Contacts of the helix formed by residues 37 - 49 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A ALA 3.5 15.9 - - - +
35A ARG 3.1 1.0 + - - -
36A GLY* 1.3 74.5 - - - +
38A ALA* 1.3 66.4 + - - +
39A HIS 3.0 1.1 - - - -
40A ILE* 3.0 44.4 + - + +
41A GLY 3.9 0.2 + - - -
61A MSE 4.4 17.0 - - + -
65A VAL* 4.9 2.7 - - + -
82A ALA* 4.3 6.5 - - + -
87A TRP* 4.2 21.1 - - + -
287A PHE* 4.0 20.2 - - + -
290A VAL* 3.8 33.4 - - + -
293A LEU* 4.2 13.7 - - + -
294A ILE* 3.7 13.5 - - + +
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Residues in contact with ALA 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ARG 3.1 15.6 + - - +
37A LEU* 1.3 78.5 - - - +
39A HIS* 1.3 62.0 + - - +
41A GLY 3.0 11.4 + - - -
42A VAL* 3.3 10.3 + - - +
232A ILE* 4.3 12.3 - - + -
277A PRO* 4.5 4.7 - - + -
279A LEU* 4.4 14.4 - - + -
293A LEU* 3.2 29.4 + - - +
294A ILE* 4.3 0.2 - - - +
297A GLY* 3.5 19.0 - - - +
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Residues in contact with HIS 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 3.5 18.5 - - + +
30A SER 2.9 36.7 + - - -
36A GLY* 3.0 28.4 + - - +
37A LEU 3.0 0.8 - - - -
38A ALA* 1.3 77.0 - - - +
40A ILE* 1.3 63.1 + - - +
42A VAL* 3.2 8.6 + - - +
43A LEU* 3.0 24.8 + - - +
61A MSE 4.4 0.4 - - - -
62A GLY* 3.4 23.0 - - - -
65A VAL* 3.9 17.3 - - + -
230A VAL* 3.3 40.3 - - + +
232A ILE* 3.8 13.4 - - + +
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Residues in contact with ILE 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LEU* 3.0 37.9 + - + +
39A HIS* 1.3 77.7 - - - +
41A GLY* 1.3 57.7 + - - +
43A LEU* 3.2 7.7 + - - +
44A LYS* 2.9 26.5 + - + +
65A VAL* 4.0 27.1 - - + -
75A PRO* 3.7 24.1 - - + +
78A LEU* 4.0 28.0 - - + +
79A GLU* 4.1 10.1 - - + +
82A ALA* 4.1 9.4 - - + -
294A ILE* 3.8 18.8 - - + -
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Residues in contact with GLY 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ALA 3.0 5.6 + - - -
40A ILE* 1.3 76.3 - - - +
42A VAL* 1.3 64.6 + - - +
44A LYS* 3.5 7.7 + - - +
45A ALA* 3.0 17.2 + - - +
294A ILE* 3.3 34.8 - - - +
298A TYR* 3.2 23.0 - - - -
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Residues in contact with VAL 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LEU* 5.1 1.1 - - + -
29A LEU* 5.7 1.3 - - + -
38A ALA 3.3 14.1 + - - +
39A HIS* 3.2 8.2 + - - +
41A GLY* 1.3 75.0 - - - +
43A LEU* 1.3 60.6 + - + +
45A ALA* 3.1 2.8 + - - +
46A LEU* 2.8 52.9 + - + +
230A VAL* 4.0 36.3 - - + -
275A ILE* 4.0 19.1 - - + -
277A PRO* 4.8 0.7 - - + -
297A GLY* 3.6 11.2 - - - +
301A THR* 3.4 25.4 - - - +
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Residues in contact with LEU 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 3.6 31.0 - - + -
29A LEU* 5.2 5.8 - - + -
39A HIS 3.0 13.1 + - - +
40A ILE* 3.2 7.6 + - - +
42A VAL* 1.3 74.9 - - + +
44A LYS* 1.3 57.8 + - - +
46A LEU* 3.2 8.9 + - + +
47A ASP* 2.9 35.7 + - - +
53A ILE* 5.3 1.1 - - + -
56A ILE* 5.7 0.2 - - + -
65A VAL* 3.5 31.4 - - + -
69A TYR* 3.7 48.7 - - + +
75A PRO* 3.8 14.4 - - + -
78A LEU* 4.0 9.0 - - + -
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Residues in contact with LYS 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ILE* 2.9 16.4 + - + +
41A GLY* 3.5 5.2 - - - +
43A LEU* 1.3 75.9 - - - +
45A ALA* 1.3 60.5 + - - +
47A ASP* 4.1 2.2 - - - +
48A GLU* 3.3 23.4 + - - +
75A PRO* 3.6 23.7 - - + +
76A ALA* 5.2 3.6 - - + +
79A GLU* 2.8 35.6 + - + +
294A ILE* 4.3 16.2 - - + +
298A TYR* 4.3 24.2 - - + -
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Residues in contact with ALA 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A GLY 3.0 13.4 + - - +
42A VAL 3.6 6.7 - - - +
44A LYS* 1.3 72.6 - - - +
46A LEU* 1.3 67.9 + - - +
47A ASP 3.1 0.5 + - - -
48A GLU* 3.2 5.2 + - - +
49A GLN* 2.9 38.1 + - - +
298A TYR* 3.7 26.1 - - + +
301A THR* 3.6 28.0 - - + -
302A THR* 4.2 0.7 - - - +
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Residues in contact with LEU 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LEU* 4.1 25.8 - - + -
42A VAL* 2.8 41.0 + - + +
43A LEU* 3.7 7.4 - - + +
45A ALA* 1.3 72.7 - - - +
47A ASP* 1.3 61.2 + - - +
49A GLN* 3.3 5.1 + - - -
50A GLY 3.2 3.6 + - - -
51A ILE* 3.0 39.7 + - + +
53A ILE* 4.2 26.0 - - + -
228A ILE* 4.1 18.8 - - + -
275A ILE* 5.0 1.6 - - + -
301A THR* 3.9 6.3 - - + -
308A LEU* 3.8 29.8 - - + -
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Residues in contact with ASP 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LEU* 2.9 20.3 + - - +
44A LYS 4.1 3.8 - - - +
46A LEU* 1.3 77.0 - - - +
48A GLU* 1.3 57.3 + - - +
50A GLY* 2.8 26.3 + - - -
51A ILE 4.7 6.5 - - - +
69A TYR* 2.7 30.3 + - - -
75A PRO* 3.4 27.5 - - + +
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Residues in contact with GLU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A LYS* 3.3 11.4 + - - +
45A ALA* 3.3 9.9 - - - +
47A ASP* 1.3 76.5 - - - +
49A GLN* 1.3 64.7 + - + +
50A GLY 3.1 3.9 + - - -
298A TYR* 2.7 35.1 + - - -
302A THR* 4.9 2.9 + - - +
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Residues in contact with GLN 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ALA* 2.9 31.6 + - - +
46A LEU* 3.8 5.8 - - - +
47A ASP 3.1 0.4 - - - -
48A GLU* 1.3 83.1 + - + +
50A GLY* 1.3 62.4 + - - +
51A ILE* 3.3 16.4 + - + +
301A THR* 3.4 22.2 + - - +
302A THR* 3.6 16.4 + - - +
305A ALA* 3.3 33.8 - - + +
308A LEU* 3.7 19.0 - - - +
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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