Contacts of the helix formed by residues 4 - 20 (chain B) in PDB entry 3PL7
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 4 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ASN* 1.3 68.0 + - - +
6B ARG* 3.2 12.1 - - - +
7B GLU* 3.6 32.3 + - - +
8B LEU* 3.1 24.6 + - - +
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Residues in contact with ASN 5 (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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4B SER* 1.3 76.2 + - - +
6B ARG* 1.3 64.5 + - - +
8B LEU* 3.3 9.3 + - - +
9B VAL* 3.0 26.1 + - - +
171B ALA* 4.9 2.7 - - + +
174B LEU* 3.4 36.1 - - + +
175B ASN* 2.8 39.8 + - - +
179B GLU* 3.4 27.0 + - - +
182B ILE* 5.7 0.9 - - - +
188B TRP* 4.3 14.6 + - - -
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Residues in contact with ARG 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B SER 3.2 7.9 - - - +
5B ASN* 1.3 80.3 - - - +
7B GLU* 1.3 57.9 + - + +
9B VAL* 3.3 4.3 + - + +
10B VAL* 2.9 54.1 + - - +
24B TRP* 4.4 9.1 - - - +
28B SER* 4.2 16.8 + - - -
29B ASP* 5.5 2.8 + - - -
164B SER* 5.2 6.9 + - - -
167B ALA* 5.1 9.5 + - - +
168B ALA* 5.7 7.5 - - - +
171B ALA* 4.2 23.4 - - + +
175B ASN* 5.5 1.0 - - - +
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Residues in contact with GLU 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B SER* 3.4 27.9 + - - +
5B ASN 3.2 0.8 - - - -
6B ARG* 1.3 76.0 - - + +
8B LEU* 1.3 61.3 + - - +
10B VAL* 3.9 5.2 - - - +
11B ASP* 2.9 33.4 + - - +
83B SER* 6.1 0.9 - - - -
87B LYS* 4.4 21.1 + - - +
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Residues in contact with LEU 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B SER 3.1 15.4 + - - +
5B ASN* 3.4 14.6 - - - +
7B GLU* 1.3 77.0 - - - +
9B VAL* 1.3 63.3 - - - +
11B ASP* 3.3 5.2 + - + +
12B PHE* 3.1 25.0 + - + +
86B VAL* 3.8 22.9 - - + -
87B LYS* 4.1 24.3 - - + +
90B LEU* 4.0 17.5 - - + -
144B PHE* 4.6 9.4 - - + -
174B LEU* 5.2 1.3 - - + -
188B TRP* 3.6 48.9 - - + +
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Residues in contact with VAL 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ASN 3.0 16.9 + - - +
6B ARG* 3.3 10.7 + - + +
8B LEU* 1.3 76.0 - - - +
10B VAL* 1.3 60.4 + - + +
12B PHE* 3.4 1.2 + - - +
13B LEU* 3.0 38.3 + - + +
143B PHE* 5.7 0.7 - - + -
144B PHE* 4.1 22.2 - - + -
167B ALA* 3.5 37.9 - - + +
170B MET* 4.0 15.3 - - + -
171B ALA* 4.0 22.0 - - + +
174B LEU* 4.3 7.4 - - + -
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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
----------------------------------------------------------
6B ARG* 2.9 56.6 + - - +
7B GLU* 3.9 5.2 - - - +
9B VAL* 1.3 73.9 - - + +
11B ASP* 1.3 67.8 + - - +
13B LEU* 4.2 3.5 - - - +
14B SER* 2.9 30.5 + - - -
24B TRP* 3.6 39.8 - - + +
167B ALA* 4.8 4.5 - - + -
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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
----------------------------------------------------------
7B GLU 2.9 19.1 + - - +
8B LEU* 3.6 4.7 - - - +
10B VAL* 1.3 76.8 - - - +
12B PHE* 1.3 60.6 + - - +
14B SER* 3.6 5.2 - - - -
15B TYR* 3.0 28.1 + - - +
84B GLU* 4.7 1.6 - - - +
87B LYS* 3.4 51.2 + - + +
91B ARG* 3.4 35.8 + - - +
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Residues in contact with PHE 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU 3.1 14.1 + - - +
9B VAL 3.9 2.2 - - - +
11B ASP* 1.3 82.5 - - - +
