Contacts of the helix formed by residues 32 - 47 (chain B) in PDB entry 3QNQ
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 THR 32 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29B LEU* 2.7 24.5 + - + +
31B LEU* 1.3 81.3 - - + +
33B MET* 1.3 57.3 + - - +
34B PRO 3.5 0.4 - - - -
35B PHE* 2.8 33.6 + - - +
36B LEU* 3.0 30.4 + - - +
80B MET* 3.8 30.7 - - + +
83B ILE* 4.1 5.6 - - + -
84B ALA* 3.8 26.2 - - + +
146B LEU* 6.2 0.7 - - + -
264B LEU* 4.8 8.2 - - + +
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Residues in contact with MET 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A SER* 5.4 2.0 - - - +
26B ARG 5.3 1.8 - - - +
29B LEU* 4.1 6.7 - - + +
30B VAL* 3.5 41.5 - - + +
32B THR* 1.3 78.3 + - - +
34B PRO* 1.3 74.7 - - + +
35B PHE 2.8 1.4 + - - -
36B LEU* 3.2 8.3 + - - +
37B ILE* 3.1 29.0 + - + +
382B TRP* 5.4 4.3 - - - -
1G NAG 3.5 51.8 - - + +
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Residues in contact with PRO 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A SER* 3.9 28.5 - - - +
187A LEU* 3.7 22.0 - - + +
443A ZDM 3.4 39.0 - - + -
30B VAL 3.4 11.9 - - - +
31B LEU 4.2 4.5 - - - +
32B THR 3.8 1.6 - - - -
33B MET* 1.3 94.7 - - + +
35B PHE* 1.3 57.3 + - - +
37B ILE* 3.4 7.2 - - + +
38B ILE* 3.0 33.9 + - + +
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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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105A ALA* 3.6 27.4 - - + -
106A LEU* 3.7 29.2 - - + -
109A VAL* 4.0 19.5 - - + -
194A VAL* 5.9 0.9 - - + -
443A ZDM 3.8 25.6 - - + -
31B LEU 3.2 27.8 - - - -
32B THR* 2.8 9.6 + - - +
33B MET 2.8 1.0 + - - -
34B PRO* 1.3 73.0 - - - +
36B LEU* 1.3 56.3 + - + +
37B ILE 2.8 14.4 + - - -
38B ILE* 2.8 16.4 + - + +
39B GLY* 2.8 25.6 + - - -
76B THR* 3.9 19.5 - - + +
83B ILE* 3.6 30.3 - - + -
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Residues in contact with LEU 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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32B THR* 3.0 23.7 + - - +
33B MET* 3.2 8.9 + - - +
35B PHE* 1.3 75.3 - - + +
37B ILE* 1.3 52.8 + - + +
39B GLY 4.1 0.9 - - - -
40B SER* 2.6 31.7 + - - -
76B THR* 4.0 12.1 - - - +
77B PHE* 3.7 25.6 - - + -
80B MET* 3.4 30.3 - - + -
264B LEU* 3.6 31.2 - - + -
267B MET* 4.1 20.2 - - + -
379B ALA* 3.7 14.4 - - + +
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Residues in contact with ILE 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A PHE* 4.9 4.5 - - + -
187A LEU* 3.4 35.9 - - + -
33B MET* 3.1 16.9 + - + +
34B PRO* 3.4 10.8 - - + +
35B PHE 2.8 0.8 + - - -
36B LEU* 1.3 77.1 - - + +
38B ILE* 1.3 59.4 + - - +
39B GLY 3.0 0.9 - - - -
40B SER* 2.7 24.5 + - - -
41B ILE* 3.1 23.2 + - + +
379B ALA* 4.1 16.6 - - + +
381B THR* 3.2 39.3 - - + +
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Residues in contact with ILE 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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187A LEU* 4.3 9.6 - - + +
190A GLY* 3.5 11.9 - - - +
191A PHE* 3.3 44.4 - - + +
194A VAL* 3.4 32.1 - - + -
443A ZDM 5.8 0.9 - - + -
34B PRO* 3.0 24.2 - - + +
35B PHE* 2.8 28.0 + - + +
37B ILE* 1.3 76.6 - - - +
39B GLY* 1.3 62.4 + - - +
40B SER 3.3 0.2 + - - -
41B ILE* 3.3 20.4 + - - +
42B PHE* 3.3 17.7 - - + -
72B PRO* 5.5 1.3 - - + -
76B THR* 5.1 6.1 - - + -
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Residues in contact with GLY 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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35B PHE 2.8 11.6 + - - -
36B LEU 4.4 1.3 - - - -
38B ILE* 1.3 76.8 - - - +
40B SER* 1.3 58.1 + - - +
42B PHE* 3.7 4.1 + - - +
43B LEU* 3.0 24.6 + - - +
72B PRO* 4.4 9.0 - - - -
