Contacts of the helix formed by residues 9 - 25 (chain D) in PDB entry 1NVP
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 THR 9 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336C VAL* 4.6 13.2 - - + -
357C ILE* 4.0 38.5 - - + +
359C ASN* 6.6 0.2 - - - -
6D TYR* 2.7 37.6 + - + +
7D ARG 3.1 0.6 + - - -
8D ASN* 1.3 80.5 - - - +
10D THR* 1.3 67.4 + - - +
11D LEU* 3.7 6.8 + - - +
12D GLY 3.0 13.0 + - - -
13D ASN* 2.8 26.1 + - - +
40D PHE* 4.5 0.5 - - - -
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Residues in contact with THR 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B TYR* 4.9 1.3 - - + -
49B LYS 5.7 1.1 - - - +
50B LEU* 3.7 29.2 - - + +
357C ILE* 5.5 0.2 - - - +
359C ASN* 3.6 11.7 + - - +
364C ASP* 2.7 38.9 + - - +
9D THR* 1.3 74.8 - - - +
11D LEU* 1.3 66.0 + - - +
13D ASN* 4.0 2.5 - - - +
14D SER* 2.9 26.6 + - - +
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Residues in contact with LEU 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B TYR* 3.9 47.3 - - + +
17B VAL* 4.1 14.4 - - + -
18B ILE* 4.4 4.9 - - + -
46B TRP* 3.1 36.3 + - + +
50B LEU* 4.1 15.4 - - + +
357C ILE* 5.6 2.2 - - + -
364C ASP* 4.8 1.0 + - - -
9D THR* 4.0 6.7 - - - +
10D THR* 1.3 79.7 - - - +
12D GLY* 1.3 60.5 + - - +
14D SER* 2.7 19.2 + - - -
15D LEU* 3.3 3.5 + - - +
40D PHE* 3.7 24.2 - - + -
44D ILE* 3.9 21.5 - - + -
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Residues in contact with GLY 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D ARG* 3.0 18.7 - - - -
9D THR* 3.0 14.4 + - - -
11D LEU* 1.3 75.8 - - - +
13D ASN* 1.3 58.1 + - - +
15D LEU* 3.3 7.5 - - - +
16D GLN* 3.1 30.1 + - - +
37D LEU* 4.9 0.7 - - - +
40D PHE* 3.7 23.3 - - - -
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Residues in contact with ASN 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D ARG 3.1 8.0 + - - +
8D ASN* 3.2 40.6 + - - +
9D THR 2.8 27.5 + - - +
10D THR* 4.0 2.5 - - - +
12D GLY* 1.3 68.0 - - - +
14D SER* 1.3 68.0 + - - +
15D LEU 3.0 1.6 - - - -
16D GLN* 3.1 14.9 + - - +
17D GLU* 2.9 43.1 + - + +
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Residues in contact with SER 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B TRP* 3.1 17.0 + - - -
49B LYS* 3.7 29.1 - - - +
50B LEU* 4.2 6.6 - - - +
10D THR* 2.9 16.3 + - - -
11D LEU* 2.7 24.4 + - - -
13D ASN* 1.3 76.2 - - - +
15D LEU* 1.3 55.8 + - - +
17D GLU* 3.5 14.2 + - - +
18D SER* 2.7 34.6 + - - -
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Residues in contact with LEU 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B VAL* 5.3 0.4 - - + -
42B LEU* 4.5 9.4 - - + -
46B TRP* 3.7 41.1 - - + +
11D LEU 3.3 8.2 + - - +
12D GLY 3.3 9.0 - - - +
13D ASN 3.0 0.2 - - - -
14D SER* 1.3 83.0 + - - +
16D GLN* 1.3 57.6 + - - +
18D SER* 3.2 5.0 + - - -
19D LEU* 2.9 51.4 + - + +
36D VAL* 4.2 15.5 - - + -
37D LEU* 4.1 12.6 - - + -
40D PHE* 3.6 44.0 - - + -
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Residues in contact with GLN 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D ARG* 3.5 38.2 + - - +
8D ASN* 5.1 0.8 - - - +
12D GLY 3.2 9.9 - - - +
13D ASN* 3.1 19.1 + - - +
15D LEU* 1.3 77.0 - - - +
17D GLU* 1.3 59.0 + - + +
19D LEU* 3.2 11.2 + - - +
20D ASP* 2.8 41.2 + - - +
37D LEU* 3.7 29.5 - - + +