13B LEU* 1.3 76.2 + - + +
15B TYR* 3.3 5.0 + + - +
16B LYS* 3.0 52.6 + - + +
90B LEU* 3.5 46.7 - - + -
91B ARG* 4.3 11.2 - - + -
94B GLY* 4.2 13.2 - - - -
144B PHE* 3.3 55.2 - + + -
145B SER* 4.2 5.2 - - - -
148B GLY* 4.4 5.8 - - - -
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Residues in contact with LEU 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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9B VAL* 3.0 23.0 + - + +
10B VAL 4.2 0.4 - - - +
12B PHE* 1.3 84.0 - - + +
14B SER* 1.3 64.0 + - - +
16B LYS* 3.2 3.5 + - - +
17B LEU* 2.9 32.6 + - + +
24B TRP* 3.9 15.3 - - + -
147B GLY 4.1 2.2 - - - -
148B GLY* 3.6 35.0 - - - +
151B CYS* 3.7 26.7 - - + -
167B ALA* 3.6 37.5 - - + -
170B MET* 3.9 10.5 - - + -
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Residues in contact with SER 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B VAL* 2.9 23.4 + - - -
11B ASP* 3.6 5.8 - - - -
13B LEU* 1.3 77.4 - - - +
15B TYR* 1.3 58.1 + - - +
17B LEU* 3.5 3.8 + - - +
18B SER* 3.0 31.2 + - - -
22B TYR 4.8 0.5 - - - +
24B TRP* 3.6 34.8 + - - +
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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 3.0 18.1 + - - +
12B PHE* 3.7 4.5 - + - +
13B LEU 3.2 0.2 - - - -
14B SER* 1.3 74.2 - - - +
16B LYS* 1.3 76.8 + - + +
18B SER* 2.8 23.8 + - - -
19B GLN* 3.1 33.3 + - + +
88B GLN* 6.2 1.1 - - - -
91B ARG* 3.6 59.5 + - + +
95B ASP* 2.6 38.4 + - - -
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Residues in contact with LYS 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 PHE* 3.0 48.9 + - + +
13B LEU* 3.7 5.8 - - - +
15B TYR* 1.3 86.3 - - + +
17B LEU* 1.3 62.6 + - + +
19B GLN* 3.3 29.7 + - - +
20B LYS* 3.4 19.1 - - - +
94B GLY 3.9 11.5 + - - -
95B ASP* 3.1 34.4 + - - +
98B GLU* 2.5 33.1 + - - +
145B SER* 5.7 1.9 + - - +
148B GLY* 4.9 17.3 - - - +
152B VAL* 4.9 5.2 - - + -
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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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13B LEU* 2.9 22.9 + - + +
14B SER* 3.7 4.0 - - - +
16B LYS* 1.3 75.3 - - + +
18B SER* 1.3 64.2 + - - +
20B LYS* 2.9 18.2 + - - +
21B GLY 3.0 0.7 + - - -
22B TYR* 2.9 36.4 + - + +
24B TRP* 3.8 29.2 - - + +
27B PHE* 3.7 39.0 - - + -
151B CYS* 4.4 22.0 - - + +
152B VAL* 4.8 7.0 - - + -
155B VAL* 4.3 13.5 - - + -
163B VAL* 4.3 5.6 - - + -
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Residues in contact with SER 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 SER* 3.0 18.5 + - - -
15B TYR* 2.8 27.2 + - - -
17B LEU* 1.3 77.2 - - - +
19B GLN* 1.3 55.8 + - - +
21B GLY* 2.8 22.0 + - - -
22B TYR 3.2 14.8 + - - +
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Residues in contact with GLN 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 TYR* 3.1 34.5 + - + +
16B LYS* 3.3 28.3 + - - +
18B SER* 1.3 82.9 + - - +
20B LYS* 1.3 72.5 + - + +
21B GLY 3.2 0.4 + - - -
95B ASP* 3.1 31.8 + - - +
98B GLU* 5.4 0.3 - - - -
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Residues in contact with LYS 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 LYS* 3.4 20.2 - - - +
17B LEU 2.9 7.8 + - - +
19B GLN* 1.3 89.8 + - + +
21B GLY* 1.3 59.4 + - - +
22B TYR* 3.6 24.0 - - + -
98B GLU* 2.8 34.5 + - - -
152B VAL* 4.0 33.7 - - + -
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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