Contacts of the helix formed by residues 46 - 61 (chain A) in PDB entry 3QPV
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 GLY 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A ALA 3.5 1.4 - - - -
45A ARG* 1.3 80.4 - - - +
47A LYS* 1.3 58.2 + - - +
49A TYR* 3.3 1.4 + - - +
50A ILE* 2.9 38.9 + - - +
700A ADP 3.1 48.3 + - - -
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Residues in contact with LYS 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A MET* 4.0 18.5 - - + +
40A VAL 3.3 42.8 - - - +
41A GLY* 3.1 11.2 + - - +
42A LEU 3.0 20.8 + - - -
43A PRO* 3.9 5.1 - - - +
45A ARG* 4.6 1.8 - - + -
46A GLY* 1.3 78.0 - - - +
48A THR* 1.3 53.8 + - - +
50A ILE* 3.5 3.0 + - - +
51A SER* 2.7 38.1 + - - -
124A ASP* 3.9 10.3 - - - +
125A ALA 3.4 22.0 - - - +
126A THR* 3.9 6.6 - - - +
152A SER* 4.4 12.8 - - - -
700A ADP 2.8 33.3 + - - +
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Residues in contact with THR 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LYS* 1.3 72.9 - - - +
49A TYR* 1.3 52.9 + - - +
51A SER* 3.1 2.9 + - - -
52A LYS* 2.7 55.6 + - + +
67A VAL* 6.1 1.3 - - + -
69A ASN* 3.7 11.9 + - + +
124A ASP* 2.8 25.1 + - - +
168A LYS* 5.1 0.9 + - - -
424A TYR* 3.5 23.3 - - + -
524A FDP 4.1 5.5 + - - -
700A ADP 2.9 31.0 + - - -
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Residues in contact with TYR 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A GLY* 3.4 4.5 - - - +
48A THR* 1.3 73.2 - - - +
50A ILE* 1.3 72.8 + - + +
52A LYS* 3.2 4.0 + - - +
53A LYS* 2.9 55.2 + - + +
241A ILE* 5.0 8.7 - - + -
242A HIS 4.0 8.0 + - - -
243A VAL* 3.8 21.4 - - + +
421A PRO* 6.0 3.1 - - + +
423A ALA 3.7 23.6 - - - -
424A TYR* 3.7 23.1 - + + +
700A ADP 2.8 65.5 + + - +
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Residues in contact with ILE 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A MET* 3.8 22.2 - - + -
46A GLY 2.9 25.7 + - - +
47A LYS 3.8 2.9 - - - +
49A TYR* 1.3 83.2 - - + +
51A SER* 1.3 57.8 + - - +
53A LYS* 4.6 3.4 - - - -
54A LEU* 2.8 45.0 + - + +
150A ILE* 4.5 13.0 - - + -
152A SER* 4.7 10.8 - - - +
214A VAL* 4.8 11.0 - - + -
238A LEU* 3.9 27.4 - - + -
241A ILE* 5.4 6.1 - - + -
700A ADP 4.4 22.9 - - - +
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Residues in contact with SER 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A MET* 3.4 23.0 - - - +
47A LYS 2.7 25.7 + - - -
48A THR* 3.1 10.7 + - - -
50A ILE* 1.3 73.8 - - - +
52A LYS* 1.3 64.7 + - - +
54A LEU* 3.9 3.6 - - - +
55A THR* 3.0 27.5 + - - -
67A VAL* 4.1 20.0 - - - -
122A VAL* 3.6 19.8 - - - +
124A ASP* 3.5 7.9 - - - -
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Residues in contact with LYS 52 (chain A).
