Contacts of the helix formed by residues 4 - 18 (chain A) in PDB entry 1P4A
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 ARG 4 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A LYS 4.3 0.6 + - - -
3A PHE* 1.3 78.5 - - - +
5A ARG* 1.3 69.6 + - - +
6A SER* 2.9 41.9 + - - +
7A GLY* 3.3 5.9 + - - +
8A ARG* 3.0 16.3 + - - +
5B ARG* 4.3 19.0 - - - +
46B ILE* 4.8 10.3 - - - +
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Residues in contact with ARG 5 (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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3A PHE 3.9 0.6 + - - -
4A ARG* 1.3 81.1 - - + +
6A SER* 1.3 60.1 + - - +
8A ARG* 3.0 36.1 + - - +
9A LEU* 2.9 42.0 + - - +
42A GLU* 5.0 5.5 + - - +
43A ASP* 3.7 15.7 + - - +
46A ILE* 2.7 37.1 - - - +
6B SER* 3.9 12.0 + - - -
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Residues in contact with SER 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ARG* 2.9 43.4 + - - +
5A ARG* 1.3 82.3 - - - +
7A GLY* 1.3 62.4 + - - +
9A LEU* 3.2 15.8 + - - +
10A VAL* 3.2 17.3 + - - +
5B ARG* 4.6 2.3 + - - +
9B LEU* 3.7 21.3 - - - +
46B ILE* 3.9 23.0 - - - +
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Residues in contact with GLY 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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3A PHE* 4.4 8.3 - - - -
4A ARG* 3.3 10.8 + - - +
6A SER* 1.3 78.1 - - - +
8A ARG* 1.3 56.7 + - - +
10A VAL* 3.4 1.7 + - - -
11A ASP* 2.8 31.9 + - - +
46B ILE* 4.4 3.0 - - - +
50B THR* 3.3 29.2 - - - +
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Residues in contact with ARG 8 (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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3A PHE* 4.3 18.4 + - + +
4A ARG 3.0 13.0 + - - +
5A ARG* 3.0 31.2 + - - +
7A GLY* 1.3 75.5 - - - +
9A LEU* 1.3 65.7 + - - +
12A LEU* 2.9 30.0 + - + +
33A TYR* 3.5 48.2 - - + -
35A SER* 3.0 24.6 + - - -
39A SER* 4.1 15.9 + - - -
40A ILE* 3.6 13.2 - - - +
43A ASP* 2.7 37.4 + - - +
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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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5A ARG* 2.9 29.6 + - - +
6A SER* 3.2 9.6 + - - +
8A ARG* 1.3 75.7 - - - +
10A VAL* 1.3 62.6 + - + +
12A LEU* 3.7 3.5 - - - +
13A THR* 2.8 30.8 + - - -
43A ASP* 3.8 36.0 + - + +
46A ILE* 4.4 6.3 - - + -
47A ILE* 4.0 19.7 - - + +
6B SER* 3.6 46.0 - - - +
9B LEU* 4.7 11.2 - - + -
10B VAL* 4.1 10.8 - - + -
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Residues in contact with VAL 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 3.2 14.9 + - - +
7A GLY 3.8 5.6 - - - +
8A ARG 3.2 0.4 - - - -
9A LEU* 1.3 73.7 - - - +
11A ASP* 1.3 65.4 + - - +
13A THR* 3.2 5.2 + - - -
14A ASN* 3.0 21.2 + - - +
9B LEU* 4.3 17.7 - - + -
13B THR* 3.5 26.8 - - + +
46B ILE* 4.4 6.7 - - + -
47B ILE* 3.9 22.2 - - + -
50B THR* 4.1 14.1 - - + -
51B PHE* 3.6 30.7 - - + -
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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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3A PHE* 4.3 4.0 - - + -
7A GLY 2.8 22.2 + - - +
8A ARG 4.0 1.6 - - - +
10A VAL* 1.3 73.6 - - - +
12A LEU* 1.3 56.9 + - - +
