Contacts of the helix formed by residues 36 - 48 (chain A) in PDB entry 4QA7
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 LYS 36 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ASP* 3.2 36.0 + - + +
34A ILE 3.4 0.6 + - - -
35A PRO* 1.3 75.2 - - + +
37A ARG* 1.3 62.4 + - - +
39A SER* 3.6 6.0 + - - -
40A MET* 3.2 31.6 + - + +
308A LEU* 5.6 0.2 - - + -
336A PHE* 4.9 15.1 - - + -
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Residues in contact with ARG 37 (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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29A ASP* 3.5 0.4 + - - -
34A ILE* 3.3 49.5 + - + +
35A PRO 3.0 3.0 + - - -
36A LYS* 1.3 75.9 - - - +
38A ALA* 1.3 61.5 + - - +
40A MET* 3.2 7.1 + - - +
41A VAL* 2.9 41.4 + - + +
137A TRP 4.6 3.8 + - - -
138A SER* 5.6 1.6 - - - +
139A GLY 5.6 0.2 + - - -
141A TRP* 3.8 8.3 - - - -
303A GLY 3.0 30.3 + - - +
304A GLY* 3.5 11.9 + - - -
305A GLY* 2.8 30.5 + - - +
306A PHE* 5.2 0.6 - - - -
308A LEU* 3.6 31.0 - - + +
311A THR* 4.0 10.1 - - + -
315A TRP* 3.4 24.7 - - - -
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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
----------------------------------------------------------
25A VAL* 4.0 16.0 - - + +
28A CYS* 3.6 23.0 + - + +
29A ASP* 3.0 9.9 + - - +
34A ILE* 4.9 1.9 + - + +
37A ARG* 1.3 80.4 - - - +
39A SER* 1.3 61.8 + - - +
41A VAL* 3.4 7.2 + - - +
42A HIS* 3.1 25.1 + - - +
138A SER* 3.6 23.3 - - - +
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Residues in contact with SER 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A VAL* 3.2 13.9 - - - +
29A ASP* 2.3 35.1 + - - -
36A LYS* 3.8 9.5 - - - +
37A ARG 3.3 0.2 - - - -
38A ALA* 1.3 74.8 - - - +
40A MET* 1.3 58.9 + - - +
42A HIS* 3.4 3.3 + - - +
43A SER* 2.8 33.4 + - - -
335A GLU* 5.7 0.7 - - - -
336A PHE* 4.1 17.9 - - - -
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Residues in contact with MET 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LYS* 3.2 18.5 + - + +
37A ARG* 3.2 7.4 + - - +
39A SER* 1.3 76.8 - - - +
41A VAL* 1.3 62.6 + - - +
43A SER* 3.8 0.9 - - - -
44A LEU* 3.1 25.6 + - - +
308A LEU* 3.6 29.8 - - + +
309A ALA* 3.8 32.8 - - + +
312A ALA* 3.9 8.3 - - + +
333A ASP* 4.4 0.3 - - - +
336A PHE* 3.7 38.6 - - + -
339A ALA* 4.2 22.4 - - + -
340A TYR* 4.0 12.3 + - + +
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Residues in contact with VAL 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A TYR* 5.4 1.1 - - - +
37A ARG* 2.9 29.3 + - + +
38A ALA* 3.8 7.6 - - - +
40A MET* 1.3 78.0 - - - +
42A HIS* 1.3 62.5 + - - +
44A LEU 3.5 0.2 + - - -
45A ILE* 3.2 36.5 + - + +
137A TRP* 4.1 17.3 - - + -
311A THR* 4.5 0.2 - - + -
312A ALA* 4.0 25.4 - - + +
315A TRP* 3.8 42.0 - - + -
316A THR* 3.9 3.4 + - - +
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Residues in contact with HIS 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A TYR* 2.8 39.9 + + - +
