Contacts of the helix formed by residues 45 - 54 (chain B) in PDB entry 4L57
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 LEU 45 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41B ARG* 3.9 4.1 + - - -
42B ARG 5.1 0.9 - - - +
43B GLY 3.3 3.1 - - - +
44B PHE* 1.3 92.1 - - + +
46B ALA* 1.3 65.9 + - - +
47B ARG* 3.2 4.9 - - + +
48B GLU* 3.1 37.0 + - + +
49B GLN* 3.5 7.1 + - - +
203B GOL 3.4 31.0 - - - +
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Residues in contact with ALA 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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18B PHE* 5.5 2.2 - - + -
19B GLU* 4.1 5.4 - - - +
22B LEU* 3.7 29.8 - - + -
41B ARG* 3.3 38.4 - - - +
44B PHE 3.5 1.6 + - - -
45B LEU* 1.3 72.0 - - - +
47B ARG* 1.3 64.5 + - - +
49B GLN* 3.0 3.8 + - - +
50B TYR* 3.0 34.1 + - + -
65B TYR* 6.1 0.2 - - + -
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Residues in contact with ARG 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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45B LEU* 3.2 4.8 - - + -
46B ALA* 1.3 79.1 - - - +
48B GLU* 1.3 74.2 + - + +
50B TYR* 3.4 2.6 + - - +
51B ARG* 2.9 37.9 + - - +
58B ALA* 3.4 24.2 + - + +
59B ASP* 2.5 33.3 + - - +
61B VAL* 3.9 16.0 - - + +
62B ALA* 3.6 23.5 - - + +
65B TYR* 3.6 28.0 + - + +
66B GLU* 4.6 6.7 + - - -
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Residues in contact with GLU 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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45B LEU* 3.1 33.8 + - + +
46B ALA 3.1 0.8 - - - -
47B ARG* 1.3 84.0 - - - +
49B GLN* 1.3 65.3 + - - +
51B ARG* 2.8 50.8 + - - +
52B ALA* 3.1 21.5 + - - +
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Residues in contact with GLN 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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36B VAL* 3.7 26.0 - - + +
40B GLN* 2.9 33.5 + - - +
41B ARG* 2.8 35.4 + - - +
42B ARG* 2.9 25.5 + - - +
45B LEU 3.5 3.4 + - - +
46B ALA* 3.0 8.3 + - - +
48B GLU* 1.3 74.2 - - - +
50B TYR* 1.3 67.2 + - + +
52B ALA* 3.3 8.9 + - + +
53B LEU* 3.1 20.3 + - - +
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Residues in contact with TYR 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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22B LEU* 5.5 2.4 - - + +
23B LEU* 3.6 22.9 - - - +
26B PHE* 3.9 34.6 - + - +
35B HIS* 3.8 4.5 - - - +
36B VAL* 3.1 47.9 + - + -
41B ARG* 5.0 4.5 - - - -
46B ALA* 3.0 36.6 + - + +
47B ARG 3.7 6.7 - - - +
49B GLN* 1.3 74.8 - - + +
51B ARG* 1.3 65.5 + - - +
53B LEU* 3.0 16.0 + - + +
54B ARG 3.0 15.7 + - - +
57B LEU* 3.7 30.0 - - + +
61B VAL* 4.0 30.3 - - + -
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Residues in contact with ARG 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 ARG* 2.9 36.1 + - - +
48B GLU* 2.8 46.3 + - - +
49B GLN 3.3 0.2 - - - -
50B TYR* 1.3 75.2 - - - +
52B ALA* 1.3 61.2 + - - +
54B ARG* 3.3 22.3 - - - -
55B PRO* 3.3 23.1 + - + +
58B ALA* 3.6 26.8 - - + +
59B ASP* 5.1 4.6 + - - -
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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 GLU 3.1 13.2 + - - +
49B GLN* 3.5 13.2 - - + +
50B TYR 3.2 0.2 - - - -
51B ARG* 1.3 76.8 - - - +
53B LEU* 1.3 62.9 + - - +
54B ARG* 4.5 0.3 - - - -
55B PRO* 5.5 0.7 - - - +
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Residues in contact with LEU 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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34B PRO* 4.2 27.6 - - + +
35B HIS* 4.2 9.4 - - - +
36B VAL* 4.1 23.8 - - + -
49B GLN 3.1 12.0 + - - +
50B TYR* 3.0 12.0 + - + +
52B ALA* 1.3 79.0 - - - +
54B ARG* 1.3 60.6 + - + +
57B LEU* 3.8 20.4 - - + -
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Residues in contact with ARG 54 (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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33B GLU* 2.9 24.6 + - - -
34B PRO* 3.8 20.5 - - + +
50B TYR 3.0 12.7 + - - +
51B ARG 3.3 2.9 - - - -
52B ALA 3.4 0.4 - - - -
53B LEU* 1.3 80.4 - - + +
55B PRO* 1.3 79.9 - - + +
56B ASP* 2.7 39.0 + - - +
57B LEU* 3.0 30.0 + - + +
60B LYS* 2.8 18.0 - - - +
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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