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* 2.7 40.1 + - + +
49A TYR 4.0 1.8 - - - +
51A SER* 1.3 74.4 - - - +
53A LYS* 1.3 56.9 - - - +
55A THR* 3.2 3.6 + - - +
56A ARG* 2.9 30.8 + - - +
67A VAL* 4.4 20.5 - - + +
72A GLU* 4.7 12.5 + - - -
424A TYR* 3.6 47.8 - - + +
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Residues in contact with LYS 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A TYR* 2.9 47.9 + - + +
50A ILE* 4.0 3.6 - - - +
52A LYS* 1.3 74.1 - - - +
54A LEU* 1.3 67.7 + - - +
56A ARG* 3.0 36.1 + - - +
57A TYR* 3.0 22.2 + - - +
237A TYR* 3.3 27.0 + - + +
241A ILE* 3.9 20.6 - - + +
242A HIS 4.7 4.4 + - - -
246A ARG* 5.5 0.8 - - - +
377A GLU* 2.6 34.9 + - - -
424A TYR 5.5 4.5 - - - +
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Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ILE* 4.2 14.1 - - + -
39A MET* 5.8 0.4 - - - -
50A ILE* 2.8 26.8 + - + +
51A SER* 3.9 3.6 - - - +
53A LYS* 1.3 76.8 - - - +
55A THR* 1.3 55.2 + - - +
57A TYR* 3.4 4.3 + - + +
58A LEU* 3.1 46.1 + - + +
122A VAL* 5.2 7.6 - - + -
150A ILE* 3.9 28.0 - - + -
234A ILE* 3.9 32.3 - - + -
237A TYR* 3.9 30.6 - - + -
238A LEU* 4.6 4.9 - - + -
241A ILE* 6.1 0.2 - - - +
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Residues in contact with THR 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A SER 3.0 21.0 + - - -
52A LYS* 3.6 4.7 - - - +
54A LEU* 1.3 72.6 - - - +
56A ARG* 1.3 60.9 + - - +
58A LEU* 3.8 0.3 - - - +
59A ASN* 2.9 53.1 + - - +
65A THR* 3.3 36.1 - - + +
66A LYS* 4.3 2.2 - - - +
67A VAL* 3.2 26.0 - - + +
122A VAL* 3.6 7.3 - - - +
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Residues in contact with ARG 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A LYS 2.9 12.4 + - - +
53A LYS* 3.2 50.3 - - - +
55A THR* 1.3 78.6 - - - +
57A TYR* 1.3 59.9 + - - +
59A ASN* 4.1 2.2 - - - +
60A TRP* 3.1 24.3 + - - +
377A GLU* 4.7 0.8 + - - -
397A TYR* 3.0 57.4 + - + +
398A PHE* 3.8 19.8 + - - +
400A ASP* 3.8 39.9 - - + +
424A TYR 5.0 4.0 + - - -
425A GLY* 4.9 18.0 - - - -
426A CYS* 5.1 8.0 - - - -
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Residues in contact with TYR 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LYS 3.0 5.7 + - - +
54A LEU* 3.6 9.4 - - + +
56A ARG* 1.3 76.2 - - - +
58A LEU* 1.3 72.1 + - + +
60A TRP* 3.0 6.8 + + - +
61A ILE* 2.9 56.4 + - + +
233A ARG* 3.3 25.1 + - + +
234A ILE* 5.8 0.4 - - - -
237A TYR* 3.3 61.2 - + + +
370A GLU* 2.6 29.8 + - - -
373A ILE* 4.6 10.3 - - + -
374A MET* 3.6 14.9 - - + +
397A TYR* 3.8 20.6 - + + -
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Residues in contact with LEU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ILE* 5.1 0.7 - - + -
54A LEU* 3.1 35.9 + - + +
55A THR 3.8 3.1 - - - +
57A TYR* 1.3 87.0 - - + +
59A ASN* 1.3 62.6 + - - +
61A ILE* 3.2 16.9 - - + +
62A GLY 3.2 4.7 + - - -
63A VAL* 2.8 33.7 + - + +
65A THR* 3.4 32.8 - - + +
120A ILE* 4.5 11.9 - - + -
122A VAL* 5.8 0.2 - - + -
230A ILE* 4.0 31.0 - - + -
233A ARG* 5.9 0.7 - - + -
234A ILE* 4.4 16.4 - - + -
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Residues in contact with ASN 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A THR* 2.9 27.2 + - - +
56A ARG* 4.1 4.0 - - - +
58A LEU* 1.3 76.7 - - - +
60A TRP* 1.3 63.8 + - - +
62A GLY* 2.8 15.9 + - - -
63A VAL 3.7 2.0 - - - -
64A PRO* 3.3 11.9 - - - +
65A THR 2.8 45.9 + - - +
112A TYR* 5.0 0.4 + - - -
400A ASP* 5.3 7.4 - - - +
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Residues in contact with TRP 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ARG 3.1 17.8 + - - +
57A TYR* 3.0 6.0 + + - +
59A ASN* 1.3 78.3 - - - +
61A ILE* 1.3 79.6 + - + +
62A GLY* 3.1 4.9 + - - -
352A TYR* 4.6 5.5 + - - -
366A VAL* 3.3 55.9 - - + +
369A LEU* 3.9 9.4 - - + -
370A GLU* 3.7 26.0 - - + -
373A ILE* 3.4 33.4 - - + -
393A CYS* 2.8 28.2 + - + -
394A LEU* 5.2 0.2 - - + -
396A ALA 4.1 2.0 - - - +
397A TYR* 3.4 44.1 - + + +
401A LYS 5.4 3.1 - - - +
406A MET* 3.9 23.1 - - + +
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Residues in contact with ILE 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A TYR* 2.9 50.3 + - + +
58A LEU* 3.2 26.7 - - + +
60A TRP* 1.3 96.8 - - + +
62A GLY* 1.3 56.1 + - - +
63A VAL* 4.1 15.7 - - + +
230A ILE* 4.5 6.1 - - + -
233A ARG* 4.0 23.1 - - + +
366A VAL* 4.0 11.2 - - + +
370A GLU* 4.2 9.9 - - + +
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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