Contacts of the helix formed by residues 34 - 47 (chain D) 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 PRO 34 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183C SER* 4.2 21.3 - - - +
187C LEU* 3.7 27.3 - - + +
443C ZDM 3.7 38.6 - - + -
30D VAL 3.6 9.2 - - - +
31D LEU 4.3 6.3 - - - +
32D THR 3.7 1.8 - - - -
33D MET* 1.3 95.4 - - + +
35D PHE* 1.3 56.6 + - - +
37D ILE* 3.2 6.8 - - + +
38D ILE* 2.8 37.0 + - + +
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Residues in contact with PHE 35 (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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105C ALA* 3.6 33.7 - - + -
106C LEU* 3.9 18.2 - - + -
109C VAL* 3.5 37.2 - - + -
194C VAL* 5.4 0.4 - - + -
443C ZDM 4.0 26.2 - - + -
31D LEU 3.3 26.7 - - - -
32D THR* 3.2 6.5 + - - +
33D MET 3.0 1.4 + - - -
34D PRO* 1.3 73.0 - - + +
36D LEU* 1.3 55.8 + - + +
37D ILE 2.8 5.7 + - - -
38D ILE* 3.0 15.6 + - + +
39D GLY* 2.7 32.9 + - - -
76D THR* 3.5 21.6 - - + +
83D ILE* 3.7 20.4 - - + -
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Residues in contact with LEU 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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32D THR* 3.2 22.3 + - - +
33D MET* 3.3 6.0 + - - +
35D PHE* 1.3 76.9 - - + +
37D ILE* 1.3 56.1 + - - +
40D SER* 2.5 31.5 + - - -
76D THR* 4.1 5.6 - - - +
77D PHE* 4.0 32.3 - - + -
80D MET* 3.5 35.7 - - + -
83D ILE* 6.4 0.9 - - + -
264D LEU* 3.7 30.1 - - + -
267D MET* 4.5 12.6 - - + -
379D ALA* 3.3 12.3 - - + +
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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
----------------------------------------------------------
184C PHE* 4.9 8.3 - - + -
187C LEU* 3.4 33.9 - - + -
33D MET* 3.2 19.1 - - + +
34D PRO* 3.2 9.9 - - + +
35D PHE 2.8 0.2 - - - -
36D LEU* 1.3 81.0 - - + +
38D ILE* 1.3 65.1 + - - +
39D GLY 3.1 0.9 - - - -
40D SER* 3.9 4.3 - - - -
41D ILE* 3.2 29.2 + - + +
379D ALA 4.5 6.7 - - - +
380D VAL* 6.1 1.8 - - + +
381D THR* 3.2 42.0 - - + +
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Residues in contact with ILE 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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187C LEU* 4.3 10.1 - - + +
190C GLY* 3.4 12.6 - - - +
191C PHE* 3.3 49.8 - - + +
194C VAL* 3.4 39.0 - - + -
443C ZDM 5.8 1.1 - - + -
34D PRO* 2.8 26.0 + - + +
35D PHE* 3.6 20.2 - - + +
37D ILE* 1.3 78.4 - - - +
39D GLY* 1.3 61.6 + - - +
41D ILE* 3.3 16.2 - - - +
42D PHE* 3.3 12.5 - - + -
72D PRO* 5.8 0.9 - - + -
76D THR* 4.9 5.4 - - + -
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Residues in contact with GLY 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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35D PHE 2.7 15.6 + - - -
38D ILE* 1.3 72.1 - - - +
40D SER* 1.3 59.2 + - - +
41D ILE 3.0 6.6 + - - -
42D PHE* 3.3 9.2 + - - +
43D LEU* 3.1 20.3 + - - +
72D PRO 4.2 5.8 - - - -
73D VAL* 4.2 4.3 - - - +
76D THR* 3.4 28.7 - - - +
77D PHE* 3.8 8.2 - - - -
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Residues in contact with SER 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 LEU 2.5 26.3 + - - -
37D ILE* 3.4 6.3 + - - -
39D GLY* 1.3 75.6 - - - +
41D ILE* 1.3 60.2 + - - +
43D LEU* 3.8 6.0 - - - +
44D ILE* 2.8 33.6 + - - +
77D PHE* 2.9 25.1 - - - -
