Contacts of the helix formed by residues 20 - 31 (chain A) in PDB entry 4EOH
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 GLY 20 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A GLN* 3.5 18.8 + - - -
12A SER 3.7 2.9 - - - -
19A VAL* 1.3 71.4 - - - +
21A ASN* 1.3 58.2 + - - -
23A ALA* 2.9 18.5 + - - +
24A ALA* 3.1 12.3 + - - +
235A ASP* 2.6 20.6 + - - +
402A TEP 3.3 23.1 - - - -
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Residues in contact with ASN 21 (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 SER* 2.5 42.4 + - - +
11A GLN* 3.2 17.0 + - - +
12A SER 2.8 16.0 + - - +
13A HIS* 5.1 3.1 - - - +
20A GLY* 1.3 71.6 - - - -
22A ARG* 1.3 56.3 + - - +
24A ALA* 4.3 3.0 - - - +
25A THR* 2.8 46.0 + - - +
35A ILE* 4.7 1.2 - - - +
37A ALA* 3.9 9.3 - - + +
38A VAL 3.1 26.3 + - - +
39A ASN* 3.5 15.8 + - - +
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Residues in contact with ARG 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A SER 4.1 0.4 + - - -
13A HIS* 3.6 26.9 - - - +
14A VAL* 3.4 29.0 + - + +
15A ILE 3.9 7.9 + - - -
17A GLY 3.1 26.4 + - - +
18A TYR* 3.4 50.4 + - - -
19A VAL 2.9 15.7 + - - +
21A ASN* 1.3 77.4 - - - +
23A ALA* 1.3 58.5 + - - +
25A THR* 4.5 2.6 + - - -
26A PHE* 4.7 8.1 + - - +
293A MET* 4.9 3.6 - - - +
25B THR* 4.6 8.1 - - - +
29B GLN* 3.7 17.4 + - - +
35B ILE 3.0 28.8 + - - -
36B ASP* 3.6 14.8 + - - -
37B ALA* 4.3 10.3 - - - +
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Residues in contact with ALA 23 (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 TYR* 4.0 12.1 - - + +
19A VAL* 3.5 18.2 + - - +
20A GLY 2.9 10.0 + - - +
22A ARG* 1.3 81.7 - - - +
24A ALA* 1.3 57.0 + - - +
25A THR 3.7 0.2 - - - -
27A PRO* 3.0 20.9 - - - +
232A GLY 3.9 22.2 - - - +
235A ASP* 4.0 6.1 - - + -
236A LEU* 3.5 17.8 - - + +
291A LEU* 4.9 4.3 - - + -
293A MET* 4.3 5.0 - - + +
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Residues in contact with ALA 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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9A SER* 4.8 0.4 - - - +
11A GLN* 3.9 18.2 - - - +
20A GLY 3.1 12.7 + - - +
21A ASN* 4.4 5.8 - - - +
23A ALA* 1.3 80.3 - - - +
25A THR* 1.3 63.0 + - - +
27A PRO* 3.5 2.8 - - - +
28A LEU* 3.2 30.6 + - + +
35A ILE* 4.3 0.9 - - + -
81A LEU* 4.2 9.4 - - + -
235A ASP 4.3 6.3 - - - +
239A ALA* 3.6 24.0 - - + +
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Residues in contact with THR 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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21A ASN* 2.8 32.8 + - - +
22A ARG* 5.3 0.4 - - - -
24A ALA* 1.3 74.5 - - - +
26A PHE* 1.3 69.1 + - - +
28A LEU* 3.1 3.3 + - - +
29A GLN* 2.8 54.9 + - + +
35A ILE* 3.8 23.9 - - + +
37A ALA* 4.1 9.0 - - + +
22B ARG* 4.5 10.3 - - - +
29B GLN* 5.9 0.2 - - - +
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Residues in contact with PHE 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 TYR* 5.9 0.4 - - + -
