Contacts of the helix formed by residues 25 - 38 (chain A) in PDB entry 4PAR
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 TYR 25 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ARG* 1.3 115.6 + - + +
26A GLU* 1.3 62.0 + - - +
27A ALA 3.6 0.9 - - - -
28A TYR* 3.6 8.9 + + + +
29A VAL* 3.3 28.1 + - + +
73A VAL* 4.1 4.0 - - + -
75A GLU* 2.8 20.2 + - - +
125A VAL* 3.8 43.5 - - + -
126A PHE* 4.0 17.7 - + - -
133A PRO* 3.2 28.5 - - + +
139A ILE* 4.5 7.0 - - + -
10B THR* 3.9 16.8 - - + +
11B ASP* 4.6 1.6 - - - -
14B ILE* 3.7 32.3 - - + +
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Residues in contact with GLU 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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19A ARG* 5.7 0.2 - - - +
21A LYS* 3.4 10.1 - - - -
22A ASN* 2.9 30.3 + - - -
23A LYS* 3.4 22.3 + - + +
24A ARG 3.3 2.0 - - - -
25A TYR* 1.3 75.6 - - - +
27A ALA* 1.3 69.8 + - - +
28A TYR 3.2 0.3 + - - -
29A VAL* 3.9 0.7 - - - +
30A VAL* 3.0 33.1 + - + +
46A THR* 5.0 3.8 - - - +
47A GLN* 3.3 31.1 + - - +
61A ASP* 3.6 35.1 - - + +
73A VAL* 4.1 10.9 - - - +
75A GLU* 4.3 0.8 + - - -
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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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17A LEU 5.8 4.0 - - - +
21A LYS* 3.0 37.1 - - + +
26A GLU* 1.3 76.5 - - - +
28A TYR* 1.3 54.1 + - - +
30A VAL* 4.9 2.5 - - - -
31A SER* 2.7 39.5 + - - -
17B LEU 5.5 6.5 - - - +
18B GLY* 6.5 0.4 - - - -
21B LYS* 5.9 2.9 - - - +
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Residues in contact with TYR 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LYS* 4.8 0.4 - - - +
24A ARG 5.5 0.2 + - - -
25A TYR* 3.6 11.3 + + + +
26A GLU 3.2 0.6 - - - -
27A ALA* 1.3 79.8 - - - +
29A VAL* 1.3 67.6 - - + +
31A SER* 3.1 5.1 + - - -
32A ARG* 2.9 40.1 + - - +
136A LEU* 3.8 18.9 - - + +
139A ILE* 4.7 11.0 - - + -
140A HIS* 2.8 38.9 + + - -
143A ILE* 5.1 0.2 - - + -
13B VAL* 3.8 19.7 - - + -
14B ILE* 3.5 32.5 - - + -
17B LEU* 4.1 17.5 - - + -
34B ILE* 5.7 0.2 - - + -
35B HIS* 3.3 26.8 + + - -
40B PHE* 3.7 13.6 - + - -
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Residues in contact with VAL 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A TYR* 3.3 20.3 + - + +
28A TYR* 1.3 86.4 - - + +
30A VAL* 1.3 61.0 + - + +
32A ARG* 3.8 1.6 - - - +
33A ILE* 2.9 45.4 + - + +
71A ILE* 4.8 3.4 - - + -
73A VAL* 3.6 26.9 - - + -
123A VAL* 3.9 35.0 - - + -
125A VAL* 4.5 10.8 - - + -
139A ILE* 4.7 3.8 - - + -
143A ILE* 4.1 18.2 - - + +
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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
----------------------------------------------------------
17A LEU* 3.9 21.3 - - + -
26A GLU* 3.0 26.0 + - + +
27A ALA* 4.3 2.7 - - - +
29A VAL* 1.3 78.6 - - + +
31A SER* 1.3 66.8 - - - +
33A ILE* 3.1 9.0 + - + +
34A ILE* 2.9 23.2 + - + +
46A THR* 4.0 9.2 - - + -
61A ASP* 4.1 23.3 - - + +
62A LEU* 3.8 42.0 - - + -
71A ILE* 5.8 1.6 - - + -
73A VAL* 5.3 1.3 - - + -
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Residues in contact with SER 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 4.7 14.8 - - - +
27A ALA* 2.7 25.2 + - - -
28A TYR* 3.1 2.3 + - - -
30A VAL* 1.3 78.8 - - - +
32A ARG* 1.3 59.4 + - - +
34A ILE* 3.4 5.1 + - - +
