Contacts of the helix formed by residues 4 - 19 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3B PHE* 1.3 75.9 - - - +
5B ARG* 1.3 66.3 + - - +
6B SER* 3.2 10.5 + - - +
7B GLY* 3.3 8.1 + - - +
8B ARG* 3.0 20.9 + - - +
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Residues in contact with ARG 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ARG* 4.3 17.9 - - - +
6A SER* 5.5 0.7 - - - +
4B ARG* 1.3 73.0 - - - +
6B SER* 1.3 66.8 + - - +
8B ARG* 3.3 27.5 + - - +
9B LEU* 3.0 37.3 + - + +
39B SER* 4.3 2.6 + - - -
42B GLU* 4.4 14.6 + - - +
43B ASP* 2.3 43.8 + - - +
46B ILE* 3.4 28.9 - - - +
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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
----------------------------------------------------------
5A ARG* 3.9 18.7 + - - -
9A LEU* 3.6 19.1 - - - +
46A ILE* 3.8 25.2 - - - +
4B ARG* 3.2 8.0 - - - +
5B ARG* 1.3 82.0 - - - +
7B GLY* 1.3 62.4 + - - +
9B LEU* 3.3 7.7 + - - +
10B VAL* 3.2 25.3 + - - +
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Residues in contact with GLY 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ILE* 4.3 3.0 - - - +
50A THR* 3.5 27.0 - - - +
3B PHE* 4.0 11.4 - - - -
4B ARG* 3.3 12.3 + - - +
6B SER* 1.3 76.5 - - - +
8B ARG* 1.3 59.7 + - - +
10B VAL* 3.3 1.6 + - - -
11B ASP* 2.9 31.4 + - - +
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Residues in contact with ARG 8 (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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2B LYS* 5.8 0.2 - - - +
3B PHE* 4.0 20.2 + - + -
4B ARG 3.0 12.1 + - - +
5B ARG* 3.3 31.7 - - - +
7B GLY* 1.3 76.7 - - - +
9B LEU* 1.3 56.9 + - - +
11B ASP* 3.8 1.0 - - - +
12B LEU* 2.9 34.4 + - + +
33B TYR* 3.4 51.1 + - + -
35B SER* 2.9 28.2 + - - -
39B SER* 4.0 18.3 - - - -
40B ILE* 4.0 5.6 - - - +
43B ASP* 2.5 39.4 + - - +
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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
----------------------------------------------------------
6A SER* 3.7 36.6 - - - +
9A LEU* 4.7 14.1 - - + -
10A VAL* 4.3 8.7 - - + -
5B ARG* 3.0 35.0 + - + +
6B SER* 3.7 5.4 - - - +
8B ARG* 1.3 76.1 - - - +
10B VAL* 1.3 55.6 + - + +
12B LEU* 3.9 3.6 - - - +
13B THR* 2.7 38.0 + - - -
43B ASP* 3.8 39.0 - - + +
46B ILE* 4.2 12.8 - - + -
47B ILE* 4.1 14.6 - - + +
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Residues in contact with VAL 10 (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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9A LEU* 4.1 17.9 - - + +
13A THR* 3.7 26.3 - - - +
46A ILE* 4.4 6.7 - - + -
47A ILE* 3.8 21.1 - - + -
50A THR* 3.8 21.8 - - + +
51A PHE* 3.9 22.9 - - + -
56A ILE* 5.6 0.2 - - + -
6B SER 3.2 15.4 + - - +
7B GLY 3.6 6.3 - - - +
8B ARG 3.2 1.0 - - - -
9B LEU* 1.3 76.9 - - - +
11B ASP* 1.3 64.5 + - - +
13B THR* 3.4 3.5 + - - -
14B ASN* 3.0 21.5 + - - +
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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
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50A THR* 4.1 11.0 - - + +
54A GLN* 3.2 29.4 - - - +
56A ILE* 4.5 5.9 - - - +
3B PHE* 4.2 3.6 - - + -
7B GLY 2.9 16.3 + - - +
8B ARG 4.0 1.6 - - - +
10B VAL* 1.3 79.3 - - - +
12B LEU* 1.3 51.2 + - - +
14B ASN* 3.2 7.5 + - - +
15B TYR* 2.7 33.1 + - - +
32B ARG* 2.8 32.8 + - - -
33B TYR* 2.5 33.6 + - + +
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Residues in contact with LEU 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ARG* 2.9 17.7 + - + +
9B LEU* 3.9 0.7 - - - +
