Contacts of the helix formed by residues 34 - 53 (chain B) in PDB entry 4QPQ
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 SER 34 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B ILE* 4.1 1.8 - - - -
24B ARG* 5.8 1.3 - - - +
31B LYS* 4.0 14.3 + - - +
32B ASP 3.3 4.1 + - - -
33B VAL* 1.3 79.8 - - - +
35B PHE* 1.3 63.8 + - - +
37B ALA* 3.3 11.2 + - - +
38B THR* 3.2 22.9 + - - +
14P C 2.7 46.6 + - - -
15P G 3.3 12.8 - - - -
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Residues in contact with PHE 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B ILE* 4.5 1.1 - - + -
13B TYR* 3.6 35.7 - + - -
16B ILE* 3.6 36.1 - - + -
17B ASN* 3.4 27.1 - - - -
20B ILE* 3.7 11.5 - - + +
34B SER* 1.3 69.8 - - - +
36B SER* 1.3 66.0 + - - +
38B THR* 3.2 1.6 + - - -
39B ALA* 3.0 39.7 + - + +
4C VAL* 3.5 35.4 - - + -
5C ASN 5.0 1.8 - - - -
6C LEU* 4.4 1.3 - - + -
43C LEU* 6.3 0.2 - - + -
15P G 2.7 23.8 + - - +
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Residues in contact with SER 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B SER 3.4 0.4 - - - -
35B PHE* 1.3 75.8 - - - +
37B ALA* 1.3 56.2 + - - +
40B SER* 3.0 30.8 + - - -
5C ASN 3.7 11.4 - - - -
6C LEU* 3.7 13.7 - - - +
7C TYR* 2.8 32.2 + - - -
14P C 2.6 31.2 + - - -
15P G 3.0 18.8 + - - -
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Residues in contact with ALA 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ASP 4.3 8.5 - - - +
33B VAL* 5.2 0.2 - - - -
34B SER* 3.3 26.9 + - - +
35B PHE 3.2 0.6 - - - -
36B SER* 1.3 76.6 - - - +
38B THR* 1.3 63.2 + - + +
40B SER* 3.2 5.5 + - - -
41B MET* 2.8 29.7 + - - +
7C TYR 6.1 0.2 - - - -
14P C 3.4 13.2 + - - +
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Residues in contact with THR 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ILE* 3.7 8.5 - - - +
19B ILE* 5.3 8.7 - - + -
20B ILE* 3.6 29.3 - - + +
23B ARG* 5.3 7.0 - - + +
33B VAL* 4.3 22.7 - - + -
34B SER 3.2 18.0 + - - +
35B PHE 3.2 5.0 + - - -
37B ALA* 1.3 75.8 - - + +
39B ALA* 1.3 58.1 + - - +
41B MET* 3.3 19.2 + - + +
42B LEU* 3.1 34.7 + - - +
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Residues in contact with ALA 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ILE* 3.9 23.6 - - + -
35B PHE* 3.0 23.0 + - + +
38B THR* 1.3 76.3 + - - +
40B SER* 1.3 60.6 + - - +
42B LEU* 3.2 12.5 + - - +
43B LEU* 3.0 25.6 + - - +
6C LEU* 3.5 26.5 - - + +
43C LEU* 4.0 8.5 - - + +
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Residues in contact with SER 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B SER 3.0 20.6 + - - -
37B ALA* 3.6 5.2 - - - -
39B ALA* 1.3 74.4 - - - +
41B MET* 1.3 64.3 + - - +
43B LEU* 3.5 7.2 - - - +
44B GLU* 3.1 38.5 + - - +
6C LEU* 4.1 5.8 - - - +
7C TYR 4.2 7.5 + - - -
8C ILE* 3.3 34.5 - - - +
9C SER 4.8 0.2 + - - -
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Residues in contact with MET 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ILE* 5.6 3.4 - - + -
23B ARG* 3.9 25.8 - - - +
37B ALA 2.8 14.1 + - - +
38B THR* 3.4 26.9 - - + +
39B ALA 3.2 0.2 - - - -
40B SER* 1.3 78.3 - - - +
42B LEU* 1.3 69.4 + - + +
44B GLU* 4.1 7.3 - - - +
45B LEU* 3.2 44.9 + - - +
48B ARG* 5.4 1.0 + - - -
50C HIS* 5.1 4.3 - - + -
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Residues in contact with LEU 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ILE* 4.1 11.2 - - + -
19B ILE* 4.1 13.9 - - + -
38B THR* 3.1 20.9 + - - +
39B ALA* 3.2 7.6 + - - +
41B MET* 1.3 93.3 - - + +
43B LEU* 1.3 61.1 + - - +
45B LEU* 3.4 8.4 - - + +
46B GLY 3.0 21.8 + - - -
42C LEU 3.8 1.9 - - - +
43C LEU* 3.9 25.4 - - + +
46C GLY* 3.5 28.0 - - - +
47C LEU* 3.7 26.0 - - + +
50C HIS* 4.2 20.9 - - + +
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Residues in contact with LEU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B VAL* 6.0 1.8 - - + -
6B LEU* 4.4 3.1 - - + -
39B ALA 3.0 13.0 + - - +
