU* 4.3 18.4 - - + +
86L LEU* 3.8 40.3 - - + +
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Residues in contact with ALA 19 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14L ILE* 3.3 38.4 - - + +
15L HIS* 3.0 19.7 + - - +
16L ALA 2.9 5.4 + - - +
18L PRO* 1.3 76.9 - - - +
20L THR* 1.3 63.1 + - - +
21L THR 2.9 5.6 + - - -
22L LEU* 3.0 12.9 + - - +
23L VAL* 3.1 19.5 + - + +
47L ILE* 5.3 0.7 - - - -
50L VAL* 5.2 3.4 - - + -
51L MET* 3.7 11.9 - - + -
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Residues in contact with THR 20 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84G ASP* 4.9 4.0 - - + +
85G ILE* 3.2 32.8 - - + -
88G MET* 4.1 3.5 - - - +
295G TYR* 3.0 24.9 + - - +
299G ALA* 5.5 0.3 - - - +
16L ALA 2.9 16.0 + - - -
17L ARG* 3.4 6.1 - - - -
19L ALA* 1.3 74.8 - - - +
21L THR* 1.3 56.7 + - - +
23L VAL* 3.6 1.6 + - - +
24L GLN* 2.7 51.6 + - - +
47L ILE* 4.0 20.1 - - + +
51L MET* 5.3 2.2 - - - +
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Residues in contact with THR 21 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17L ARG* 2.7 18.9 + - - +
18L PRO 3.9 4.0 - - - -
20L THR* 1.3 75.7 - - - +
22L LEU* 1.3 58.7 + - - +
23L VAL 3.0 4.5 - - - -
24L GLN* 3.0 8.2 + - - +
25L ALA* 2.9 29.9 + - + +
80L THR* 3.8 11.9 - - + -
84L GLU* 2.9 43.0 + - + +
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Residues in contact with LEU 22 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14L ILE* 4.9 16.2 - - + -
18L PRO 3.6 10.0 + - - +
19L ALA* 3.0 10.3 + - - +
21L THR* 1.3 78.0 - - - +
23L VAL* 1.3 59.9 + - + +
25L ALA* 4.0 4.6 + - - +
26L ALA* 3.8 14.6 - - - +
35L LEU* 6.2 1.1 - - + -
44L LEU* 3.8 21.8 - - + +
50L VAL* 6.4 0.7 - - + -
63L ILE* 6.1 4.7 - - + -
77L LEU* 4.1 23.1 - - + +
80L THR* 3.4 36.3 - - + -
81L MET* 4.0 17.5 - - + +
86L LEU* 3.8 20.2 - - + -
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Residues in contact with VAL 23 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88G MET* 4.1 8.5 - - + -
19L ALA* 3.1 15.2 + - + +
20L THR 4.0 1.6 - - - +
21L THR 3.0 0.8 - - - -
22L LEU* 1.3 77.8 - - + +
24L GLN* 1.3 62.9 + - - +
25L ALA 3.2 1.6 - - - -
26L ALA* 3.6 8.4 + - - +
27L SER* 3.1 19.2 + - - +
44L LEU* 3.8 9.2 - - + +
45L LYS* 3.9 24.9 - - - +
46L SEP 4.1 1.8 - - - +
47L ILE* 3.6 34.8 - - + +
50L VAL* 3.5 35.7 - - + -
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Residues in contact with GLN 24 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84G ASP 4.7 2.5 + - - +
87G THR* 5.6 1.9 - - - +
88G MET* 3.1 48.5 - - + +
20L THR* 2.7 46.3 + - - +
21L THR* 3.0 8.0 + - - +
23L VAL* 1.3 78.4 - - - +
25L ALA* 1.3 54.4 + - - +
26L ALA 3.2 4.0 + - - -
27L SER* 3.8 8.8 + - - -
28L LYS* 3.3 32.8 + - - +
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Residues in contact with ALA 25 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21L THR* 2.9 16.2 + - + +
22L LEU* 4.2 2.9 - - - -
23L VAL 3.2 0.2 - - - -
24L GLN* 1.3 76.8 - - - +
26L ALA* 1.3 57.2 + - - +
28L LYS* 4.0 16.2 - - + +
29L PHE* 4.1 10.0 - - + -
77L LEU* 2.9 21.3 - - + +
80L THR* 3.6 32.9 + - + +
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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