11B ASP* 1.3 72.7 - - - +
13B THR* 1.3 61.3 + - - +
15B TYR* 3.7 2.2 - - - -
16B LEU* 2.8 40.4 + - + +
29B PHE* 3.5 45.1 - - + -
33B TYR* 3.3 20.5 + - + +
40B ILE* 4.5 7.2 - - + -
43B ASP* 3.7 33.2 - - + +
44B LEU* 3.8 28.0 - - + -
47B ILE* 3.8 12.3 - - + -
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Residues in contact with THR 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 3.5 43.7 - - + +
13A THR* 3.9 19.5 - - + -
14A ASN* 4.4 0.9 - - - +
9B LEU 2.7 23.8 + - - -
10B VAL 3.5 4.9 - - - -
12B LEU* 1.3 77.0 - - - +
14B ASN* 1.3 62.5 + - - +
16B LEU* 3.8 4.9 - - - +
17B LEU* 3.0 39.6 + - + +
47B ILE* 3.9 8.5 - - - +
51B PHE* 4.0 15.0 - - + -
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Residues in contact with ASN 14 (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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13A THR* 4.4 2.4 - - + +
17A LEU* 3.3 38.7 - - + +
51A PHE* 5.0 0.4 - - + -
56A ILE* 3.5 39.6 - - + +
10B VAL 3.0 12.9 + - - +
11B ASP* 3.5 9.3 + - - +
13B THR* 1.3 76.6 - - - +
15B TYR* 1.3 69.6 + - - +
17B LEU* 3.2 1.6 + - - -
18B THR* 2.9 44.5 + - - +
32B ARG* 6.0 1.0 - - - +
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Residues in contact with TYR 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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11B ASP* 2.7 23.2 + - - +
12B LEU* 3.8 4.0 - - - +
14B ASN* 1.3 78.0 - - - +
16B LEU* 1.3 61.8 + - - +
18B THR* 3.2 4.5 + - - -
19B HIS* 2.8 66.8 + + - +
22B GLU* 5.0 4.0 + - - -
24B ILE* 3.7 24.2 - - + +
28B PHE* 3.5 35.9 - + - -
29B PHE* 3.7 28.3 - + + -
32B ARG* 3.9 25.8 - - - -
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Residues in contact with LEU 16 (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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12B LEU* 2.8 28.4 + - + +
13B THR* 3.8 3.4 - - - +
15B TYR* 1.3 72.7 - - - +
17B LEU* 1.3 63.0 + - - +
19B HIS 3.1 18.8 + - - +
24B ILE* 4.3 13.9 - - + -
29B PHE* 4.6 4.5 - - + -
44B LEU* 3.9 22.9 - - + -
47B ILE* 3.9 28.0 - - + -
51B PHE* 4.7 4.5 - - + -
59B LEU* 4.0 9.0 - - + -
69B VAL* 4.0 30.3 - - + -
71B TYR* 3.2 38.6 - - + +
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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
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14A ASN* 3.3 37.0 - - + +
17A LEU* 3.7 28.3 - - + -
18A THR* 5.5 2.5 - - + -
13B THR* 3.0 30.3 + - + +
14B ASN* 3.7 4.0 - - - +
16B LEU* 1.3 76.8 - - - +
18B THR* 1.3 62.9 + - + +
20B PRO* 3.5 12.1 - - - +
51B PHE* 3.7 23.3 - - + -
56B ILE* 4.1 2.2 - - + -
71B TYR* 3.8 30.4 - - + +
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Residues in contact with THR 18 (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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17A LEU* 5.7 2.0 - - + -
151A TYR* 5.9 2.5 - - - +
14B ASN* 2.9 38.9 + - - +
15B TYR* 3.2 2.9 + - - -
17B LEU* 1.3 78.4 - - + +
19B HIS* 1.3 85.6 + - - +
20B PRO* 3.3 8.2 - - - +
153B ASN* 5.9 0.9 + - - -
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Residues in contact with HIS 19 (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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117A LYS* 6.4 0.4 - - - -
15B TYR* 2.8 67.7 + + - +
16B LEU 3.1 7.9 + - - +
18B THR* 1.3 98.7 + - - +
20B PRO* 1.3 66.6 - - - +
22B GLU* 3.5 41.8 + - - +
24B ILE* 4.3 15.9 - - + +
71B TYR* 4.9 3.5 + - - +
153B ASN* 5.8 2.5 - - - +
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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