Contacts of the helix formed by residues 25 - 34 (chain A) in PDB entry 1R18
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 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A LYS* 5.0 1.6 - - - -
23A ILE* 3.4 10.7 - - - +
24A ALA* 1.3 78.8 - - - +
26A ASP* 1.3 63.6 + - - +
27A ALA* 4.3 7.9 - - - +
28A VAL* 2.9 33.8 + - - +
29A ALA* 3.3 14.6 + - - +
70A GLU* 3.1 10.3 + - - -
73A ARG* 4.2 16.1 - - - -
99A TYR* 5.0 0.8 + - - -
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Residues in contact with ASP 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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18A LYS* 2.6 40.0 + - - +
24A ALA 4.0 1.9 + - - +
25A SER* 1.3 70.3 - - - +
27A ALA* 1.3 60.7 + - - +
29A ALA* 3.2 3.2 + - - +
30A GLN* 2.9 35.6 + - + +
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Residues in contact with ALA 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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25A SER* 3.3 5.0 - - - +
26A ASP* 1.3 79.8 - - - +
28A VAL* 1.3 62.4 + - - +
30A GLN* 3.3 7.0 + - - +
31A ALA* 3.1 23.7 + - - +
99A TYR* 3.6 31.1 - - + +
102A ALA* 6.5 0.9 - - + -
103A LYS* 4.2 17.0 - - - +
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Residues in contact with VAL 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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23A ILE* 4.1 8.7 - - + -
25A SER* 2.9 27.9 + - - +
26A ASP 3.3 0.6 - - - -
27A ALA* 1.3 77.7 - - - +
29A ALA* 1.3 62.5 + - - +
31A ALA* 3.4 3.1 + - - +
32A MET* 3.2 30.8 + - - +
66A ALA* 4.4 8.7 - - - +
69A LEU* 3.8 39.4 - - + +
70A GLU* 3.4 22.2 - - + +
73A ARG* 4.7 3.1 - - + -
99A TYR* 3.9 20.6 - - + -
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Residues in contact with ALA 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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14A ILE* 3.6 19.3 - - + +
18A LYS* 4.0 24.9 - - + +
23A ILE* 3.8 21.1 - - + +
25A SER 3.3 4.9 + - - +
26A ASP 3.2 9.3 + - - +
28A VAL* 1.3 79.5 - - - +
30A GLN* 1.3 57.6 + - + +
32A MET* 3.4 0.9 + - - -
33A LYS* 2.8 38.4 + - + +
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Residues in contact with GLN 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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18A LYS* 6.0 0.6 + - - +
26A ASP* 2.9 23.1 + - + +
27A ALA* 3.7 7.6 - - - +
29A ALA* 1.3 75.9 - - + +
31A ALA* 1.3 65.6 + - - +
33A LYS* 3.2 24.3 + - - +
34A GLU* 3.0 52.8 + - - +
102A ALA* 6.4 2.7 - - + -
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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 ALA 3.1 16.3 + - - +
28A VAL* 3.8 4.3 - - - +
30A GLN* 1.3 76.3 - - - +
32A MET* 1.3 61.4 + - - +
34A GLU* 3.5 4.8 + - - +
35A THR* 3.1 27.7 + - - -
69A LEU* 5.2 3.4 - - + -
95A CYS* 3.8 27.9 - - + +
98A ARG* 4.4 10.3 - - - +
99A TYR* 3.9 23.8 - - + +
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Residues in contact with MET 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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10A ASN* 3.0 15.2 - - - +
14A ILE* 3.7 26.3 - - + +
17A LEU* 4.8 2.7 - - + -
23A ILE* 4.2 13.7 - - - -
28A VAL* 3.2 15.7 + - - +
29A ALA 3.8 2.7 - - - +
31A ALA* 1.3 77.4 - - - +
33A LYS* 1.3 64.7 + - - +
35A THR 3.1 12.0 - - - +
37A ARG* 6.5 0.2 - - - -
62A PRO* 3.5 32.8 - - + +
65A HIS* 4.0 14.6 - - + -
66A ALA* 4.0 24.7 - - + +
69A LEU* 3.7 20.0 - - + -
91A TYR* 3.8 22.5 + - + +
95A CYS* 4.2 5.8 - - - -
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Residues in contact with LYS 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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10A ASN* 3.2 17.2 - - - +
11A GLU* 4.4 37.6 - - + +
14A ILE* 3.8 28.0 - - + +
15A ARG* 4.0 20.0 - - - +
18A LYS* 5.0 7.7 - - - +
29A ALA* 2.8 28.4 + - - +
30A GLN* 3.2 30.9 + - - +
32A MET* 1.3 77.7 - - - +
34A GLU* 1.3 60.1 + - + +
35A THR 3.2 0.6 - - - -
36A ASP* 4.6 1.2 + - - +
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Residues in contact with GLU 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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30A GLN* 3.0 36.9 + - - +
31A ALA* 4.1 1.2 - - - +
32A MET 3.3 0.2 - - - -
33A LYS* 1.3 76.8 - - + +
35A THR* 1.3 59.8 + - - +
36A ASP 3.8 2.5 + - - -
98A ARG* 3.2 46.3 + - - +
101A LYS* 5.0 9.2 + - - -
102A ALA* 6.0 1.7 - - - +
131A ASP* 4.7 1.4 - - - +
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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