Contacts of the helix formed by residues 29 - 50 (chain A) in PDB entry 5GNA
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 GLU 29 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LEU* 2.8 34.1 + - + +
27A ARG* 3.9 28.2 - - + +
28A GLY* 1.3 74.5 - - - +
30A TRP* 1.3 59.4 + - - +
31A ASP 3.5 2.2 - - - -
32A LEU* 3.5 23.4 + - + +
33A LEU* 3.0 27.3 + - - +
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Residues in contact with TRP 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ALA* 3.7 36.3 - - + -
28A GLY* 3.2 34.4 + - - -
29A GLU* 1.3 69.9 - - - +
31A ASP* 1.3 66.3 + - - +
33A LEU* 3.5 28.9 - - + +
34A LEU* 3.1 28.7 + - - +
81A LEU* 3.9 12.3 - - + -
82A LEU* 4.3 9.6 - - + -
85A ARG* 3.3 72.2 - - + +
88A GLU* 4.8 3.5 + - - -
439B GLN* 3.5 23.3 - - + +
443B LEU* 4.1 5.8 - - + -
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Residues in contact with ASP 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLU 3.5 0.2 - - - -
30A TRP* 1.3 77.8 - - - +
32A LEU* 1.3 62.7 + - + +
34A LEU* 3.4 10.6 + - - +
35A GLN* 3.2 23.5 + - - +
439B GLN* 3.5 20.8 + - - +
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Residues in contact with LEU 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 3.9 21.0 - - + +
29A GLU* 3.5 33.7 + - + +
30A TRP 3.4 0.2 - - - -
31A ASP* 1.3 77.6 - - + +
33A LEU* 1.3 60.7 + - - +
35A GLN* 3.1 23.2 + - - +
36A GLN* 2.8 30.7 + - - +
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Residues in contact with LEU 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU* 3.1 49.4 - - + +
24A LEU* 3.8 12.2 - - + +
25A ALA* 4.1 9.9 - - + +
29A GLU 3.0 19.4 + - - +
30A TRP* 3.5 25.8 - - + +
32A LEU* 1.3 76.5 - - - +
34A LEU* 1.3 50.5 + - - +
36A GLN* 3.1 3.1 + - - +
37A GLU* 2.7 34.0 + - - +
78A LEU* 4.3 1.3 - - + -
82A LEU* 4.0 10.8 - - + -
443B LEU* 3.6 30.7 - - + -
446B MET* 4.0 14.8 - - + -
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Residues in contact with LEU 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TRP 3.1 17.3 + - - +
31A ASP* 3.4 10.1 + - - +
32A LEU 3.2 0.2 - - - -
33A LEU* 1.3 79.0 - - - +
35A GLN* 1.3 62.6 + - - +
37A GLU* 3.5 17.9 - - + +
38A VAL* 3.8 10.4 + - - +
439B GLN* 4.2 17.7 - - + -
442B GLN* 3.8 57.2 - - + +
443B LEU* 3.9 23.8 - - + -
446B MET* 4.3 12.1 - - + -
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Residues in contact with GLN 35 (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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31A ASP 3.2 13.2 + - - +
32A LEU* 3.1 31.7 + - + +
34A LEU* 1.3 76.1 - - - +
36A GLN* 1.3 63.4 + - - +
38A VAL* 3.2 24.6 + - - +
39A SER* 4.0 4.3 + - - -
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Residues in contact with GLN 36 (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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17A LEU* 3.7 25.0 - - + +
20A SER* 2.4 36.8 + - - +
21A LEU* 3.6 17.5 - - + -
24A LEU* 3.9 10.3 - - + +
32A LEU 2.8 16.6 + - - +
33A LEU 3.5 4.3 - - - +
35A GLN* 1.3 74.1 - - - +
37A GLU* 1.3 66.4 + - - +
39A SER* 3.0 22.7 + - - +
40A TYR* 3.0 10.6 + - - +
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Residues in contact with GLU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU* 3.5 15.7 - - - +
33A LEU 2.7 20.2 + - - +
34A LEU* 3.5 14.1 - - + +
36A GLN* 1.3 72.9 - - - +
38A VAL* 1.3 64.1 + - + +
40A TYR* 3.1 12.0 + - - +
41A LEU* 3.0 50.0 + - + +
446B MET* 3.5 55.9 - - + +
449B LYS* 4.2 5.5 - - - +
450B LEU* 4.8 3.9 - - - +
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Residues in contact with VAL 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU 3.8 11.0 - - - +
35A GLN* 3.4 15.9 - - - +
36A GLN 3.1 0.6 + - - -
37A GLU* 1.3 78.9 - - + +
39A SER* 1.3 63.2 + - - +
41A LEU* 3.4 6.9 + - - +
42A GLN* 3.2 42.8 + - + +
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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
----------------------------------------------------------
13A ARG* 4.3 15.3 + - - +
17A LEU* 3.7 14.7 - - - +
35A GLN 4.5 4.3 + - - -
36A GLN* 3.0 23.6 + - - -
38A VAL* 1.3 76.2 - - - +
40A TYR* 1.3 61.9 + - - +
42A GLN* 3.2 15.5 + - - +
43A SER* 2.9 30.5 + - - -
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Residues in contact with TYR 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ILE* 3.7 26.9 - - + -