73B VAL* 3.7 9.7 - - - +
76B THR* 3.5 25.7 - - - +
77B PHE* 4.1 7.1 - - - -
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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
----------------------------------------------------------
36B LEU 2.6 20.7 + - - -
37B ILE* 2.7 18.3 + - - -
39B GLY* 1.3 69.9 - - - +
41B ILE* 1.3 58.3 + - - -
42B PHE 3.2 1.8 - - - -
43B LEU* 3.7 7.9 - - - -
44B ILE* 2.9 38.9 + - - +
77B PHE* 3.5 6.8 - - - -
378B ALA* 4.1 7.1 - - - -
379B ALA 3.0 36.2 + - - -
380B VAL* 4.8 2.0 - - - -
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Residues in contact with ILE 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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187A LEU* 5.4 2.5 - - + -
191A PHE* 3.7 48.0 - - + -
37B ILE* 3.1 27.5 + - + +
38B ILE* 3.3 9.6 + - - +
40B SER* 1.3 78.2 - - - +
42B PHE* 1.3 59.6 + - + +
44B ILE* 4.0 7.5 - - + +
45B ILE* 3.2 36.0 + - + +
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Residues in contact with PHE 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A PHE* 3.7 25.1 - + - -
194A VAL* 4.3 10.8 - - + -
195A THR* 3.8 21.5 - - + -
198A TRP* 3.5 46.4 - + + -
38B ILE 3.3 20.6 + - - -
39B GLY 3.7 5.4 + - - +
41B ILE* 1.3 76.5 - - + +
43B LEU* 1.3 67.1 + - - +
44B ILE 3.2 0.2 - - - -
45B ILE* 3.2 18.1 + - + +
46B SER* 3.5 13.9 + - - -
69B LEU* 3.7 25.4 - - + +
72B PRO* 3.4 38.4 - - + -
73B VAL* 4.3 1.1 - - + -
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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
----------------------------------------------------------
39B GLY 3.0 20.2 + - - +
40B SER* 3.7 9.0 - - - +
42B PHE* 1.3 78.3 - - - +
44B ILE* 1.3 73.4 - - + +
46B SER* 3.4 2.0 + - - -
47B THR* 3.2 43.3 + - + +
69B LEU 4.8 1.1 - - - -
73B VAL* 3.9 20.5 - - + +
77B PHE* 5.1 3.1 - - + -
271B ARG* 4.2 14.8 - - + +
274B PHE* 4.9 10.3 - - + -
275B GLN* 3.4 37.0 - - + +
376B SER* 5.2 0.4 - - - +
378B ALA* 3.6 20.6 - - + +
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Residues in contact with ILE 44 (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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40B SER* 2.9 25.4 + - - +
41B ILE* 4.4 6.5 - - + +
43B LEU* 1.3 79.1 - - + +
45B ILE* 1.3 58.8 + - - +
46B SER 3.4 1.3 - - - -
47B THR* 3.7 11.9 - - - +
48B LEU* 3.8 23.5 - - + +
376B SER* 5.4 0.7 - - - +
378B ALA* 3.2 33.7 - - + -
380B VAL* 5.8 8.3 - - + -
392B LEU* 3.6 41.5 - - + +
395B GLY* 6.1 3.6 - - - -
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Residues in contact with ILE 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 ILE* 3.2 26.1 + - + +
42B PHE* 3.2 15.8 + - + +
44B ILE* 1.3 78.0 - - - +
46B SER* 1.3 61.0 + - - +
47B THR 3.6 0.7 - - - -
48B LEU* 4.8 2.2 - - + -
53B TYR* 2.5 42.5 + - - +
57B MET* 5.7 4.5 - - + -
65B TRP* 4.0 4.7 - - - -
69B LEU* 3.6 29.8 - - + -
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Residues in contact with SER 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 PHE 3.7 7.2 - - - -
43B LEU* 3.4 3.8 + - - -
45B ILE* 1.3 81.1 - - - +
47B THR* 1.3 61.5 + - - +
48B LEU 3.6 1.2 - - - +
53B TYR* 5.2 0.4 - - - -
65B TRP* 3.6 12.5 - - - -
66B ASN* 2.7 52.8 + - - -
69B LEU* 3.4 34.7 - - - +
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Residues in contact with THR 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 3.2 26.6 + - + +
44B ILE* 3.7 9.7 - - - +
46B SER* 1.3 86.9 - - - +
48B LEU* 1.3 63.6 + - - +
49B PRO* 3.2 14.9 - - - +
66B ASN* 5.7 1.1 - - - +
274B PHE* 3.3 34.2 - - + -
275B GLN* 4.4 22.2 - - + +
395B GLY* 4.6 2.1 - - - +
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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