20A TYR* 3.1 55.3 + + - -
25A VAL* 4.5 11.9 - - + -
38A ALA 3.1 17.4 + - - +
39A SER* 4.0 3.8 - - - +
41A VAL* 1.3 77.7 - - - +
43A SER* 1.3 54.6 + - - +
45A ILE* 3.2 1.6 + - - +
46A GLU* 2.7 63.8 + - + +
51A HIS* 4.9 11.2 - + - -
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Residues in contact with SER 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A SER 2.8 23.3 + - - -
40A MET 3.8 1.3 - - - -
41A VAL 3.3 0.2 - - - -
42A HIS* 1.3 76.5 - - - +
44A LEU* 1.3 56.7 + - - +
46A GLU* 3.4 13.6 + - - +
47A ALA* 2.9 26.7 + - - +
333A ASP* 2.6 31.4 + - - +
335A GLU* 4.3 9.3 + - - +
336A PHE* 3.6 20.6 - - - -
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Residues in contact with LEU 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 MET 3.1 11.4 + - - +
41A VAL 4.0 1.1 - - - +
42A HIS 3.3 0.2 - - - -
43A SER* 1.3 74.0 - - - +
45A ILE* 1.3 65.7 + - - +
47A ALA* 3.3 1.9 + - + +
48A TYR* 3.1 49.7 + - + -
312A ALA* 3.4 17.7 - - + +
313A ARG* 3.8 8.7 - - - +
316A THR* 3.3 28.7 - - + +
331A ILE* 4.0 15.7 - - + -
332A PRO* 4.2 2.0 - - + -
333A ASP* 3.2 21.0 + - + -
340A TYR* 3.3 33.7 - - + +
346A LEU* 4.4 7.2 - - + -
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Residues in contact with ILE 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A TYR* 4.0 22.0 - - + +
41A VAL* 3.2 19.6 + - + +
42A HIS* 3.6 7.9 - - - +
44A LEU* 1.3 77.2 - - - +
46A GLU* 1.3 62.7 + - - +
48A TYR* 3.3 3.6 + - - +
49A ALA 3.1 14.9 + - - -
50A LEU* 3.2 26.8 + - + +
51A HIS* 4.2 11.4 - - + +
54A MET* 4.4 9.9 - - + -
137A TRP* 3.7 22.9 - - + +
315A TRP 4.4 2.7 - - - +
316A THR* 3.5 25.4 - - + +
319A THR* 3.6 22.0 - - + +
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Residues in contact with GLU 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A TYR* 4.9 2.3 + - - -
42A HIS* 2.7 45.9 + - + +
43A SER* 3.6 13.4 + - - +
44A LEU 3.2 0.2 - - - -
45A ILE* 1.3 75.3 - - - +
47A ALA* 1.3 57.2 + - - +
49A ALA* 2.9 19.2 + - - +
51A HIS* 3.4 34.0 + - + +
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Residues in contact with ALA 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A SER 2.9 17.5 + - - +
44A LEU* 3.7 5.8 - - - +
45A ILE 3.3 0.2 - - - -
46A GLU* 1.3 72.8 - - - +
48A TYR* 1.3 59.8 + - - +
49A ALA* 3.1 7.5 + - - +
332A PRO* 3.8 21.3 - - + +
333A ASP* 3.8 33.2 - - + +
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Residues in contact with TYR 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 LEU* 3.1 41.5 + - + +
45A ILE 3.9 1.1 - - - +
46A GLU 3.3 0.2 - - - -
47A ALA* 1.3 75.3 - - - +
49A ALA* 1.3 69.1 + - - +
50A LEU* 3.1 29.6 + - + +
316A THR* 3.6 15.7 - - + -
327A LEU* 3.8 21.3 - - + -
328A SER* 3.1 37.2 + - - -
330A GLU 3.4 11.1 + - - -
331A ILE* 3.8 4.3 - - - +
332A PRO* 3.4 30.8 - - + +
346A LEU* 3.8 23.4 - - + +
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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