Contacts of the helix formed by residues 23 - 37 (chain A) in PDB entry 1N35
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 SER 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A SER* 5.1 0.4 - - - -
21A ASP* 3.8 3.9 + - - -
22A GLN* 1.3 77.2 - - - +
24A ASN* 1.3 65.0 + - - +
25A ASP* 4.2 8.0 - - - +
26A VAL* 3.3 29.9 + - - +
27A PHE* 3.0 22.0 + - - +
867A MET* 3.6 6.9 - - - +
868A TRP* 5.5 2.0 - - - -
940A LEU* 6.2 4.0 - - - -
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Residues in contact with ASN 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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23A SER* 1.3 72.4 - - - +
25A ASP* 1.3 59.9 + - - +
27A PHE* 4.0 1.9 - - - -
28A GLU* 2.5 71.6 + - - +
866A PRO* 3.0 9.4 - - - +
867A MET* 2.7 42.2 + - - +
868A TRP* 4.0 8.2 - - - +
940A LEU* 3.2 27.0 - - - +
941A LYS* 3.5 21.8 - - - +
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Residues in contact with ASP 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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23A SER* 3.1 8.1 - - - +
24A ASN* 1.3 81.3 + - - +
26A VAL* 1.3 64.6 + - + +
28A GLU* 4.2 5.0 - - - +
29A ASP* 2.8 33.0 + - - +
939A GLU 5.7 1.7 - - - +
940A LEU* 6.0 2.3 - - - +
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Residues in contact with VAL 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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11A PRO* 3.8 19.3 - - + +
12A PHE* 3.4 43.3 - - + +
15A SER* 4.4 5.8 - - - +
21A ASP 6.0 0.9 - - - +
23A SER* 3.2 23.7 + - - +
25A ASP* 1.3 79.4 - - + +
27A PHE* 1.3 54.0 + - - +
29A ASP* 3.2 8.1 + - - +
30A ALA* 2.8 32.6 + - - +
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Residues in contact with PHE 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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12A PHE* 4.1 16.4 - + + -
22A GLN* 5.8 1.1 - - - -
23A SER 3.0 16.6 + - - +
24A ASN* 3.5 10.3 - - - +
26A VAL* 1.3 76.8 - - - +
28A GLU* 1.3 62.9 + - + +
30A ALA* 3.1 9.1 + - - +
31A ALA* 2.8 24.3 + - - +
843A TRP* 4.0 22.9 - + - -
847A CYS* 3.3 43.7 - - + -
850A SER* 3.6 10.1 - - - -
864A GLN* 4.3 0.7 - - - -
865A TYR 3.3 24.2 - - - -
867A MET* 3.5 30.1 - - + -
870A PHE* 3.7 22.0 - + - -
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Residues in contact with GLU 28 (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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24A ASN* 2.5 55.9 + - - +
25A ASP* 4.3 5.4 - - - +
27A PHE* 1.3 77.2 - - + +
29A ASP* 1.3 58.7 + - - +
31A ALA* 3.2 10.1 + - - +
32A LYS* 2.9 27.2 + - - +
851A ARG* 4.4 2.4 + - - +
864A GLN* 3.6 23.4 + - + +
866A PRO* 3.7 5.9 - - - +
941A LYS* 5.3 0.2 - - - +
1042A ARG* 2.8 41.5 + - - -
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Residues in contact with ASP 29 (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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25A ASP* 2.8 21.4 + - - +
26A VAL* 3.2 11.1 + - - +
28A GLU* 1.3 73.6 - - - +
30A ALA* 1.3 61.2 + - - +
32A LYS* 3.2 15.7 + - - +
33A ALA* 2.8 30.2 + - - +
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Residues in contact with ALA 30 (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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8A GLN 5.5 1.8 - - - -
9A PHE* 3.4 14.5 - - + +
12A PHE* 3.5 33.4 - - + -
26A VAL 2.8 13.7 + - - +
27A PHE 3.1 9.6 + - - +
