Contacts of the strand formed by residues 29 - 38 (chain D) in PDB entry 4QPL
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 29 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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-5D HIS* 3.5 20.2 + - - -
-4D HIS* 3.4 12.8 + - - -
25D PRO* 3.9 3.8 - - - +
26D VAL 3.3 9.1 + - - +
27D GLY 3.3 3.4 - - - -
28D ASP* 1.3 81.6 + - - +
30D LEU* 1.3 61.6 + - - +
31D PHE* 2.7 37.6 + - - +
32D HIS* 3.0 37.7 - - + +
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Residues in contact with LEU 30 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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-4D HIS* 3.7 7.5 + - + -
3D LEU* 3.8 29.2 - - + -
6D ILE* 3.2 26.0 - - + +
7D GLN* 4.3 21.3 - - + +
10D LEU* 3.8 28.0 - - + -
25D PRO* 4.2 17.3 - - + -
28D ASP* 3.5 14.9 + - - +
29D ASP* 1.3 74.6 + - - +
31D PHE* 1.3 57.9 + - - +
32D HIS 3.2 1.3 - - - -
33D TRP* 2.9 26.8 + - - +
56D PHE* 3.7 1.0 - - - -
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Residues in contact with PHE 31 (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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-5D HIS* 3.5 34.1 - + + +
-4D HIS* 3.9 20.0 - + - -
-1D HIS* 4.2 13.0 - - + -
2D ALA* 4.0 20.9 - - + -
3D LEU* 4.1 22.9 - - + -
6D ILE* 3.7 14.4 - - + -
29D ASP* 2.7 18.3 + - - +
30D LEU* 1.3 73.1 - - - +
32D HIS* 1.3 56.8 + - - +
55D HIS* 3.4 6.2 - - - +
56D PHE* 2.9 59.9 + - + +
57D PRO 3.7 16.8 - - - -
58D THR* 4.1 10.3 - - + -
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Residues in contact with HIS 32 (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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25D PRO* 3.4 2.1 - - - +
26D VAL* 2.7 61.3 + - + +
29D ASP* 3.0 25.3 + - + +
30D LEU 3.2 0.8 - - - -
31D PHE* 1.3 80.7 - - - +
33D TRP* 1.3 70.0 + - - +
53D THR* 4.5 10.3 - - - +
54D VAL 3.3 5.4 - - - -
55D HIS* 3.3 38.8 + + + -
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Residues in contact with TRP 33 (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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6D ILE* 3.6 20.5 - - + +
9D GLU* 4.3 9.2 - - + -
10D LEU* 3.6 50.9 - - + -
13D LEU* 4.1 14.6 - - + -
23D ALA* 4.2 15.3 - - + -
24D GLY 3.2 11.2 - - - +
25D PRO* 3.7 12.1 - - + +
26D VAL* 3.6 5.6 - - - +
30D LEU* 2.9 35.4 + - - +
32D HIS* 1.3 85.7 - - - +
34D GLN* 1.3 62.5 + - - +
53D THR* 3.6 1.9 - - - -
54D VAL* 2.8 42.1 + - + +
56D PHE* 3.4 26.7 - + - -
99D VAL* 4.0 24.7 - - + -
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Residues in contact with GLN 34 (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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147B MET* 4.8 2.1 - - - +
23D ALA* 3.4 4.0 - - - +
24D GLY 2.9 31.4 + - - +
25D PRO 5.7 0.4 - - - -
26D VAL* 3.5 17.7 - - + +
33D TRP* 1.3 75.6 - - - +
35D ALA* 1.3 69.9 + - - +
36D THR* 5.1 2.0 - - - +
51D PHE* 3.9 26.8 - - + +
52D LEU 3.5 14.4 + - - +
53D THR* 4.7 8.8 - - + +
54D VAL* 5.2 0.2 - - - -
70D THR* 4.3 7.1 + - - +
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Residues in contact with ALA 35 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22D SER 3.3 12.3 - - - +
23D ALA* 4.1 8.3 - - + -
34D GLN* 1.3 79.6 - - - +
36D THR* 1.3 64.7 + - - +
37D ILE 4.4 0.2 - - - -
51D PHE* 3.4 4.2 - - - -
52D LEU* 2.9 44.8 + - + +
53D THR* 4.9 0.2 - - - +
54D VAL* 4.5 11.7 - - + -
103D LEU* 4.1 25.4 - - + -
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Residues in contact with THR 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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38B MET* 4.0 9.1 - - + +
49B VAL* 3.8 32.1 - - + +
20D HIS 3.7 0.4 - - - +
21D CYS* 3.2 6.2 - - - +
22D SER* 2.9 35.3 + - - +
34D GLN* 5.1 2.4 - - - +
35D ALA* 1.3 76.0 + - - +
37D ILE* 1.3 68.9 + - - +
38D MET* 4.2 1.8 - - + +
49D VAL* 3.7 28.7 - - + -
50D PHE 3.3 6.1 - - - +
51D PHE* 3.5 19.1 - - + -
103D LEU* 5.7 0.2 - - - +
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Residues in contact with ILE 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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20D HIS 3.5 4.0 - - - +
21D CYS* 4.0 10.3 - - - -
36D THR* 1.3 79.7 - - - +
38D MET* 1.3 76.2 + - - +
39D GLY 4.6 0.4 - - - +
40D PRO* 4.8 0.7 - - + -
49D VAL* 3.7 0.9 - - - -
50D PHE* 2.8 49.5 + - + +
52D LEU* 4.1 22.2 - - + -
69D PHE* 4.9 1.6 - - + -
103D LEU* 4.3 14.8 - - + +
106D ILE* 3.7 30.7 - - + -
107D CYS* 3.7 26.9 - - - -
110D LEU* 4.1 19.5 - - + -
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Residues in contact with MET 38 (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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20B HIS* 3.7 30.1 - - - +
21B CYS 3.5 24.5 - - - +
22B SER* 3.8 11.9 - - - -
36B THR* 4.7 7.0 - - + +
38B MET* 3.9 28.3 - - + -
20D HIS* 2.9 38.5 + - + +
36D THR* 4.2 1.1 - - + -
37D ILE* 1.3 78.1 - - - +
39D GLY* 1.3 71.3 + - - +
40D PRO* 3.1 3.1 - - - +
47D GLY* 3.9 9.6 - - - +
48D GLY 3.2 27.1 - - - +
49D VAL* 4.0 15.7 - - + -
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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