Contacts of the helix formed by residues 41 - 53 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31B ASP* 4.1 16.8 - - - +
34B LEU* 4.6 0.9 - - - -
35B GLN* 3.4 19.9 - - - +
40B MET* 1.3 94.9 - - + +
42B HIS* 1.3 67.5 + - - +
43B VAL* 3.3 5.2 + - + +
44B TYR* 3.4 40.3 + - + +
45B TYR* 3.3 17.3 + - - +
81B ARG* 4.1 5.4 - - - +
12C T 4.3 17.5 - - - +
13C C 5.4 2.5 - - - +
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Residues in contact with HIS 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TRP* 4.3 3.8 + + - -
20A ILE* 3.6 37.5 - - + +
27B GLU* 5.4 4.9 - - - +
30B LEU* 4.2 18.9 - - + +
31B ASP* 2.9 30.1 + - - +
34B LEU* 3.6 28.9 - - + +
41B PRO* 1.3 72.8 - - - +
43B VAL* 1.3 66.7 + - + +
45B TYR* 3.5 5.9 + + - +
46B GLY* 3.1 20.5 + - - -
119B HIS* 3.7 21.7 + + - -
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Residues in contact with VAL 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A THR* 6.2 3.6 - - + -
31B ASP* 5.5 2.0 - - - +
41B PRO* 3.3 4.4 - - + -
42B HIS* 1.3 79.9 - - + +
44B TYR* 1.3 68.9 + - + +
46B GLY* 3.2 11.2 + - - -
47B LEU* 3.2 19.2 + - + +
68B ALA* 5.4 3.1 - - + +
70B ILE* 4.2 27.4 - - + -
74B ARG* 3.5 33.2 - - - +
13C C 4.2 8.7 - - - +
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Residues in contact with TYR 44 (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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40B MET* 4.0 12.1 - - - -
41B PRO* 3.4 31.6 + - + +
43B VAL* 1.3 79.2 - - + +
45B TYR* 1.3 67.6 + - - +
47B LEU* 2.7 24.3 + - + +
48B LEU* 3.2 12.1 + - - +
74B ARG* 5.9 0.4 - - + -
77B HIS* 4.7 1.7 + - - +
78B ALA* 3.4 35.6 + - + -
81B ARG* 3.7 36.9 - - + +
82B LEU* 3.9 22.4 - - + +
12C T 3.3 30.6 + - - +
13C C 3.2 29.7 + - - -
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Residues in contact with TYR 45 (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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34B LEU* 3.6 29.6 - - + -
38B ALA* 5.0 0.2 - - + -
40B MET* 3.5 32.5 - - + -
41B PRO 3.3 10.2 + - - +
42B HIS* 3.6 10.8 - + - +
44B TYR* 1.3 77.4 - - - +
46B GLY* 1.3 58.6 + - - +
48B LEU* 3.1 6.6 + - - +
49B VAL* 3.0 52.6 + - + +
112B LEU* 4.4 11.6 + - + -
115B THR* 3.3 21.5 - - - -
116B ALA* 3.0 36.4 + - - +
119B HIS* 3.7 33.3 - + + +
7E TRP* 4.8 2.3 - - - -
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Residues in contact with GLY 46 (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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42B HIS* 3.1 16.5 + - - -
43B VAL* 3.5 5.8 - - - -
44B TYR 3.1 0.4 - - - -
45B TYR* 1.3 74.4 - - - +
47B LEU* 1.3 65.6 + - - +
49B VAL* 3.3 9.8 + - - +
50B LYS* 3.0 24.3 + - - +
68B ALA* 6.2 0.9 - - - -
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Residues in contact with LEU 47 (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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43B VAL* 3.2 13.6 + - + +
44B TYR* 2.7 23.3 + - + +
46B GLY* 1.3 71.7 - - - -
48B LEU* 1.3 62.1 + - + +
50B LYS* 3.2 4.8 + - - +
51B LEU* 3.1 28.2 + - + +
64B LEU* 4.1 27.7 - - + +
68B ALA* 3.7 29.8 - - + -