29A ASP* 1.3 76.9 - - - +
31A ALA* 1.3 56.4 + - - +
33A ALA* 3.1 3.0 + - - -
34A PHE* 2.8 32.6 + - - -
847A CYS* 3.4 15.7 - - - -
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Residues in contact with ALA 31 (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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27A PHE 2.8 13.4 + - - +
28A GLU* 3.3 10.1 - - - +
29A ASP 3.1 0.2 - - - -
30A ALA* 1.3 77.0 - - - +
32A LYS* 1.3 62.4 + - - +
34A PHE* 3.1 6.0 + - - +
35A SER* 3.1 22.9 + - - -
847A CYS* 3.3 15.3 - - - +
850A SER* 3.4 22.4 - - - +
851A ARG* 3.9 8.4 - - + +
864A GLN* 3.4 21.1 - - - +
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Residues in contact with LYS 32 (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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28A GLU 2.9 14.0 + - - +
29A ASP* 3.5 17.6 + - - +
31A ALA* 1.3 75.8 - - - +
33A ALA* 1.3 63.6 + - - +
35A SER* 3.2 2.4 + - - -
36A MET* 3.0 48.1 + - - +
851A ARG* 3.6 26.2 - - - +
1294A CH1 3.2 39.0 - - - +
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Residues in contact with ALA 33 (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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8A GLN* 3.9 26.3 - - - +
9A PHE* 3.4 21.8 - - + -
29A ASP 2.8 13.8 + - - +
30A ALA* 3.4 8.7 - - - +
32A LYS* 1.3 77.3 - - - +
34A PHE* 1.3 62.2 + - - +
36A MET* 3.3 6.4 + - - +
37A PHE* 3.1 28.2 + - - +
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Residues in contact with PHE 34 (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 PHE* 3.6 15.7 - + - -
12A PHE* 4.3 6.5 - + - -
30A ALA 2.8 22.9 + - - -
31A ALA 3.1 7.4 + - - +
33A ALA* 1.3 77.0 - - - +
35A SER* 1.3 61.3 + - - +
37A PHE* 3.4 18.2 + - - +
153A LYS* 4.6 10.1 + - - +
156A LEU* 3.4 43.0 - - + +
157A ALA* 4.1 7.6 - - - -
160A VAL* 3.3 32.5 - - + -
844A ALA 3.8 21.8 - - - -
847A CYS* 3.8 17.0 - - + -
848A ALA* 3.6 38.4 - - + +
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Residues in contact with SER 35 (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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31A ALA 3.1 14.9 + - - -
32A LYS 3.2 1.1 + - - -
34A PHE* 1.3 77.0 - - - +
36A MET* 1.3 59.9 + - - +
37A PHE 3.3 4.9 + - - +
153A LYS* 4.3 14.2 + - - +
848A ALA 5.4 0.7 + - - -
851A ARG* 4.0 20.8 + - - +
1294A CH1 3.2 55.9 + - - +
1295A CH1 5.5 2.1 + - - -
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Residues in contact with MET 36 (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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8A GLN* 5.7 2.9 - - - +
32A LYS* 3.0 50.8 + - - +
33A ALA* 3.3 6.7 + - - +
34A PHE 3.2 0.4 - - - -
35A SER* 1.3 78.9 - - - +
37A PHE* 1.3 63.0 + - - +
38A THR* 3.5 11.8 + - - +
41A ASP* 5.0 0.3 - - - +
1294A CH1 3.5 83.4 + - + +
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Residues in contact with PHE 37 (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 MET* 4.3 20.4 - - + -
5A ILE* 3.8 19.1 - - + -
8A GLN* 3.9 26.0 - - + -
9A PHE* 3.8 22.4 - + - -
33A ALA 3.1 15.7 + - - +
34A PHE 3.5 17.3 - - - +
35A SER 3.3 4.7 - - - +
36A MET* 1.3 78.7 - - - +
38A THR* 1.3 62.6 + - - +
39A ARG 4.0 0.3 + - - -
41A ASP* 3.6 41.3 - - + -
42A VAL* 4.0 9.8 - - + +
45A ALA* 4.7 1.1 - - + -
156A LEU* 3.7 32.8 - - + -
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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