Contacts of the helix formed by residues 37 - 49 (chain B) in PDB entry 5FQU
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 37 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34B ALA 3.5 16.8 - - - +
35B ARG 3.1 0.8 + - - -
36B GLY* 1.3 73.0 - - - +
38B ALA* 1.3 66.9 + - - +
39B HIS 3.0 1.3 - - - -
40B ILE* 3.0 44.5 + - + +
41B GLY 3.9 0.3 + - - -
61B MSE 3.9 15.9 - - + +
65B VAL* 4.9 2.2 - - + -
82B ALA* 4.3 7.0 - - + -
87B TRP* 4.2 21.3 - - + -
287B PHE* 4.0 20.2 - - + -
290B VAL* 3.8 33.2 - - + -
293B LEU* 4.2 13.2 - - + -
294B ILE* 3.7 13.6 - - + +
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Residues in contact with ALA 38 (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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35B ARG 3.1 15.6 + - - +
37B LEU* 1.3 78.5 - - - +
39B HIS* 1.3 61.1 + - - +
41B GLY 3.0 10.9 + - - -
42B VAL* 3.3 10.6 + - - +
232B ILE* 4.3 12.6 - - + -
277B PRO* 4.5 4.3 - - + -
279B LEU* 4.4 13.7 - - + -
293B LEU* 3.2 29.3 + - - +
294B ILE* 4.3 0.4 - - - +
297B GLY* 3.5 19.0 - - - +
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Residues in contact with HIS 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU* 3.5 19.5 - - + +
30B SER 2.9 36.3 + - - -
36B GLY* 3.0 27.3 + - - +
37B LEU 3.0 1.4 - - - -
38B ALA* 1.3 77.0 - - - +
40B ILE* 1.3 62.1 + - - +
42B VAL* 3.1 8.8 + - - +
43B LEU* 3.0 25.1 + - - +
61B MSE 4.3 0.4 - - - -
62B GLY* 3.5 25.7 - - - -
65B VAL* 3.8 17.3 - - + -
230B VAL* 3.3 39.5 - - + +
232B ILE* 3.9 13.2 - - + +
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Residues in contact with ILE 40 (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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37B LEU* 3.0 37.6 + - + +
39B HIS* 1.3 77.3 - - - +
41B GLY* 1.3 56.8 + - - +
43B LEU* 3.2 8.0 + - - +
44B LYS* 2.9 26.5 + - + +
65B VAL* 4.0 27.1 - - + -
75B PRO* 3.7 24.9 - - + +
78B LEU* 4.0 27.6 - - + +
79B GLU* 4.1 9.9 - - + +
82B ALA* 4.1 9.2 - - + -
294B ILE* 3.8 19.3 - - + -
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Residues in contact with GLY 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ALA 3.0 6.2 + - - -
40B ILE* 1.3 77.2 - - - +
42B VAL* 1.3 60.0 + - - +
44B LYS* 3.5 7.0 - - - +
45B ALA* 3.0 22.0 + - - +
294B ILE* 3.3 35.0 - - - +
298B TYR* 3.2 21.9 - - - -
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Residues in contact with VAL 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LEU* 5.1 1.6 - - + -
29B LEU* 5.7 1.3 - - + -
38B ALA 3.3 13.9 + - - +
39B HIS* 3.1 7.8 + - - +
41B GLY* 1.3 74.5 - - - +
43B LEU* 1.3 61.3 + - + +
45B ALA* 3.1 2.8 + - - +
46B LEU* 2.8 53.7 + - + +
230B VAL* 4.0 35.9 - - + -
275B ILE* 4.0 19.3 - - + -
277B PRO* 4.8 0.9 - - + -
297B GLY* 3.6 10.1 - - - +
301B THR* 3.4 25.6 - - - +
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Residues in contact with LEU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LEU* 3.6 31.9 - - + -
29B LEU* 5.2 4.9 - - + -
39B HIS 3.0 13.9 + - - +
40B ILE* 3.5 7.2 - - - +
42B VAL* 1.3 75.4 - - + +
44B LYS* 1.3 58.1 + - - +
46B LEU* 3.2 8.0 + - + -
47B ASP* 2.9 35.7 + - - +
53B ILE* 5.3 1.1 - - + -
65B VAL* 3.5 31.4 - - + +
69B TYR* 3.7 48.2 - - + -
75B PRO* 3.8 13.7 - - + -
78B LEU* 4.0 8.7 - - + -
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Residues in contact with LYS 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 ILE* 2.9 16.6 + - + +
41B GLY* 3.5 5.4 - - - +
42B VAL 3.2 0.2 - - - -
43B LEU* 1.3 77.9 - - - +
45B ALA* 1.3 61.2 + - - +
47B ASP* 4.1 1.6 - - - +
48B GLU* 3.3 21.9 + - - +
75B PRO* 3.6 23.7 - - + +
76B ALA* 5.2 4.5 - - + +
79B GLU* 2.7 35.2 + - + +
294B ILE* 4.3 16.7 - - + +
298B TYR* 4.3 24.5 - - + -
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Residues in contact with ALA 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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41B GLY 3.0 12.6 + - - +
42B VAL 3.5 6.1 - - - +
44B LYS* 1.3 74.1 - - - +
46B LEU* 1.3 66.3 + - - +
47B ASP 3.1 0.3 + - - -
48B GLU* 3.2 5.8 + - - +
49B GLN* 2.9 37.6 + - - +
298B TYR* 3.7 24.8 - - + +
301B THR* 3.6 28.5 - - + -
302B THR* 4.2 0.4 - - - +
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Residues in contact with LEU 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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27B LEU* 4.1 26.5 - - + -
42B VAL* 2.8 41.8 + - + +
43B LEU* 3.7 6.7 - - + +
45B ALA* 1.3 72.9 - - - +
47B ASP* 1.3 60.5 + - - +
49B GLN* 3.4 4.1 + - - -
50B GLY 3.3 3.8 + - - -
51B ILE* 3.0 40.2 + - + +
53B ILE* 4.2 24.9 - - + -
228B ILE* 4.1 19.1 - - + -
275B ILE* 5.0 1.8 - - + -
301B THR* 3.9 5.8 - - + -
308B LEU* 3.8 29.2 - - + -
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Residues in contact with ASP 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 LEU* 2.9 20.4 + - - +
44B LYS* 4.1 3.6 - - - +
46B LEU* 1.3 76.8 - - - +
48B GLU* 1.3 56.7 + - - +
50B GLY* 2.8 26.5 + - - -
51B ILE 4.7 5.9 - - - +
53B ILE* 4.8 0.7 - - - +
69B TYR* 2.7 30.4 + - - -
75B PRO* 3.4 28.0 - - + +
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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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44B LYS* 3.3 11.7 + - - +
45B ALA* 3.2 9.9 + - - +
47B ASP* 1.3 77.2 - - - +
49B GLN* 1.3 64.6 + - + +
50B GLY* 3.2 4.2 + - - -
298B TYR* 2.7 35.0 + - - -
302B THR* 4.8 3.1 + - - +
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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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45B ALA* 2.9 29.1 + - - +
46B LEU* 3.8 6.3 - - - +
47B ASP 3.2 0.2 - - - -
48B GLU* 1.3 83.2 + - + +
50B GLY* 1.3 62.3 + - - +
51B ILE* 3.4 17.8 + - + +
301B THR* 3.4 23.2 + - - +
302B THR* 3.6 17.2 + - - +
305B ALA* 3.3 33.8 - - + +
308B LEU* 3.7 19.2 - - - +
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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