70B ILE* 4.2 13.0 - - + -
75B LEU* 3.8 19.3 - - + -
78B ALA* 4.0 22.7 - - + -
79B VAL* 5.0 1.1 - - + -
82B LEU* 4.2 15.7 - - + -
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Residues in contact with LEU 48 (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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40B MET* 3.6 29.4 - - + -
44B TYR 3.9 8.1 - - - +
45B TYR 3.1 7.5 + - - +
47B LEU* 1.3 78.8 - - + +
49B VAL* 1.3 56.1 + - - +
51B LEU* 3.3 6.7 + - + +
52B ALA* 2.9 31.2 + - - +
82B LEU* 4.0 17.9 - - + -
87B TRP* 4.3 19.7 - - + +
88B VAL* 3.7 29.4 - - + -
104B LEU* 3.9 11.7 - - + +
108B GLY 4.5 3.8 - - - +
111B VAL* 5.2 1.6 - - + -
112B LEU* 3.6 32.2 - - + +
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Residues in contact with VAL 49 (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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45B TYR* 3.0 44.6 + - + +
46B GLY* 3.5 10.8 - - - +
47B LEU 3.2 0.2 - - - -
48B LEU* 1.3 77.1 - - - +
50B LYS* 1.3 63.9 + - - +
52B ALA* 3.5 2.5 + - - +
53B GLU* 3.1 34.7 + - - +
112B LEU* 4.0 11.0 - - + -
7E TRP* 3.9 28.0 - - + -
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Residues in contact with LYS 50 (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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46B GLY 3.0 16.5 + - - +
47B LEU* 3.2 4.9 + - + +
49B VAL* 1.3 77.1 - - - +
51B LEU* 1.3 55.2 + - - +
53B GLU* 3.4 14.5 + - - +
54B SER* 2.6 31.9 + - - -
59B LEU* 4.3 6.5 - - + +
64B LEU* 4.1 17.7 - - + -
67B TYR* 4.9 13.5 - - + -
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Residues in contact with LEU 51 (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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47B LEU* 3.1 17.8 + - + +
48B LEU* 3.7 6.7 - - + +
50B LYS* 1.3 72.8 - - - +
52B ALA* 1.3 58.6 + - - +
53B GLU 3.0 2.0 - - - -
54B SER* 2.7 24.1 + - - -
57B ARG* 3.3 27.4 - - - +
58B ARG 4.2 0.7 - - - -
59B LEU* 3.6 32.8 - - + +
64B LEU* 3.9 21.5 - - + -
88B VAL* 4.2 20.6 - - + -
102B ALA* 3.6 28.9 - - + +
104B LEU* 4.0 20.2 - - + +
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Residues in contact with ALA 52 (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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48B LEU 2.9 17.8 + - - +
49B VAL* 3.6 4.5 - - - +
51B LEU* 1.3 76.1 - - - +
53B GLU* 1.3 54.4 + - - +
57B ARG* 4.1 5.5 - - - +
104B LEU* 3.6 21.4 - - + +
109B TYR* 4.4 7.6 - - + -
112B LEU* 3.6 17.9 - - + -
6E ARG* 3.4 10.2 - - - +
7E TRP* 2.8 42.6 + - + -
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Residues in contact with GLU 53 (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 GLN* 5.1 4.7 - - - +
17A ARG* 4.8 14.8 + - - -
49B VAL* 3.1 29.6 + - - +
50B LYS* 3.5 13.0 - - - +
51B LEU 3.0 1.0 - - - -
52B ALA* 1.3 75.8 - - - +
54B SER* 1.3 62.1 + - - +
55B PRO* 4.1 1.0 - - - +
6E ARG* 3.7 18.1 + - - -
7E TRP* 3.8 30.6 - - + +
8E LEU 4.1 3.0 - - - +
9E THR* 3.5 45.0 - - + +
10E ALA* 4.1 3.8 + - - +
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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