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Residues in contact with GLU 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LYS* 3.6 32.2 - - - +
13D ASN* 2.9 35.4 + - + +
14D SER* 3.7 7.2 - - - +
16D GLN* 1.3 74.0 - - + +
18D SER* 1.3 66.6 + - - +
20D ASP* 3.2 10.5 + - - +
21D GLU* 3.1 26.2 + - - +
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Residues in contact with SER 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 4.0 15.9 - - - -
45B LEU* 3.4 23.4 - - - +
46B TRP* 3.2 24.2 + - - -
49B LYS* 3.6 12.0 - - - +
14D SER 2.7 18.8 + - - -
15D LEU* 3.4 9.0 - - - -
17D GLU* 1.3 78.8 - - - +
19D LEU* 1.3 62.1 + - - +
21D GLU* 3.4 4.0 + - - +
22D LEU* 3.3 25.3 + - - +
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Residues in contact with LEU 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 3.6 28.7 - - + -
15D LEU* 2.9 27.4 + - + +
16D GLN* 3.5 8.3 - - - +
17D GLU 3.2 0.2 - - - -
18D SER* 1.3 74.7 - - - +
20D ASP* 1.3 61.1 + - - +
22D LEU* 3.2 4.8 + - - +
23D ILE* 2.8 34.4 + - + +
28D ILE* 3.7 21.5 - - + +
33D ALA* 3.6 39.7 - - + +
36D VAL* 4.2 11.9 - - + -
37D LEU* 3.8 26.5 - - + -
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Residues in contact with ASP 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D GLN* 2.8 34.2 + - - +
17D GLU* 3.7 9.3 - - - +
19D LEU* 1.3 72.0 - - - +
21D GLU* 1.3 52.7 + - - +
23D ILE* 3.0 19.3 + - - +
24D GLN* 2.6 37.1 + - - +
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Residues in contact with GLU 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LEU* 3.9 27.3 - - + +
49B LYS* 2.5 32.7 + - - +
17D GLU 3.1 16.9 + - - +
18D SER 3.5 7.2 - - - +
19D LEU 3.2 0.2 - - - -
20D ASP* 1.3 74.1 - - - +
22D LEU* 1.3 54.3 + - + +
24D GLN* 2.7 28.7 + - - +
25D SER* 2.7 21.8 + - - -
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Residues in contact with LEU 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B PHE* 5.7 0.7 - - + -
38B VAL* 4.4 8.1 - - + -
41B GLU* 3.7 22.4 - - + +
42B LEU* 3.7 46.7 - - + +
45B LEU* 3.9 7.9 - - + -
18D SER 3.4 9.4 - - - +
19D LEU 3.2 7.7 + - - +
21D GLU* 1.3 79.3 - - + +
23D ILE* 1.3 58.0 + - - +
25D SER* 3.6 4.2 + - - +
26D GLN 3.3 0.9 + - - -
27D GLN* 2.6 59.3 + - + +
28D ILE* 3.1 33.2 + - + -
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Residues in contact with ILE 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D LEU* 2.8 30.2 + - + +
20D ASP* 3.3 21.1 - - - +
21D GLU 3.0 0.2 - - - -
22D LEU* 1.3 74.4 - - - +
24D GLN* 1.3 63.6 + - - +
26D GLN* 2.9 21.5 + - - +
28D ILE* 3.6 25.4 - - + +
29D THR 4.4 2.9 - - - +
30D PRO* 4.2 27.8 - - + -
33D ALA* 3.6 25.6 - - + -
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Residues in contact with GLN 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D ASP 2.6 16.8 + - - +
21D GLU* 2.7 13.0 + - - +
23D ILE* 1.3 76.0 - - - +
25D SER* 1.3 59.5 + - - +
26D GLN* 3.1 11.6 + - - +
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Residues in contact with SER 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D GLU 2.7 19.4 + - - -
22D LEU* 3.6 4.3 + - - +
24D GLN* 1.3 73.5 - - - +
26D GLN* 1.3 68.9 + - - +
27D GLN* 2.9 35.9 + - - +
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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