Contacts of the helix formed by residues 41 - 53 (chain F) in PDB entry 3ZPL
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 PRO 41 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31F ASP* 4.1 11.9 - - - +
34F LEU* 4.6 1.3 - - - -
35F GLN* 3.6 24.0 - - - +
40F MET* 1.3 96.8 - - + +
42F HIS* 1.3 67.0 + - - +
43F VAL* 3.3 6.4 + - + +
44F TYR* 3.4 39.7 + - + +
45F TYR* 3.3 17.0 + - - +
81F ARG* 4.1 5.4 - - - +
12G T 4.3 16.6 - - - +
13G C 5.5 1.6 - - - +
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Residues in contact with HIS 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E TRP* 4.3 4.4 + + - -
20E ILE* 3.6 36.9 - - + +
27F GLU* 5.4 5.3 - - - +
30F LEU* 4.2 19.3 - - + +
31F ASP* 2.9 31.8 + - - +
34F LEU* 3.6 28.0 - - + -
41F PRO* 1.3 71.6 - - - +
43F VAL* 1.3 66.0 + - + +
45F TYR* 3.4 6.2 + + - +
46F GLY* 3.1 19.9 + - - -
119F HIS* 3.7 20.7 + + - -
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Residues in contact with VAL 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E THR* 6.2 3.1 - - + -
31F ASP* 5.6 1.8 - - - +
41F PRO* 3.3 4.8 - - + +
42F HIS* 1.3 78.9 - - + +
44F TYR* 1.3 70.2 + - + +
46F GLY* 3.2 4.6 + - - -
47F LEU* 3.2 24.4 + - + +
68F ALA* 5.4 3.1 - - + +
70F ILE* 4.2 27.6 - - + -
74F ARG* 3.5 33.0 - - - +
13G C 4.1 7.4 - - - +
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Residues in contact with TYR 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F MET* 4.0 12.1 - - - -
41F PRO* 3.4 32.7 + - + +
42F HIS 3.3 0.2 - - - -
43F VAL* 1.3 78.9 - - + +
45F TYR* 1.3 57.7 + - - +
47F LEU* 2.7 33.2 + - + +
48F LEU* 3.2 12.4 + - - +
74F ARG* 5.9 0.2 - - - -
77F HIS* 4.7 2.3 + - - +
78F ALA* 3.4 36.5 + - + -
81F ARG* 3.6 37.5 - - + +
82F LEU* 3.9 22.1 - - + +
12G T 3.5 27.8 + - - +
13G C 3.2 29.3 + - - -
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Residues in contact with TYR 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A TRP* 5.0 1.0 - - - -
34F LEU* 3.6 27.4 - - + -
38F ALA* 5.0 0.4 - - + -
40F MET* 3.5 33.6 - - + -
41F PRO 3.3 10.1 + - - +
42F HIS* 3.6 11.2 - + - +
44F TYR* 1.3 76.5 - - - +
46F GLY* 1.3 63.6 + - - +
48F LEU* 3.2 6.1 + - - +
49F VAL* 3.0 47.8 + - + +
111F VAL 5.2 0.2 - - - -
112F LEU* 4.4 14.1 + - + +
115F THR* 3.3 21.3 - - - -
116F ALA* 3.0 37.1 + - - +
119F HIS* 3.7 33.3 - + + +
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Residues in contact with GLY 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F HIS* 3.1 15.0 + - - -
43F VAL* 3.5 6.1 - - - -
44F TYR 3.0 1.4 + - - -
45F TYR* 1.3 77.9 - - - +
47F LEU* 1.3 63.9 + - - +
49F VAL* 3.3 10.3 + - - +
50F LYS* 3.0 24.7 + - - +
68F ALA* 6.3 0.4 - - - -
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Residues in contact with LEU 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F VAL* 3.2 15.0 + - + +
44F TYR* 2.7 25.3 + - + +
46F GLY* 1.3 71.6 - - - +
48F LEU* 1.3 63.2 + - + +