35A HIS* 2.9 40.2 + - - -
31B SER* 4.1 19.5 - - - -
35B HIS* 3.0 21.3 - - - -
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Residues in contact with ARG 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 2.9 23.0 + - + +
29A VAL 3.8 2.5 - - - +
31A SER* 1.3 78.2 + - - +
33A ILE* 1.3 61.8 + - - +
36A LEU* 2.9 62.7 + - + +
140A HIS* 3.3 54.1 + - - +
143A ILE* 4.1 17.7 - - + +
144A ASP* 4.6 4.8 + - - -
35B HIS* 3.5 50.0 + - + +
38B ASN* 3.3 34.4 + - - +
40B PHE* 4.6 2.6 - - - -
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Residues in contact with ILE 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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29A VAL* 2.9 28.3 + - + +
30A VAL* 3.5 7.2 - - - +
32A ARG* 1.3 76.5 - - - +
34A ILE* 1.3 65.9 + - + +
36A LEU* 3.9 0.9 - - - +
37A LEU* 2.9 28.6 + - + +
62A LEU* 3.7 20.9 - - + -
64A PHE* 4.6 1.3 - - + -
71A ILE* 3.7 37.5 - - + -
143A ILE* 3.5 28.7 - - + -
146A ILE* 4.2 11.4 - - + -
147A ILE* 4.2 8.3 - - + +
150A ILE* 4.3 20.6 - - + -
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Residues in contact with ILE 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A VAL* 5.5 0.9 - - + -
17A LEU* 4.4 16.8 - - + -
30A VAL* 2.9 26.5 + - + +
31A SER* 3.8 4.7 - - - +
33A ILE* 1.3 76.4 - - - +
35A HIS* 1.3 60.0 + - + +
37A LEU* 3.6 5.4 - - + +
38A ASN* 2.5 35.6 + - - -
40A PHE* 4.5 17.5 - - + -
44A PHE* 3.9 36.3 - - + -
62A LEU* 3.8 29.2 - - + -
64A PHE* 4.0 12.3 - - + -
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Residues in contact with HIS 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 4.5 3.7 - - + +
31A SER* 2.9 26.4 + - - +
32A ARG 4.2 1.6 - - - +
34A ILE* 1.3 84.9 - - + +
36A LEU* 1.3 62.4 + - + +
38A ASN* 3.1 23.4 - - - +
40A PHE* 5.7 1.1 - + - -
28B TYR* 3.3 38.3 - + - -
31B SER* 3.1 28.2 + - - -
32B ARG* 3.3 46.0 + - + +
35B HIS* 3.8 9.2 + - + -
36B LEU* 3.8 25.3 - - + +
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Residues in contact with LEU 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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32A ARG* 2.9 66.0 + - + +
35A HIS* 1.3 76.4 - - + +
37A LEU* 1.3 64.6 + - - +
38A ASN* 4.1 3.6 + - - -
143A ILE* 4.7 0.9 - - + -
144A ASP* 3.8 17.7 - - - +
147A ILE* 3.5 22.0 - - + +
151A LYS* 5.1 4.9 + - - -
35B HIS* 3.8 32.5 - - + +
36B LEU* 4.7 4.5 - - + -
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Residues in contact with LEU 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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33A ILE* 2.9 20.1 + - + +
34A ILE* 3.6 5.4 - - + +
36A LEU* 1.3 74.8 - - - +
38A ASN* 1.3 80.0 + - - +
39A ASP* 3.0 27.4 + - + +
42A LEU* 3.9 25.8 - - + -
64A PHE* 4.1 21.3 - - + -
147A ILE* 4.3 15.8 - - + +
150A ILE* 4.0 18.8 - - + -
151A LYS* 4.2 35.0 + - + +
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Residues in contact with ASN 38 (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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34A ILE* 2.5 18.6 + - - +
35A HIS* 3.1 19.3 - - - +
36A LEU 4.1 4.6 + - - -
37A LEU* 1.3 99.4 + - - +
39A ASP* 1.3 57.9 + - - +
40A PHE* 3.9 22.3 + - + -
32B ARG* 3.9 28.2 + - - +
140B HIS* 5.1 2.0 + - + -
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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