14A ASN* 3.2 8.4 + - - +
15A TYR* 2.8 27.2 + - - +
32A ARG* 3.0 27.6 + - - -
33A TYR* 2.6 31.1 + - + +
50B THR* 4.0 11.6 - - + +
54B GLN* 3.1 34.3 - - - +
56B ILE* 4.5 6.3 - - - +
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Residues in contact with LEU 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 ARG* 2.9 18.7 + - + +
9A LEU* 3.7 4.3 - - - +
11A ASP* 1.3 75.0 - - - +
13A THR* 1.3 65.4 + - - +
15A TYR* 3.2 2.9 + - - +
16A LEU* 2.9 32.1 + - + +
29A PHE* 3.6 45.1 - - + -
33A TYR* 3.3 21.9 + - + +
40A ILE* 4.7 5.8 - - + -
43A ASP* 3.7 32.8 - - + +
44A LEU* 4.0 18.8 - - + -
47A ILE* 3.8 14.6 - - + -
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Residues in contact with THR 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 2.8 19.9 + - - -
10A VAL 3.5 4.7 - - - -
12A LEU* 1.3 77.2 - - - +
14A ASN* 1.3 64.6 + - - +
16A LEU* 3.4 5.3 + - - +
17A LEU* 3.0 48.5 + - + +
47A ILE* 3.8 9.2 - - - +
51A PHE* 4.0 15.9 - - + -
10B VAL* 3.7 41.3 - - + +
13B THR* 3.9 12.6 - - + -
14B ASN 4.4 0.2 - - - +
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Residues in contact with ASN 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 VAL 3.0 13.1 + - - +
11A ASP* 3.2 10.1 + - - +
13A THR* 1.3 77.3 - - - +
15A TYR* 1.3 66.3 + - - +
17A LEU* 3.4 1.2 + - - +
18A THR* 2.8 45.2 + - - +
32A ARG* 6.2 0.2 - - - +
13B THR* 4.4 3.3 - - + +
17B LEU* 3.3 38.5 - - + +
51B PHE* 5.0 0.9 - - + -
56B ILE* 3.5 39.9 - - + +
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Residues in contact with TYR 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* 2.8 21.0 + - - +
12A LEU* 3.2 7.6 + - - +
14A ASN* 1.3 82.9 - - - +
16A LEU* 1.3 60.8 + - - +
18A THR* 3.2 3.8 + - - -
19A HIS* 2.8 67.6 + + - +
22A GLU* 5.5 0.2 + - - -
24A ILE* 3.6 31.6 - - + +
28A PHE* 3.3 39.3 - + - -
29A PHE* 3.8 17.5 - + + -
32A ARG* 4.0 25.6 - - - +
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Residues in contact with LEU 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 LEU* 2.9 24.3 + - + +
13A THR* 3.9 3.1 - - - +
15A TYR* 1.3 74.6 - - - +
17A LEU* 1.3 64.0 + - - +
19A HIS 3.0 17.0 + - - +
24A ILE* 4.0 24.2 - - + -
29A PHE* 4.2 6.7 - - + -
44A LEU* 4.1 11.2 - - + -
47A ILE* 3.9 32.8 - - + -
51A PHE* 4.5 5.6 - - + -
59A LEU* 3.9 29.6 - - + -
69A VAL* 4.1 14.8 - - + -
71A TYR* 3.3 30.6 - - + +
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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 THR* 3.0 36.5 + - + +
14A ASN* 3.8 4.0 - - - +
16A LEU* 1.3 76.8 - - - +
18A THR* 1.3 62.6 + - + +
20A PRO* 3.6 13.0 - - - +
51A PHE* 3.7 21.1 - - + -
56A ILE* 4.0 2.7 - - + -
71A TYR* 3.9 28.8 - - + +
14B ASN* 3.3 34.3 - - + +
17B LEU* 3.7 27.8 - - + -
18B THR* 5.7 2.2 - - + -
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Residues in contact with THR 18 (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 ASN* 2.8 37.5 + - - +
15A TYR* 3.2 9.7 + - - -
17A LEU* 1.3 77.6 - - + +
19A HIS* 1.3 75.6 + - - +
20A PRO* 3.2 9.8 - - - +
22A GLU* 5.2 0.2 - - - +
153A ASN* 5.8 0.9 + - - -
17B LEU* 5.5 2.5 - - + -
151B TYR* 6.1 1.6 - - - +
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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