22A ARG 4.7 7.3 + - - +
25A THR* 1.3 74.6 - - - +
27A PRO* 1.3 66.4 - - + +
29A GLN* 3.0 10.3 + - - +
30A VAL* 2.8 56.7 + - + +
293A MET* 3.7 41.1 - - + -
294A VAL* 3.9 12.3 - - + -
297A LYS* 4.2 20.2 - - + -
300A ILE* 4.5 6.5 - - + -
26B PHE* 4.2 7.0 - + - -
29B GLN* 3.5 60.5 + - + +
30B VAL* 4.0 14.8 - - + -
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Residues in contact with PRO 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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23A ALA 3.0 29.2 - - - +
24A ALA* 3.5 11.4 - - - +
25A THR 3.6 0.4 - - - -
26A PHE* 1.3 100.1 - - + +
28A LEU* 1.3 54.3 + - - +
30A VAL* 3.4 3.9 + - + +
31A LEU* 3.0 32.4 + - - +
236A LEU* 3.8 11.9 - - + -
240A MET* 3.6 21.8 - - + -
293A MET* 4.2 7.6 - - + -
300A ILE* 3.7 29.1 - - + +
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Residues in contact with LEU 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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7A VAL* 4.7 9.0 - - + -
24A ALA 3.2 20.8 + - - +
25A THR 3.1 4.1 + - - +
27A PRO* 1.3 73.6 - - - +
29A GLN* 1.3 63.4 + - - +
31A LEU* 3.3 3.3 + - - +
32A GLY 3.2 4.0 + - - -
33A PHE* 2.9 53.1 + - + +
35A ILE* 3.6 30.5 - - + -
81A LEU* 4.1 14.1 - - + -
239A ALA* 3.5 37.0 - - + +
240A MET* 4.1 2.0 - - + -
242A LEU* 4.3 10.1 - - + -
243A ALA* 4.0 10.8 - - + -
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Residues in contact with GLN 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 THR* 2.8 36.9 + - - +
26A PHE* 3.5 11.9 - - - +
28A LEU* 1.3 73.0 - - - +
30A VAL* 1.3 58.6 + - - +
32A GLY 2.8 20.3 + - - -
33A PHE 3.9 7.6 - - - -
35A ILE* 3.6 15.5 + - + +
18B TYR* 4.3 15.4 + - - -
22B ARG* 4.0 18.0 + - - +
25B THR* 5.7 0.9 - - - +
26B PHE* 3.4 48.8 + - + +
29B GLN* 4.2 5.7 - - - +
294B VAL* 3.1 26.7 - - + +
297B LYS* 5.4 0.3 - - - +
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Residues in contact with VAL 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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26A PHE* 2.8 58.3 + - + +
27A PRO* 3.5 6.1 - - + +
29A GLN* 1.3 76.3 - - - +
31A LEU* 1.3 59.2 + - - +
32A GLY 3.3 3.5 + - - -
297A LYS* 4.1 12.6 - - + +
300A ILE* 4.0 15.5 - - + -
301A GLU* 3.3 33.7 - - + +
26B PHE* 3.8 8.7 - - + -
30B VAL* 5.1 0.2 - - + -
297B LYS* 2.8 36.6 + - + +
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Residues in contact with LEU 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 PRO 3.0 19.8 + - - +
28A LEU 3.8 4.9 - - - +
29A GLN 3.1 0.8 - - - -
30A VAL* 1.3 78.5 - - - +
32A GLY* 1.3 58.6 + - - +
33A PHE* 3.5 12.9 + - + -
240A MET* 4.1 18.4 - - + -
243A ALA* 3.5 28.5 - - + -
244A TRP* 4.1 22.7 - - + -
247A LYS* 3.4 26.3 + - - +
300A ILE* 3.4 24.7 - - + +
301A GLU* 3.9 19.5 - - - +
407A MPD 3.5 8.8 + - - +
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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