Contacts of the helix formed by residues 10 - 20 (chain D) in PDB entry 2NYM
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 LEU 10 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9D SER* 1.3 75.0 + - - +
11D TYR* 1.3 64.7 + - - +
12D PRO* 3.7 2.0 - - - -
13D ILE* 4.6 17.5 - - + +
14D ALA* 3.3 21.1 + - + +
41D ALA* 4.4 26.2 - - + +
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Residues in contact with TYR 11 (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 SER* 2.9 16.8 + - - +
10D LEU* 1.3 79.6 - - - +
12D PRO* 1.3 79.0 - - + +
14D ALA* 2.7 20.8 + - + +
15D VAL* 3.0 9.6 + - - +
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Residues in contact with PRO 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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9D SER* 3.9 18.4 - - - +
10D LEU 4.6 0.2 - - - -
11D TYR* 1.3 90.9 - - + +
13D ILE* 1.3 60.4 + - + +
15D VAL* 2.4 51.3 + - + +
16D LEU* 3.2 4.1 + - + -
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Residues in contact with ILE 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 SER 6.0 0.9 - - - +
10D LEU* 4.4 19.7 + - + +
11D TYR 3.4 0.4 - - - -
12D PRO* 1.3 82.5 - - + +
14D ALA* 1.3 62.0 + - - +
15D VAL 3.2 0.7 + - - -
16D LEU* 3.4 18.1 + - + +
17D ILE* 3.3 22.7 + - + +
37D THR* 4.0 25.8 - - - +
38D ILE* 4.6 9.9 - - + -
41D ALA* 3.6 35.0 - - + -
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Residues in contact with ALA 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 LEU* 3.3 18.6 + - + +
11D TYR* 2.7 25.1 + - + +
13D ILE* 1.3 75.8 - - - +
15D VAL* 1.3 58.5 + - - +
17D ILE* 3.7 21.1 - - - +
18D ASP* 3.8 8.7 + - - +
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Residues in contact with VAL 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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11D TYR 3.0 7.4 + - - +
12D PRO* 2.4 41.4 + - + +
14D ALA* 1.3 65.7 - - - +
16D LEU* 1.3 73.6 + - + +
17D ILE 3.0 1.8 - - - -
18D ASP* 2.6 33.7 + - + +
19D GLU* 2.8 29.3 + - + +
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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 PRO* 3.2 8.7 + - + +
13D ILE* 3.4 14.5 + - + +
15D VAL* 1.3 88.8 - - + +
17D ILE* 1.3 63.3 + - - +
19D GLU* 3.0 31.6 + - - +
20D LEU* 3.3 17.7 + - - +
30D ASN* 4.4 11.7 - - - +
31D SER* 3.6 15.0 + - - +
34D LYS* 4.0 28.5 - - + +
37D THR* 5.2 4.5 - - - +
38D ILE* 4.0 26.0 - - + -
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Residues in contact with ILE 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 ILE* 3.3 21.8 - - + +
14D ALA* 3.7 15.0 - - - +
15D VAL 3.0 0.6 - - - -
16D LEU* 1.3 79.7 - - - +
18D ASP* 1.3 58.6 + - - +
19D GLU 3.8 0.2 + - - -
20D LEU* 4.1 18.5 + - + +
21D ARG* 3.8 21.1 + - - +
38D ILE* 3.5 24.7 - - + +
41D ALA 6.2 0.4 - - - -
42D LEU* 3.6 31.0 - - + -
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Residues in contact with ASP 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 ALA 3.8 5.5 + - - +
15D VAL* 2.6 30.8 + - + +
17D ILE* 1.3 74.1 - - - +
19D GLU* 1.3 59.6 + - + -
20D LEU 3.4 2.3 + - - -
21D ARG* 3.6 35.8 + - - +
22D ASN* 4.2 4.5 + - - +
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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 VAL* 2.8 29.7 + - + +
16D LEU* 3.0 23.9 + - - +
18D ASP* 1.3 79.0 - - + +
20D LEU* 1.3 56.3 + - - +
21D ARG 3.0 9.3 + - - -
22D ASN* 3.5 21.9 + - + +
27D LEU* 3.9 33.1 - - + +
28D ARG* 3.4 16.5 - - - -
30D ASN* 4.5 5.7 - - - +
31D SER* 3.1 21.7 + - - +
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Residues in contact with LEU 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 3.6 10.1 - - - +
17D ILE* 4.1 16.1 + - + +
18D ASP 3.4 2.2 - - - -
19D GLU* 1.3 76.6 - - - +
21D ARG* 1.3 58.7 + - + +
22D ASN 3.7 0.2 - - - -
28D ARG* 3.8 15.4 - - - +
31D SER* 2.9 37.5 - - - +
32D ILE* 3.4 26.2 - - + +
35D LEU* 4.1 20.6 - - + -
38D ILE* 5.4 7.2 - - + -
51D LEU* 4.4 7.6 - - + -
54D PHE* 3.6 35.7 - - + -
58D THR* 5.8 0.3 - - - +
60D TYR* 3.1 19.2 + - - +
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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