50F LYS* 3.2 3.9 + - - +
51F LEU* 3.1 28.6 + - + +
64F LEU* 4.1 27.7 - - + +
68F ALA* 3.7 29.6 - - + -
70F ILE* 4.2 12.1 - - + -
75F LEU* 3.8 20.2 - - + -
78F ALA* 4.0 21.8 - - + -
79F VAL* 5.0 1.3 - - + -
82F LEU* 4.2 15.0 - - + -
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Residues in contact with LEU 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F MET* 3.6 31.4 - - + -
44F TYR 3.9 8.7 - - - +
45F TYR* 3.2 7.3 + - - +
47F LEU* 1.3 77.6 - - + +
49F VAL* 1.3 58.3 + - - +
51F LEU* 3.3 5.8 + - + +
52F ALA* 2.9 31.4 + - - +
82F LEU* 4.0 17.3 - - + -
87F TRP* 4.3 20.0 - - + +
88F VAL* 3.7 30.5 - - + -
104F LEU* 4.0 12.1 - - + +
108F GLY 4.5 3.4 - - - +
111F VAL* 5.2 1.3 - - + -
112F LEU* 3.6 28.4 - - + +
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Residues in contact with VAL 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A TRP* 4.1 22.2 - - + -
45F TYR* 3.0 48.4 + - + +
46F GLY* 3.5 11.4 - - - +
47F LEU 3.2 0.2 - - - -
48F LEU* 1.3 76.4 - - - +
50F LYS* 1.3 62.2 + - - +
52F ALA* 3.5 2.1 + - - +
53F GLU* 3.0 35.4 + - - +
112F LEU* 4.0 15.7 - - + -
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Residues in contact with LYS 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F GLY 3.0 15.6 + - - +
47F LEU* 3.2 4.9 + - + +
49F VAL* 1.3 77.3 - - - +
51F LEU* 1.3 56.3 + - - +
53F GLU* 3.4 15.6 + - - +
54F SER* 2.6 31.6 + - - -
59F LEU* 4.4 6.4 - - + +
64F LEU* 4.2 17.3 - - + -
67F TYR* 5.0 13.5 - - + -
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Residues in contact with LEU 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F LEU* 3.1 19.0 + - + +
48F LEU* 3.7 7.0 - - + +
50F LYS* 1.3 73.8 - - - +
52F ALA* 1.3 57.2 + - - +
53F GLU 3.0 1.8 - - - -
54F SER* 2.7 24.7 + - - -
57F ARG* 3.3 27.2 - - - +
58F ARG 4.2 0.7 - - - -
59F LEU* 3.6 32.3 - - + +
64F LEU* 3.9 21.3 - - + -
79F VAL* 6.6 0.2 - - + -
88F VAL* 4.2 21.1 - - + -
102F ALA* 3.6 29.8 - - + +
104F LEU* 4.0 20.4 - - + +
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Residues in contact with ALA 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ARG* 3.2 13.2 - - - +
7A TRP* 2.8 42.5 + - + -
48F LEU 2.9 17.7 + - - +
49F VAL 3.6 4.3 - - - +
51F LEU* 1.3 74.8 - - - +
53F GLU* 1.3 52.5 + - - +
57F ARG* 4.1 5.4 - - - -
104F LEU* 3.6 17.1 - - + +
109F TYR* 4.4 8.5 - - + -
112F LEU* 3.6 22.9 - - + -
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Residues in contact with GLU 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ARG* 3.3 21.9 + - - -
7A TRP* 3.9 26.5 - - + -
8A LEU 4.1 2.9 - - - +
9A THR* 3.5 43.9 - - + +
10A ALA* 4.1 5.4 + - - +
13E GLN* 5.0 4.9 - - - +
17E ARG* 4.9 14.9 + - - -
49F VAL* 3.0 29.3 + - - +
50F LYS* 3.5 13.2 - - - +
51F LEU 3.0 0.6 - - - -
52F ALA* 1.3 77.5 - - - +
54F SER* 1.3 59.8 - - - +
55F PRO* 4.5 1.0 - - - +
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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