Contacts of the helix formed by residues 5 - 25 (chain D) in PDB entry 2NS7
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 ASP 5 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D LEU* 1.3 92.6 - - + +
6D LYS* 1.3 62.9 + - - +
7D SER* 3.6 13.2 + - - +
8D LYS* 3.0 27.0 + - - +
9D VAL* 3.2 22.9 + - - +
44D HIS* 4.1 4.0 - - - -
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Residues in contact with LYS 6 (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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5D ASP* 1.3 72.0 - - - +
7D SER* 1.3 66.1 + - - +
9D VAL* 3.4 8.7 + - - +
10D ILE* 3.0 35.6 + - + +
44D HIS* 4.2 19.3 + - + +
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Residues in contact with SER 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D ASP* 3.2 15.1 + - - +
6D LYS* 1.3 79.2 - - - +
8D LYS* 1.3 59.3 + - - +
10D ILE* 3.3 3.6 + - - +
11D ASN* 3.0 37.8 + - - +
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Residues in contact with LYS 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D LEU* 6.4 1.3 - - + -
5D ASP* 3.0 20.5 + - - +
7D SER* 1.3 70.8 - - - +
9D VAL* 1.3 65.7 + - - +
11D ASN* 3.4 33.0 - - - +
12D SER* 3.0 44.6 + - - +
15D GLU* 4.1 14.1 + - - -
34D LEU* 4.0 12.3 - - + +
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Residues in contact with VAL 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D LEU 4.8 8.3 - - - +
5D ASP 3.2 19.3 + - - +
6D LYS* 3.6 9.2 - - - +
7D SER 3.3 0.2 - - - -
8D LYS* 1.3 78.0 - - - +
10D ILE* 1.3 65.9 + - + +
12D SER* 3.7 1.6 - - - -
13D ALA* 2.9 31.3 + - + +
30D LEU* 4.2 15.2 - - + +
34D LEU* 4.3 21.5 - - + -
41D LEU* 4.4 4.5 - - + -
44D HIS* 4.3 21.8 - - + +
45D VAL* 3.8 28.5 - - + -
51D LEU* 5.5 1.1 - - + -
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Residues in contact with ILE 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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6D LYS* 3.0 22.6 + - + +
7D SER* 3.9 3.6 - - - +
9D VAL* 1.3 81.2 - - + +
11D ASN* 1.3 56.3 + - - +
13D ALA* 3.1 4.4 + - - +
14D LEU* 2.7 48.3 + - + +
45D VAL* 6.3 0.7 - - + -
51D LEU* 5.6 2.2 - - + -
54D ALA* 3.5 37.7 - - + +
55D LEU* 4.1 7.6 - - + -
58D GLU* 3.5 41.5 - - + +
62D ARG* 4.8 1.6 - - - +
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Residues in contact with ASN 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D SER* 3.0 28.5 + - - +
8D LYS* 3.4 28.0 + - - +
10D ILE* 1.3 74.8 - - - +
12D SER* 1.3 57.1 + - - +
14D LEU* 3.5 4.6 + - - +
15D GLU* 3.0 28.9 + - - +
62D ARG* 2.6 38.3 - - - +
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Residues in contact with SER 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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8D LYS* 3.0 33.6 + - - +
9D VAL 3.7 2.7 - - - -
11D ASN* 1.3 76.4 - - - +
13D ALA* 1.3 57.3 + - - +
15D GLU* 3.2 8.8 - - - +
16D LEU* 2.8 25.3 + - - +
30D LEU* 4.0 9.1 - - - +
33D LYS* 3.3 40.2 + - - +
34D LEU* 4.1 12.1 - - - +
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Residues in contact with ALA 13 (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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9D VAL 2.9 18.1 + - - +
10D ILE* 3.6 4.3 - - - +
12D SER* 1.3 76.5 - - - +
14D LEU* 1.3 53.4 + - - +
16D LEU* 3.3 7.9 + - - +
17D LEU* 2.8 35.0 + - - +
25D LEU* 4.0 4.6 - - + +
30D LEU* 4.0 14.3 - - + +
51D LEU* 3.8 20.0 - - + -
55D LEU* 3.7 22.9 - - + +
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Residues in contact with LEU 14 (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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10D ILE* 2.7 29.6 + - + +
11D ASN* 3.6 5.4 - - - +
13D ALA* 1.3 71.1 - - - +
15D GLU* 1.3 65.2 + - - +
17D LEU* 3.6 7.2 - - + +
18D ASN* 3.3 28.2 + - - -
55D LEU* 3.5 43.7 - - + +
58D GLU* 4.3 4.5 - - + -
59D MET* 5.2 4.5 - - + -
62D ARG* 3.2 46.2 - - - +
93D HIS* 3.4 32.9 - - + +
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Residues in contact with GLU 15 (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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8D LYS* 4.1 16.2 + - - -
11D ASN 3.0 13.8 + - - +
12D SER* 3.2 11.4 - - - +
14D LEU* 1.3 75.9 - - - +
16D LEU* 1.3 56.4 + - - +
18D ASN* 3.3 11.1 + - - +
19D GLU* 3.0 37.8 + - - +