17A LEU* 3.8 25.5 - - + +
18A SER* 3.8 13.9 - - - -
21A LEU* 3.6 25.6 - - + -
36A GLN 3.0 11.6 + - - +
37A GLU* 3.4 17.5 - - - +
39A SER* 1.3 77.4 - - - +
41A LEU* 1.3 70.7 + - + +
43A SER* 2.8 23.2 + - - -
44A ILE* 3.1 23.2 + - + +
71A THR* 3.4 14.6 - - - +
75A GLU* 2.5 38.2 + - + +
450B LEU* 4.3 10.3 - - + -
453B THR* 4.5 2.9 - - - -
457B LEU* 3.8 5.0 - - - +
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Residues in contact with LEU 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A GLU* 3.0 41.4 + - + +
38A VAL* 3.9 6.3 - - - +
40A TYR* 1.3 86.6 - - + +
42A GLN* 1.3 66.6 + - + +
44A ILE* 3.2 7.5 + - + +
45A GLU* 3.1 32.5 + - - +
449B LYS* 3.6 42.6 - - + +
450B LEU* 6.0 1.1 - - + -
453B THR* 4.2 14.4 - - + -
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Residues in contact with GLN 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ARG* 5.8 5.0 + - - +
38A VAL* 3.2 31.9 + - + +
39A SER* 3.2 16.4 + - - +
41A LEU* 1.3 76.9 - - + +
43A SER* 1.3 60.6 + - - +
45A GLU* 3.2 16.8 + - - +
46A THR* 3.1 24.8 + - - -
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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
----------------------------------------------------------
10A ARG 4.9 1.5 - - - +
13A ARG* 4.2 21.5 - - - +
14A ILE* 3.4 36.4 - - - +
17A LEU* 3.7 20.1 - - - +
39A SER 2.9 13.5 + - - -
40A TYR* 2.8 21.3 + - - -
42A GLN* 1.3 73.6 - - - +
44A ILE* 1.3 64.6 + - - +
46A THR* 3.4 20.3 + - - -
47A VAL* 3.7 1.9 + - - +
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Residues in contact with ILE 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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14A ILE* 3.7 33.2 - - + -
40A TYR* 3.1 37.4 + - + +
41A LEU* 3.2 9.6 + - + +
43A SER* 1.3 75.2 - - - +
45A GLU* 1.3 66.4 + - + +
47A VAL* 3.2 18.9 + - - +
48A MET* 3.4 30.3 + - + +
453B THR* 4.5 20.4 - - + -
456B TYR* 4.1 12.1 - - + -
457B LEU* 3.9 21.3 - - + -
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Residues in contact with GLU 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 LEU* 3.1 23.3 + - - +
42A GLN* 3.2 17.6 + - - +
44A ILE* 1.3 76.3 - - + +
46A THR* 1.3 57.4 + - - +
48A MET* 3.0 19.0 + - - +
49A GLU* 2.9 46.3 + - + +
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Residues in contact with THR 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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10A ARG* 3.3 32.8 - - + +
13A ARG* 5.9 1.2 + - - -
42A GLN 3.1 13.4 + - - -
43A SER* 3.5 14.7 - - - +
44A ILE 3.1 0.4 - - - -
45A GLU* 1.3 76.3 - - - +
47A VAL* 1.3 57.2 + - - +
49A GLU* 3.3 7.3 + - - +
50A LYS* 3.0 39.1 + - + +
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Residues in contact with VAL 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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10A ARG* 3.8 28.5 - - + +
11A TRP* 3.6 44.4 - - + +
14A ILE* 3.6 28.7 - - + -
43A SER 3.7 1.1 + - - +
44A ILE* 3.2 15.2 + - - +
46A THR* 1.3 73.8 - - - +
48A MET* 1.3 59.5 + - - +
50A LYS 2.9 19.1 - - - +
51A GLN* 5.2 0.7 - - - +
456B TYR* 3.4 23.2 + - + +
460B GLN* 5.0 2.3 - - - +
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Residues in contact with MET 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ILE* 3.4 24.4 + - + +
45A GLU* 3.0 22.0 + - - +
47A VAL* 1.3 78.4 - - - +
49A GLU* 1.3 63.7 + - + +
50A LYS 3.4 0.4 - - - -
51A GLN* 3.6 13.3 - - - +
453B THR* 6.4 0.4 - - + -
456B TYR* 3.4 55.4 - - + +
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Residues in contact with GLU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A GLU* 2.9 33.9 + - + +
46A THR* 3.3 7.1 + - - +
48A MET* 1.3 78.9 - - + +
50A LYS* 1.3 65.2 + - + +
51A GLN* 4.2 5.7 + - - +
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Residues in contact with LYS 50 (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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10A ARG* 3.4 44.3 + - - +
46A THR* 3.0 21.5 + - + +
47A VAL* 2.9 24.6 - - - +
49A GLU* 1.3 84.4 + - + +
51A GLN* 1.3 66.2 + - - +
52A THR 4.2 0.2 + - - -
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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
------------------------------------------------------------
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