40B SER* 3.3 10.1 + - - +
42B LEU* 1.3 75.3 - - - +
44B GLU* 1.3 61.1 + - + +
46B GLY* 2.9 4.9 + - - -
47B LEU* 2.9 32.8 + - + +
6C LEU* 4.1 21.8 - - + -
8C ILE* 4.2 17.3 - - + -
12C ALA* 5.6 1.6 - - + -
16C ILE* 3.7 33.0 - - + -
39C ALA* 4.0 22.4 - - + +
42C LEU* 3.8 28.2 - - + +
43C LEU* 4.5 5.6 - - + +
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Residues in contact with GLU 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B SER* 3.1 26.0 + - - +
41B MET* 4.2 5.8 - - - +
43B LEU* 1.3 76.9 - - + +
45B LEU* 1.3 62.0 + - - +
47B LEU* 3.2 12.4 + - + +
48B ARG* 3.1 44.3 + - + +
8C ILE* 6.3 0.2 - - + -
9C SER* 3.4 26.7 + - - -
12C ALA* 4.2 18.3 - - + +
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Residues in contact with LEU 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B MET* 3.2 37.0 + - - +
42B LEU* 3.4 13.0 - - + +
43B LEU 3.1 0.2 - - - -
44B GLU* 1.3 78.0 - - - +
46B GLY* 1.3 59.7 + - - +
48B ARG* 3.6 25.0 + - - +
49B VAL* 3.3 29.7 + - + +
46C GLY* 3.9 16.6 - - - +
49C VAL* 3.6 39.0 - - + -
50C HIS* 5.1 10.3 - - + +
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Residues in contact with GLY 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B LEU 3.0 7.9 + - - -
43B LEU 2.9 7.6 + - - -
45B LEU* 1.3 75.8 - - - +
47B LEU* 1.3 58.4 + - - +
49B VAL* 3.5 3.3 + - - +
50B HIS* 3.1 27.0 + - - +
42C LEU* 3.5 26.9 - - - +
45C LEU* 3.9 19.9 - - - +
46C GLY* 4.1 3.6 - - - -
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Residues in contact with LEU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B LEU* 2.9 18.7 + - + +
44B GLU* 3.2 21.9 + - + +
46B GLY* 1.3 76.2 - - - +
48B ARG* 1.3 65.7 + - + +
50B HIS* 3.2 15.0 + - + +
51B GLU* 3.3 24.8 + - + +
12C ALA* 4.0 36.3 - - + +
15C LYS* 4.2 26.0 - - + +
16C ILE* 4.6 2.9 - - + -
19C ILE* 4.2 15.9 - - + -
42C LEU* 3.7 25.1 - - + -
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Residues in contact with ARG 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B MET 5.4 1.0 + - - -
44B GLU* 3.1 37.5 + - - +
45B LEU* 4.0 28.8 + - - +
46B GLY 3.4 0.2 - - - -
47B LEU* 1.3 76.0 - - + +
49B VAL* 1.3 62.2 + - + +
51B GLU* 3.7 17.5 + - - +
52B ALA* 3.5 17.0 + - - +
15C LYS* 6.1 2.5 - - - +
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Residues in contact with VAL 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B LEU* 3.3 20.8 + - + +
46B GLY 3.8 1.6 - - - +
47B LEU 3.2 0.6 - - - -
48B ARG* 1.3 76.5 - - + +
50B HIS* 1.3 65.8 + - - +
51B GLU 3.1 2.0 - - - -
52B ALA* 3.0 23.6 + - + +
53B GLN* 3.3 21.3 + - + +
45C LEU* 3.6 28.0 - - + -
49C VAL* 4.2 25.1 - - + -
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Residues in contact with HIS 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B GLY 3.1 15.4 + - - +
47B LEU* 3.4 12.1 - - + +
49B VAL* 1.3 77.6 - - - +
51B GLU* 1.3 65.5 + - + +
53B GLN* 3.9 15.0 - - - +
19C ILE* 3.7 32.8 - - + +
22C LYS* 6.4 0.2 - - - -
23C ARG* 3.6 27.8 + - - -
41C MET* 5.0 5.2 - - + +
42C LEU* 4.2 15.8 - - + +
45C LEU* 5.1 10.0 - - + +
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Residues in contact with GLU 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B LEU* 3.3 21.7 + - + +
48B ARG* 3.9 16.6 - - - +
49B VAL 3.1 0.4 - - - -
50B HIS* 1.3 79.7 - - + +
52B ALA* 1.3 68.6 + - - +
53B GLN 4.2 3.1 - - - -
15C LYS* 3.7 30.7 + - - +
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Residues in contact with ALA 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B ARG 3.5 10.0 + - - +
49B VAL* 3.0 15.2 + - + +
51B GLU* 1.3 82.1 - - - +
53B GLN* 1.3 66.5 + - + +
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Residues in contact with GLN 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B VAL* 3.3 22.2 + - + +
50B HIS* 3.9 14.8 - - - +
51B GLU 4.2 2.6 - - - +
52B ALA* 1.3 85.8 - - + +
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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