Contacts of the helix formed by residues 5 - 17 (chain B) 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 ALA 5 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A LYS* 5.2 10.5 - - - +
6B SER* 1.3 69.1 + - - +
7B SER* 3.2 10.8 + - - +
8B ASP* 2.9 29.4 + - - +
9B LEU* 4.3 1.4 + - - +
168B ILE* 5.1 1.9 - - - +
169B GLU* 2.9 32.3 + - - +
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Residues in contact with SER 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A ASN* 3.7 26.3 - - - +
136A LEU 5.1 1.4 + - - -
5B ALA* 1.3 78.9 - - - +
7B SER* 1.3 65.2 + - - +
8B ASP 3.1 2.7 - - - -
9B LEU* 3.0 25.2 + - - +
10B THR* 3.0 14.5 + - - -
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Residues in contact with SER 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A LYS* 4.4 10.8 + - - +
132A GLN* 3.5 15.3 + - - -
133A PRO* 3.3 37.7 - - - +
134A GLN 4.2 4.0 + - - -
135A ASN* 4.9 1.2 - - - +
5B ALA* 3.7 13.4 + - - +
6B SER* 1.3 80.0 - - - +
8B ASP* 1.3 60.3 + - - +
10B THR* 3.2 11.2 + - - -
11B ASP* 2.9 30.1 + - - +
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Residues in contact with ASP 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ALA 2.9 34.8 + - - +
6B SER 3.1 0.2 - - - -
7B SER* 1.3 81.3 + - - +
9B LEU* 1.3 59.3 + - - +
11B ASP* 3.5 6.6 + - - +
12B TYR* 2.9 31.5 + - - +
168B ILE* 3.7 24.1 - - + +
169B GLU* 3.5 10.1 - - - +
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Residues in contact with LEU 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LEU* 3.8 23.8 - - + +
5B ALA 4.3 0.8 + - - +
6B SER* 3.0 18.9 + - - +
8B ASP* 1.3 78.8 - - - +
10B THR* 1.3 64.9 + - - +
12B TYR* 3.2 3.5 + - - +
13B VAL* 2.9 38.9 + - + +
40B PHE* 4.5 19.7 - - + +
166B TRP* 3.6 38.4 - - + -
168B ILE* 4.2 14.3 - - + +
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Residues in contact with THR 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A TYR* 3.9 30.5 - - + +
133A PRO* 4.0 3.6 - - + -
134A GLN 2.6 28.8 + - - +
136A LEU* 3.3 40.2 + - + +
139A ILE* 4.7 4.9 - - + -
6B SER 3.0 9.6 + - - -
7B SER* 3.2 8.3 + - - -
9B LEU* 1.3 78.2 - - - +
11B ASP* 1.3 65.6 + - - +
13B VAL* 3.3 2.3 + - - +
14B ILE* 3.0 27.7 + - + +
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Residues in contact with ASP 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ARG* 2.7 29.0 + - - +
25A TYR* 4.6 4.5 + - - -
133A PRO* 4.6 10.4 - - + +
7B SER 2.9 19.3 + - - +
8B ASP* 3.8 6.5 - - - +
10B THR* 1.3 73.9 - - - +
12B TYR* 1.3 59.8 + - - +
14B ILE* 3.3 5.8 + - - +
15B ARG* 2.9 63.1 + - - +
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Residues in contact with TYR 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ASP 2.9 18.8 + - - +
9B LEU* 3.5 5.2 - - - +
11B ASP* 1.3 80.4 + - - +
13B VAL* 1.3 68.9 + - + +
15B ARG* 3.3 4.9 + - - +
16B GLN* 2.9 58.6 + - + +
43B LYS* 3.3 25.7 - - + -
44B PHE* 2.8 31.7 + + - -
45B VAL* 3.8 4.0 - - - +
166B TRP* 3.3 37.5 - + - -
168B ILE* 4.6 11.0 - - + -
172B TYR* 5.8 3.1 - - - -
278B ASN* 5.3 2.0 + - - -
279B LEU* 3.7 16.8 - - + -
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Residues in contact with VAL 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 3.8 28.5 - - + +
136A LEU* 3.8 14.4 - - + -
9B LEU* 2.9 40.0 + - + +
10B THR 3.6 3.8 - - - +
12B TYR* 1.3 80.2 - - + +
14B ILE* 1.3 63.2 + - + +
16B GLN* 3.1 2.6 + - - +
17B LEU* 3.0 27.4 + - + +
40B PHE* 4.1 19.7 - - + -
44B PHE* 4.0 26.7 - - + -
166B TRP* 5.2 0.2 - - + -
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Residues in contact with ILE 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ARG* 4.2 33.0 - - + +
25A TYR* 3.7 39.0 - - + +
28A TYR* 3.5 47.3 - - + -
136A LEU* 5.5 1.6 - - + -
139A ILE* 6.4 0.2 - - + -
10B THR* 3.0 25.4 + - + +
11B ASP* 3.6 6.1 - - - +
13B VAL* 1.3 74.7 - - + +
15B ARG* 1.3 60.1 + - - +
17B LEU* 3.2 6.1 + - - +
18B GLY* 2.9 26.7 + - - -
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Residues in contact with ARG 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ARG* 4.4 16.2 - - - +
11B ASP* 2.9 47.9 + - - +
12B TYR* 3.7 3.6 - - - +
13B VAL 3.2 0.2 - - - -
14B ILE* 1.3 76.3 - - - +
16B GLN* 1.3 62.9 + - - +
18B GLY* 3.2 11.6 + - - +
19B ARG* 3.5 15.6 + - - +
279B LEU* 3.6 37.3 - - + +
280B SER* 3.4 38.4 - - - +
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Residues in contact with GLN 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B TYR* 2.9 57.5 + - + +
13B VAL 3.1 4.4 + - - +
15B ARG* 1.3 76.5 - - - +
17B LEU* 1.3 60.3 + - - +
18B GLY 3.2 0.7 + - - -
19B ARG* 2.9 26.9 + - - +
44B PHE* 3.8 21.5 - - + +
45B VAL* 3.8 4.5 - - - +
46B THR* 2.7 50.3 + - + +
278B ASN* 3.2 16.2 + - - +
279B LEU* 3.2 23.7 - - + +
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Residues in contact with LEU 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ALA* 5.5 5.9 - - - +
28A TYR* 4.1 32.3 - - + -
13B VAL* 3.0 21.1 + - + +
14B ILE* 3.6 4.5 - - - +
16B GLN* 1.3 79.7 - - - +
18B GLY* 1.3 57.4 + - - +
19B ARG 3.6 1.3 - - - -
21B LYS* 3.4 18.8 + - - -
30B VAL* 4.1 17.3 - - + -
31B SER* 4.8 13.9 - - - -
34B ILE* 4.3 18.4 - - + -
35B HIS* 4.5 7.9 - - + +
44B PHE* 3.6 24.5 - - + -
46B THR* 4.0 8.7 - - + -
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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