33D LYS* 2.8 31.9 + - - -
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Residues in contact with LEU 16 (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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12D SER 2.8 19.8 + - - +
13D ALA* 3.5 5.2 - - - +
15D GLU* 1.3 71.3 - - - +
17D LEU* 1.3 55.4 + - - +
19D GLU* 2.9 21.6 + - - +
20D VAL* 2.8 53.5 + - + +
25D LEU* 3.5 22.2 - - + -
26D THR 4.2 2.5 - - - +
29D LYS* 4.0 18.2 - - + +
30D LEU* 3.8 39.5 - - + +
33D LYS* 3.9 13.4 - - + +
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Residues in contact with LEU 17 (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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13D ALA 2.8 20.6 + - - +
14D LEU* 3.6 7.6 - - + +
16D LEU* 1.3 71.7 - - - +
18D ASN* 1.3 58.8 + - - +
21D GLY* 2.8 34.8 + - - +
22D ILE* 3.7 28.5 - - - +
25D LEU* 3.7 18.1 - - + +
55D LEU* 4.4 16.6 - - + -
59D MET* 5.0 4.0 - - - -
93D HIS* 4.0 20.0 - - + -
94D ARG* 3.2 31.2 - - - +
99D VAL* 3.8 24.5 - - + -
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Residues in contact with ASN 18 (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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14D LEU 3.3 15.0 + - - -
15D GLU* 3.3 11.7 + - - +
16D LEU 3.2 0.6 - - - -
17D LEU* 1.3 79.9 - - - +
19D GLU* 1.3 58.6 + - + +
92D SER 5.2 1.8 + - - -
93D HIS* 3.5 21.9 - - - +
94D ARG* 2.8 60.4 + - + +
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Residues in contact with GLU 19 (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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15D GLU* 3.0 24.4 + - - +
16D LEU* 2.9 21.1 + - - +
18D ASN* 1.3 79.3 - - + +
20D VAL* 1.3 66.5 + - + +
33D LYS* 3.4 29.6 + - - -
94D ARG* 3.4 8.8 + - - -
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Residues in contact with VAL 20 (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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16D LEU* 2.8 44.3 + - + +
19D GLU* 1.3 81.9 - - + +
21D GLY* 1.3 71.1 + - - +
24D GLY* 3.4 20.4 + - - +
25D LEU* 3.4 22.2 - - - +
29D LYS* 4.8 14.1 - - + +
94D ARG* 3.6 13.5 + - - +
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Residues in contact with GLY 21 (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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17D LEU* 2.8 31.1 + - - +
20D VAL* 1.3 73.0 - - - +
22D ILE* 1.3 60.2 + - - -
23D GLU 3.3 2.9 - - - -
25D LEU* 3.1 28.8 + - - +
94D ARG* 3.5 16.3 - - - -
95D ASP* 3.4 10.5 - - - -
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Residues in contact with ILE 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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17D LEU* 3.7 11.9 - - + +
21D GLY* 1.3 72.1 - - - -
23D GLU* 1.3 66.6 + - + +
25D LEU* 3.6 6.4 - - - +
48D LYS* 2.7 33.2 + - - +
52D LEU* 3.9 27.8 - - + -
95D ASP* 2.7 36.4 + - + +
98D LYS* 3.7 29.2 - - + +
99D VAL* 3.5 36.8 - - + +
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Residues in contact with GLU 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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49C ARG* 5.4 5.9 + - - -
21D GLY* 3.3 0.4 - - - -
22D ILE* 1.3 87.1 - - + +
24D GLY* 1.3 63.4 + - - +
25D LEU 3.2 1.7 - - - +
26D THR* 5.0 3.3 - - - +
48D LYS* 3.4 14.7 + - - +
98D LYS* 4.5 12.7 + - + -
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Residues in contact with GLY 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 VAL* 3.4 25.6 + - - +
21D GLY 3.6 2.2 + - - -
22D ILE 3.5 0.2 - - - -
23D GLU* 1.3 75.6 - - - +
25D LEU* 1.3 63.6 + - - +
26D THR* 3.3 2.9 + - - +
29D LYS* 2.9 39.0 + - - +
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Residues in contact with LEU 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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13D ALA* 4.0 6.5 - - - +
16D LEU* 3.5 37.9 - - + -
17D LEU* 3.7 27.4 - - + +
20D VAL* 3.7 3.4 - - + -
21D GLY 3.1 15.4 + - - +
22D ILE 3.6 6.7 - - - +
23D GLU 3.2 0.6 - - - -
24D GLY* 1.3 74.9 - - - +
26D THR* 1.3 62.3 + - - +
48D LYS* 2.9 34.4 + - - +
51D LEU* 3.9 21.5 - - + -
52D LEU* 4.0 19.3 - - + -
55D LEU* 3.8 25.6 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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