Contacts of the helix formed by residues 6 - 17 (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 SER 6 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A ALA* 1.3 70.8 - - - +
7A SER* 1.3 61.8 + - - +
8A ASP* 3.2 3.4 - - - -
9A LEU* 3.4 32.2 + - - +
10A THR* 3.7 6.6 + - - -
127B LYS* 5.2 5.9 - - - +
135B ASN* 4.0 26.3 - - - +
136B LEU 5.2 0.7 + - - -
137B GLU* 4.9 6.7 + - - -
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Residues in contact with SER 7 (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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5A ALA* 4.0 7.4 - - - +
6A SER* 1.3 76.8 - - - +
8A ASP* 1.3 64.9 + - - +
9A LEU 3.2 0.2 - - - -
10A THR* 3.2 8.9 + - - -
11A ASP* 2.9 29.5 + - - +
127B LYS* 5.2 3.7 - - - +
132B GLN* 3.2 26.7 + - - +
133B PRO* 3.2 45.3 - - - +
134B GLN 4.8 0.7 - - - -
135B ASN* 5.3 0.6 - - - +
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Residues in contact with ASP 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ALA* 3.8 21.4 - - - +
6A SER 3.2 0.6 - - - -
7A SER* 1.3 79.8 + - - +
9A LEU* 1.3 60.4 + - - +
11A ASP* 3.4 6.8 + - - +
12A TYR* 2.9 30.5 + - - +
168A ILE* 3.6 28.5 - - + +
169A GLU* 6.0 0.7 - - - -
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Residues in contact with LEU 9 (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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6A SER* 3.4 23.4 + - - +
8A ASP* 1.3 78.7 - - - +
10A THR* 1.3 57.2 + - - +
12A TYR* 3.1 4.0 + - - +
13A VAL* 2.9 42.6 + - + +
40A PHE* 4.7 15.9 - - + +
166A TRP* 3.6 38.4 - - + -
168A ILE* 4.2 15.2 - - + +
136B LEU* 3.8 26.9 - - + +
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Residues in contact with THR 10 (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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6A SER 3.7 2.3 + - - -
7A SER* 3.2 10.8 + - - -
9A LEU* 1.3 77.8 - - - +
11A ASP* 1.3 63.8 + - - +
13A VAL* 3.4 0.9 + - - +
14A ILE* 2.9 30.9 + - + +
25B TYR* 3.7 32.8 - - + +
133B PRO* 4.0 4.9 - - + -
134B GLN 2.9 27.7 + - - +
135B ASN* 3.8 2.3 - - - -
136B LEU* 3.3 38.7 + - + +
139B ILE* 4.8 3.8 - - + -
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Residues in contact with ASP 11 (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 SER 2.9 16.5 + - - +
8A ASP* 3.8 7.9 - - - +
10A THR* 1.3 78.0 - - - +
12A TYR* 1.3 64.2 + - - +
14A ILE* 3.4 4.1 + - - +
15A ARG* 2.9 52.4 + - - +
24B ARG* 2.5 36.0 + - - +
25B TYR* 4.9 3.3 + - - -
133B PRO* 4.8 6.8 - - + +
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Residues in contact with TYR 12 (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 ASP 2.9 17.8 + - - +
9A LEU* 3.4 6.1 - - - +
11A ASP* 1.3 79.3 + - - +
13A VAL* 1.3 64.1 + - + +
15A ARG* 3.3 1.6 + - - +
16A GLN* 2.9 61.6 + - + +
43A LYS* 3.6 24.8 - - + -
44A PHE* 2.6 34.6 + + - -
45A VAL* 3.8 5.5 - - - +
166A TRP* 3.5 34.5 - + - -
168A ILE* 4.6 10.3 - - + -
171A GLU* 6.1 0.4 - - - -
172A TYR* 5.8 3.4 - - - -
278A ASN* 4.9 5.0 + - - -
279A LEU* 3.9 17.8 - - + +
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Residues in contact with VAL 13 (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 LEU* 2.9 35.9 + - + +
10A THR* 3.8 3.4 - - - +
12A TYR* 1.3 77.6 - - + +
14A ILE* 1.3 64.2 + - + +
16A GLN* 3.3 1.9 + - - +
17A LEU* 3.1 27.7 + - + +
34A ILE* 5.5 0.7 - - + -
40A PHE* 4.0 17.9 - - + -
44A PHE* 4.0 24.0 - - + -
166A TRP* 5.2 0.4 - - + -
28B TYR* 3.7 30.5 - - + +
136B LEU* 3.7 22.9 - - + -
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Residues in contact with ILE 14 (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 THR* 2.9 24.5 + - + +
11A ASP* 3.8 5.4 - - - +
13A VAL* 1.3 76.5 - - + +
15A ARG* 1.3 60.6 + - + +
17A LEU* 3.3 4.0 + - - +
18A GLY* 2.8 27.2 + - - -
24B ARG* 3.9 40.4 - - + +
25B TYR* 3.5 32.8 - - + -
28B TYR* 3.4 48.2 - - + -
136B LEU* 5.5 1.6 - - + -
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Residues in contact with ARG 15 (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 ASP* 2.9 43.3 + - - +
14A ILE* 1.3 76.5 - - + +
16A GLN* 1.3 64.3 + - - +
18A GLY* 3.3 10.5 + - - +
19A ARG* 3.6 17.0 + - - +
279A LEU* 3.7 35.4 - - + +
280A SER* 2.6 46.1 + - - +
24B ARG* 3.9 17.0 - - - +
31H T 4.9 9.1 + - - -
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Residues in contact with GLN 16 (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 TYR* 2.9 57.3 + - + +
13A VAL 3.8 1.1 - - - +
14A ILE 3.3 0.4 - - - -
15A ARG* 1.3 76.4 - - - +
17A LEU* 1.3 60.2 + - - +
18A GLY 3.2 0.8 + - - -
19A ARG* 2.8 28.5 + - - +
44A PHE* 3.8 23.1 - - + +
45A VAL* 3.6 2.1 - - - +
46A THR* 2.5 51.3 + - + +
278A ASN* 2.9 27.3 + - - -
279A LEU* 3.2 14.8 - - - +
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Residues in contact with LEU 17 (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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13A VAL* 3.1 23.0 + - + +
14A ILE* 3.5 3.6 - - - +
16A GLN* 1.3 80.6 - - - +
18A GLY* 1.3 57.0 + - - +
19A ARG 3.5 2.7 + - - +
27A ALA* 5.8 4.0 - - - +
30A VAL* 3.9 28.5 - - + -
31A SER* 4.7 14.8 - - - +
34A ILE* 4.4 17.7 - - + -
35A HIS* 4.5 8.5 - - + +
44A PHE* 4.2 15.9 - - + -
46A THR* 4.2 1.8 - - + -
27B ALA* 5.3 8.1 - - - +
28B TYR* 3.9 35.4 - - + -
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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