378D ALA* 4.7 2.7 - - - -
379D ALA 3.0 30.4 + - - -
380D VAL* 4.6 2.7 - - - -
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Residues in contact with ILE 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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191C PHE* 3.3 38.1 - - + -
37D ILE* 3.2 22.0 + - + +
38D ILE 3.3 9.2 - - - +
39D GLY 3.0 0.8 - - - -
40D SER* 1.3 75.5 - - - +
42D PHE* 1.3 65.7 + - + +
44D ILE* 2.8 35.7 + - + +
45D ILE* 2.9 23.3 + - + +
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Residues in contact with PHE 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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191C PHE* 4.4 14.1 - + - -
194C VAL* 4.2 15.5 - - + -
195C THR* 3.7 22.4 - - + -
198C TRP* 3.9 27.6 - + - -
38D ILE* 3.3 21.3 - - + -
39D GLY 3.3 4.4 + - - +
41D ILE* 1.3 78.1 - - + +
43D LEU* 1.3 63.0 + - - +
45D ILE* 3.0 26.1 + - + +
46D SER* 3.1 18.0 + - - -
69D LEU* 3.8 38.6 - - + +
72D PRO* 3.3 33.7 - - + -
73D VAL* 4.2 4.5 - - + -
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Residues in contact with LEU 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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39D GLY 3.1 15.7 + - - +
40D SER* 3.8 7.6 - - - +
41D ILE 3.2 0.2 - - - -
42D PHE* 1.3 77.2 - - - +
44D ILE* 1.3 57.4 + - - +
46D SER* 4.5 3.6 - - - +
47D THR* 3.1 36.4 + - + +
73D VAL* 3.9 21.8 - - + +
77D PHE* 4.8 1.8 - - + -
271D ARG* 4.0 17.9 - - + +
274D PHE* 5.3 3.4 - - + -
275D GLN* 3.3 42.0 - - + +
376D SER* 4.8 5.4 - - - +
378D ALA* 3.2 42.4 - - + +
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Residues in contact with ILE 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 SER* 2.8 23.8 - - - +
41D ILE* 2.8 22.9 + - + +
43D LEU* 1.3 77.4 - - - +
45D ILE* 1.3 79.0 + - + +
46D SER 3.3 0.2 - - - -
47D THR* 3.3 5.6 + - - -
48D LEU* 3.2 42.0 + - + +
378D ALA* 4.2 18.4 - - + -
380D VAL* 5.9 7.6 - - + -
392D LEU* 4.5 29.4 - - + +
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Residues in contact with ILE 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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191C PHE* 6.3 0.2 - - + -
41D ILE* 2.9 33.8 + - + +
42D PHE* 3.0 19.0 + - + +
44D ILE* 1.3 91.4 - - + +
46D SER* 1.3 63.2 + - - +
48D LEU* 3.7 6.9 + - - +
53D TYR* 2.8 35.5 + - - +
57D MET* 5.2 7.9 - - + -
65D TRP* 4.0 3.1 - - + -
69D LEU* 3.6 21.1 - - + -
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Residues in contact with SER 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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42D PHE 3.1 14.5 + - - -
43D LEU* 3.8 3.5 + - - +
45D ILE* 1.3 78.2 - - - +
47D THR* 1.3 76.1 + - - +
48D LEU 3.3 4.4 + - - +
65D TRP* 3.4 13.6 - - - -
66D ASN* 3.3 38.1 + - - +
69D LEU* 3.6 26.1 + - - +
275D GLN* 5.4 1.7 + - - -
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Residues in contact with THR 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 LEU* 3.1 23.8 + - + +
44D ILE* 3.3 7.4 + - - -
45D ILE 3.3 0.6 - - - -
46D SER* 1.3 89.5 - - - +
48D LEU* 1.3 57.6 + - - -
49D PRO* 3.2 16.6 - - - +
274D PHE* 3.2 29.3 - - + -
275D GLN* 4.4 26.0 - - + +
395D GLY* 3.9 5.7 + - - +
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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