Contacts of the helix formed by residues 35 - 52 (chain D) in PDB entry 1GQA
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 ASP 35 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27D MET* 3.7 7.2 - - - +
32D MET* 6.2 3.1 - - + -
33D PRO* 3.4 8.6 + - + +
34D TYR* 1.3 75.4 - - - +
36D ALA* 1.3 58.5 + - - +
37D ALA* 3.1 21.8 + - - +
38D ALA* 3.3 21.9 + - + +
39D ALA* 2.8 29.9 + - - +
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Residues in contact with ALA 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D TYR* 3.6 34.6 - - + +
35D ASP* 1.3 74.1 + - - +
37D ALA* 1.3 57.6 + - - +
39D ALA* 3.8 3.2 - - - +
40D LYS* 2.9 35.3 + - - +
102D GLY* 4.1 17.5 - - - +
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Residues in contact with ALA 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D ASP* 3.1 10.1 + - - +
36D ALA* 1.3 74.5 - - - +
38D ALA* 1.3 61.8 + - - +
40D LYS* 3.2 11.8 + - - +
41D ALA* 2.9 28.5 + - - +
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Residues in contact with ALA 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D MET* 5.3 4.5 - - - -
32D MET* 6.0 6.1 - - + -
35D ASP* 3.3 27.5 + - + +
37D ALA* 1.3 76.9 - - - +
39D ALA* 1.3 67.2 + - - +
41D ALA* 3.3 7.0 + - - +
42D HIS* 3.0 41.7 + - + +
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Residues in contact with ALA 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D LEU* 3.7 18.2 - - + +
27D MET* 3.6 25.7 - - + -
35D ASP 2.8 18.5 + - - +
36D ALA* 3.8 2.2 - - - +
37D ALA 3.2 0.2 - - - -
38D ALA* 1.3 75.9 - - - +
40D LYS* 1.3 57.6 + - - +
42D HIS* 3.4 0.4 + - - -
43D ALA* 3.0 30.7 + - - +
101D ALA* 3.4 28.7 - - + +
108D LEU* 4.6 1.1 - - + -
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Residues in contact with LYS 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D ALA* 2.9 22.2 + - - +
37D ALA* 3.5 10.4 - - - +
38D ALA 3.2 0.2 - - - -
39D ALA* 1.3 77.4 - - - +
41D ALA* 1.3 56.4 + - - +
43D ALA* 3.5 2.0 + - - +
44D SER* 3.0 32.9 + - - -
98D GLU* 5.1 12.9 - - + +
101D ALA* 4.2 9.8 - - + +
102D GLY* 4.3 15.9 - - - +
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Residues in contact with ALA 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D ALA 2.9 16.4 + - - +
38D ALA* 3.6 9.0 - - - +
39D ALA 3.2 0.2 - - - -
40D LYS* 1.3 74.0 - - - +
42D HIS* 1.3 68.7 + - + +
44D SER* 3.4 5.8 + - - -
45D ASP* 3.1 25.6 + - - +
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Residues in contact with HIS 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ASP* 2.8 30.2 + - - -
19D LEU 5.2 0.4 - - - -
20D GLU* 2.7 40.1 + - - +
23D PRO* 3.4 39.9 - - + +
24D LEU* 3.9 15.7 - - + -
27D MET* 6.2 1.1 - - - -
32D MET* 6.2 0.8 - - - +
38D ALA* 3.0 38.1 + - + +
39D ALA* 4.9 0.2 - - - -
41D ALA* 1.3 77.2 - - + +
43D ALA* 1.3 65.3 + - - +
45D ASP* 3.2 4.0 + - - +
46D LEU* 3.0 24.3 + - - +
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Residues in contact with ALA 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D LEU* 4.0 10.6 - - + +
39D ALA 3.0 18.8 + - - +
40D LYS 3.7 4.0 - - - +
41D ALA 3.3 0.2 - - - -
42D HIS* 1.3 77.1 - - - +
44D SER* 1.3 57.1 + - - +
46D LEU* 3.1 7.0 + - - +
47D VAL* 3.0 31.0 + - - +
94D VAL* 4.9 0.3 - - - +
97D LEU* 3.9 18.6 - - + -
98D GLU* 4.2 13.5 - - + -
101D ALA* 3.9 19.7 - - + -
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Residues in contact with SER 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D LYS* 3.0 20.5 + - - -
41D ALA* 4.0 5.1 + - - -
42D HIS 3.3 0.2 - - - -
43D ALA* 1.3 74.2 - - - +
45D ASP* 1.3 67.8 + - - +
47D VAL* 3.2 5.4 + - - +
