Contacts of the helix formed by residues 12 - 24 (chain B) in PDB entry 1PH3
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 12 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281A THR* 3.9 6.5 - - - +
10B GLN* 2.8 24.3 - - - +
11B GLN* 1.3 75.5 - - - +
13B ALA* 1.3 64.7 + - - +
15B LYS* 3.1 19.8 + - - -
16B GLN* 3.1 17.4 + - - +
54B ASP* 2.8 15.7 + - - -
56B TYR* 3.7 13.2 - - - -
57B PHE* 3.1 25.0 - - - -
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Residues in contact with ALA 13 (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 GLN 3.3 6.3 + - - +
12B SER* 1.3 72.5 - - - +
14B PHE* 1.3 68.5 + - + +
16B GLN* 3.4 8.3 + - - +
17B LEU* 3.0 30.1 + - + +
35B LEU* 6.1 0.2 - - - +
39B LEU* 4.9 14.8 - - + -
54B ASP* 3.1 17.5 + - + +
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Residues in contact with PHE 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B SER* 4.1 0.9 - - - +
13B ALA* 1.3 76.2 - - + +
15B LYS* 1.3 57.2 + - - +
17B LEU* 3.1 10.0 + - + -
18B TYR* 2.9 43.8 + + + +
39B LEU* 4.4 24.9 - - + -
41B CYS* 4.1 16.2 - - + -
52B VAL* 3.7 17.9 - - + -
53B THR 3.6 4.3 - - - -
54B ASP* 2.7 52.1 + - + +
57B PHE* 3.6 12.3 - - + -
59B VAL* 3.5 46.2 - - + -
116B LEU* 5.2 4.7 - - + -
138B LEU* 4.1 5.4 - - + -
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Residues in contact with LYS 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A THR* 3.0 23.9 + - - +
282A SER* 3.6 6.5 + - - -
10B GLN* 3.6 15.7 - - - +
12B SER* 3.1 22.8 + - - +
14B PHE* 1.3 75.7 - - - +
16B GLN* 1.3 57.1 + - - +
18B TYR* 3.8 0.7 - - - +
19B THR* 2.6 46.4 + - - +
57B PHE* 3.7 22.2 - - + -
138B LEU* 3.9 18.1 - - + +
141B ASP* 2.9 26.5 + - - +
143B GLU* 2.7 36.9 + - - +
144B PHE* 4.6 4.9 - - + +
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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
----------------------------------------------------------
10B GLN* 3.5 44.5 + - + +
12B SER 3.1 11.3 + - - +
13B ALA* 3.8 7.3 - - - +
15B LYS* 1.3 76.6 - - - +
17B LEU* 1.3 63.7 + - + +
19B THR* 3.7 5.1 - - - -
20B GLU* 3.1 41.6 + - + +
35B LEU* 3.7 27.0 - - + +
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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
----------------------------------------------------------
13B ALA* 3.0 25.2 + - + +
14B PHE* 3.1 8.5 + - + +
16B GLN* 1.3 78.7 - - + +
18B TYR* 1.3 68.6 + - + +
20B GLU* 3.4 3.6 + - - +
21B LEU* 3.1 22.5 + - - +
28B PHE* 5.9 1.1 - - + -
31B VAL* 4.6 8.9 - - + +
35B LEU* 3.4 46.7 - - + +
36B LYS* 6.3 0.2 - - + -
39B LEU* 4.3 25.1 - - + -
93B TRP* 3.8 28.3 - - + -
95B LEU* 4.0 18.1 - - + +
116B LEU* 6.1 0.4 - - + -
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Residues in contact with TYR 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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14B PHE* 2.9 35.1 + + + +
15B LYS 4.2 0.4 - - - +
17B LEU* 1.3 80.1 - - + +
19B THR* 1.3 61.8 + - - +
21B LEU* 3.5 7.3 + - - +
22B PHE* 3.2 29.1 + - - -
59B VAL* 3.5 32.5 - - + +
60B ALA 5.1 0.9 + - - -
95B LEU* 4.1 21.5 - - + -
114B ALA* 3.1 40.1 + - + -
116B LEU* 3.2 32.1 + - + +
138B LEU* 3.6 15.3 - - + -
139B PHE* 4.1 16.6 - + - -
144B PHE* 3.5 17.3 - + + -
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Residues in contact with THR 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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15B LYS* 2.6 36.2 + - - +
16B GLN* 3.7 6.7 - - - +
17B LEU 3.2 0.2 - - - -
18B TYR* 1.3 75.5 - - - +
20B GLU* 1.3 61.9 + - + +
22B PHE* 3.2 4.9 + - - +
23B ASN* 2.9 46.6 + - - +
144B PHE* 3.7 18.7 - - - +
147B THR* 4.1 17.4 + - - +
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Residues in contact with GLU 20 (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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16B GLN* 3.1 27.2 + - + +
17B LEU 3.9 0.4 - - - +
19B THR* 1.3 80.0 - - + +
21B LEU* 1.3 66.3 + - - +
23B ASN* 3.1 7.2 + - + +
24B ASN* 2.8 41.0 + - - +
31B VAL* 3.3 15.0 - - + +
32B SER* 2.8 37.8 + - - -
35B LEU* 3.2 25.7 - - - +
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Residues in contact with LEU 21 (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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17B LEU 3.1 16.5 + - - +
18B TYR* 3.6 5.8 - - - +
20B GLU* 1.3 76.2 - - - +
22B PHE* 1.3 60.6 + - - +
24B ASN* 3.2 9.5 + - - +
26B GLY* 2.9 58.1 + - - +
27B ASP 4.1 0.7 - - - -
28B PHE* 3.8 28.0 - - + +
31B VAL* 4.7 6.3 - - + +
95B LEU* 3.9 29.8 - - + +
96B GLU* 4.2 9.0 - - - +
97B LEU* 3.6 23.3 - - + -
114B ALA* 3.8 17.5 - - + -
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Residues in contact with PHE 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B TYR 3.2 18.6 + - - +
19B THR 3.2 8.5 + - - +
21B LEU* 1.3 74.4 - - - +
23B ASN* 1.3 59.7 + - - +
24B ASN 3.0 9.8 + - - -
25B GLU 3.4 5.4 + - - -
26B GLY* 4.6 2.0 - - - +
97B LEU* 3.8 31.0 - - + -
112B LEU* 4.4 18.6 - - + -
113B GLU 4.8 0.4 - - - -
114B ALA* 3.9 22.4 - - + -
139B PHE* 4.6 1.3 - + - -
144B PHE* 3.6 22.9 - + - -
147B THR* 3.9 15.5 - - + +
148B ILE* 3.5 36.1 - - + -
151B PHE* 3.3 54.1 - + + +
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Residues in contact with ASN 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B THR* 2.9 38.6 + - - +
20B GLU* 3.5 8.5 - - + +
22B PHE* 1.3 75.6 - - - +
24B ASN* 1.3 65.5 + - - +
25B GLU 3.6 1.7 + - - -
147B THR* 3.7 17.9 + - - +
150B HIS* 4.4 15.7 + - - -
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Residues in contact with ASN 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B GLU* 2.8 43.4 + - - +
21B LEU* 3.9 2.2 - - - +
22B PHE 3.0 1.0 - - - -
23B ASN* 1.3 84.9 - - - +
25B GLU* 1.3 64.3 + - - +
26B GLY 3.1 2.5 - - - -
27B ASP* 2.7 34.1 + - - +
30B LYS* 4.0 40.1 + - + +
31B VAL* 4.5 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