48D THR* 3.0 24.0 + - - -
98D GLU* 3.6 26.2 + - - +
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Residues in contact with ASP 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A TYR* 3.4 24.7 - - + -
53A ASP* 3.0 49.5 + - - +
56A ASP* 5.0 1.7 - - - +
20D GLU* 3.7 21.4 - - - +
41D ALA 3.1 16.4 + - - +
42D HIS 3.7 6.7 - - - +
44D SER* 1.3 77.2 + - - +
46D LEU* 1.3 58.5 + - - +
48D THR* 3.2 9.2 + - - -
49D LEU* 3.0 31.1 + - - +
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Residues in contact with LEU 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D VAL* 3.9 40.4 - - + +
20D GLU* 3.9 15.5 - - + +
21D PHE* 4.3 20.9 - - + +
24D LEU* 3.8 29.4 - - + -
42D HIS 3.0 7.1 + - - +
43D ALA 3.3 8.7 - - - +
45D ASP* 1.3 73.8 - - - +
47D VAL* 1.3 64.8 + - - +
49D LEU* 3.1 11.2 + - + +
50D THR* 3.0 26.2 + - - +
90D PHE* 4.9 9.4 - - + -
94D VAL* 3.9 15.7 - - + -
97D LEU* 4.2 10.3 - - + -
115D VAL* 5.4 1.8 - - + -
131D HEC 5.5 0.2 - - + -
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Residues in contact with VAL 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D ALA 3.0 17.9 + - - +
44D SER* 3.2 9.6 + - - +
46D LEU* 1.3 76.5 - - - +
48D THR* 1.3 63.3 + - - +
50D THR* 2.6 23.8 + - - +
51D LYS* 3.2 33.8 + - + +
94D VAL* 3.8 26.9 - - + +
95D ALA* 4.7 5.4 - - - -
98D GLU* 3.5 33.7 - - + +
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Residues in contact with THR 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A THR* 3.9 32.2 - - + +
51A LYS* 4.5 9.3 + - + +
52A TYR* 4.0 24.5 - - + +
44D SER* 3.0 14.1 + - - -
45D ASP* 3.2 14.1 + - - -
47D VAL* 1.3 76.6 - - - +
49D LEU* 1.3 63.2 + - + +
51D LYS* 3.1 22.3 + - + +
52D TYR* 3.4 4.9 + - - +
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Residues in contact with LEU 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU* 5.9 0.7 - - + -
49A LEU* 5.8 7.2 - - + -
52A TYR* 4.0 27.8 - - + -
13D TYR* 3.1 31.7 + - + +
16D LEU* 3.8 27.4 - - + +
17D VAL* 3.7 40.4 - - + +
20D GLU* 4.6 2.5 - - + -
45D ASP 3.0 18.4 + - - +
46D LEU* 3.1 16.5 + - + +
48D THR* 1.3 77.5 - - + +
50D THR* 1.3 62.5 + - + +
51D LYS 3.1 1.2 + - - -
52D TYR* 3.1 22.0 + - + +
90D PHE* 6.5 0.2 - - + -
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Residues in contact with THR 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D TYR* 4.2 5.4 - - - -
46D LEU* 3.0 12.9 + - + +
47D VAL* 2.6 24.8 + - - +
49D LEU* 1.3 75.2 - - + +
51D LYS* 1.3 61.2 + - - +
52D TYR 4.0 4.7 - - - +
54D PRO* 6.0 0.2 - - - +
90D PHE* 3.9 23.1 - - + -
91D PHE* 3.3 41.4 + - + -
94D VAL* 3.7 32.8 - - + +
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Residues in contact with LYS 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A THR* 4.4 12.3 + - + +
47D VAL* 3.3 34.3 - - + +
48D THR* 3.1 14.5 + - + +
49D LEU 3.0 0.4 - - - -
50D THR* 1.3 76.6 - - - +
52D TYR* 1.3 67.3 + - - +
53D ASP* 3.1 5.0 + - - +
91D PHE* 3.3 38.0 - - + -
95D ALA* 6.3 0.4 - - - +
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Residues in contact with TYR 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU* 3.7 29.4 + - + +
19A LEU* 5.4 1.6 - - - +
20A GLU* 2.8 26.3 + - + +
45A ASP* 3.3 35.0 - - + -
48A THR* 4.0 15.4 - - + +
49A LEU* 3.5 39.9 - - + -
13D TYR* 3.9 19.6 + + + -
48D THR 3.4 2.9 + - - +
49D LEU* 3.1 21.4 + - + +
50D THR 4.0 4.7 - - - +
51D LYS* 1.3 79.2 - - - +
53D ASP* 1.3 74.3 + - - +
54D PRO* 3.3 22.4 - - + +
56D ASP* 5.4 0.9 - - - +
57D LEU* 4.3 11.8 - - + +
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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