Contacts of the helix formed by residues 46 - 62 (chain D) in PDB entry 2V3W
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 GLN 46 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B GLN* 4.6 13.2 + - - +
48B ALA* 4.8 8.1 - - - +
77B ASN 5.3 0.2 + - - -
433B TYR* 3.4 46.0 + - + +
23D ASN* 5.1 0.4 - - - -
44D ALA* 3.4 0.8 - - - +
45D LEU* 1.3 77.4 - - - +
47D GLU* 1.3 70.4 + - - +
48D ALA* 3.1 29.6 + - - +
49D CYS* 3.1 14.8 + - - +
50D VAL* 3.1 27.6 + - - +
77D ASN* 3.4 34.4 + - - +
433D TYR 5.1 3.2 - - - +
436D SER* 4.1 14.7 + - - +
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Residues in contact with GLU 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B TYR* 3.4 12.6 - - - -
1531B TPP 2.7 34.4 + - - +
23D ASN* 3.3 15.6 - - + +
46D GLN* 1.3 71.5 - - - +
48D ALA* 1.3 64.9 + - - +
49D CYS 3.2 1.6 - - - -
50D VAL* 3.6 7.4 - - - +
51D VAL* 3.1 30.0 + - - +
69D LEU* 3.7 18.8 - - + -
70D HIS* 4.9 0.9 - - - +
74D GLY* 3.2 39.2 - - - +
77D ASN* 3.0 24.7 + - + -
78D ALA* 3.4 6.2 - - + +
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Residues in contact with ALA 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B GLN* 4.6 11.7 - - - +
77B ASN* 4.9 6.5 - - - +
46D GLN* 3.1 17.7 + - - +
47D GLU* 1.3 78.1 - - - +
49D CYS* 1.3 58.1 + - - +
52D GLY* 3.0 23.6 + - - -
77D ASN 3.6 17.4 + - - +
78D ALA* 4.2 4.9 - - - +
81D ALA* 3.9 14.9 - - + +
404D GLY 4.7 2.4 - - - +
408D PRO* 4.5 2.9 - - - +
433D TYR 5.4 0.7 - - - +
434D SER* 4.4 13.9 + - - +
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Residues in contact with CYS 49 (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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44D ALA* 3.8 13.2 - - + -
45D LEU 5.1 0.2 - - - +
46D GLN* 3.1 19.8 + - - +
48D ALA* 1.3 75.2 - - - +
50D VAL* 1.3 60.6 + - - +
53D ILE* 2.8 38.8 + - + +
408D PRO* 3.9 7.0 - - - -
434D SER* 3.9 20.9 - - - -
436D SER* 3.8 13.0 - - - -
437D ALA* 3.6 38.8 - - + -
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Residues in contact with VAL 50 (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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21D PHE* 3.5 35.1 - - + +
22D GLY* 3.6 28.5 - - - +
23D ASN* 3.9 5.2 - - + +
42D ILE 5.4 0.4 - - - +
44D ALA* 3.7 17.4 - - + +
46D GLN 3.1 13.0 + - - +
47D GLU* 3.6 14.6 - - - +
49D CYS* 1.3 77.8 - - - +
51D VAL* 1.3 57.7 + - - +
53D ILE* 3.8 3.8 - - - +
54D ALA* 2.9 31.4 + - - +
67D ILE* 3.6 19.1 - - + -
69D LEU* 3.8 5.4 - - + -
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Residues in contact with VAL 51 (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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47D GLU 3.1 18.7 + - - +
50D VAL* 1.3 76.8 - - + +
52D GLY* 1.3 53.2 + - - +
54D ALA* 3.6 5.9 - - - +
55D ASP* 2.8 36.9 + - + +
67D ILE* 4.3 13.5 - - + -
69D LEU* 4.2 13.7 - - + -
78D ALA* 3.3 19.5 - - + -
81D ALA* 3.6 28.0 - - + +
82D LEU* 4.1 16.8 - - + -
92D LEU* 3.8 22.8 - - + +
94D VAL* 5.3 0.7 - - + -
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Residues in contact with GLY 52 (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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48D ALA 3.0 19.2 + - - -
49D CYS 3.8 0.9 - - - -
51D VAL* 1.3 75.5 - - - +
53D ILE* 1.3 62.8 + - - +
55D ASP* 3.2 6.8 + - - +
56D GLY 3.0 19.8 + - - -
81D ALA* 4.5 4.6 - - - +
404D GLY 5.4 0.9 - - - -
405D PHE* 4.8 8.5 - - - -
408D PRO* 4.1 10.8 - - - -
409D ALA* 3.3 18.3 - - - +
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Residues in contact with ILE 53 (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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21D PHE* 3.7 21.8 - - + -
42D ILE* 4.7 7.4 - - + -
44D ALA* 3.7 24.9 - - + -
49D CYS* 2.8 32.8 + - + +
50D VAL* 3.8 3.1 - - - +
52D GLY* 1.3 71.0 - - - +
54D ALA* 1.3 65.5 + - - +
55D ASP 3.1 0.7 + - - -
56D GLY 3.1 0.3 + - - -
57D TYR* 3.0 19.4 + - - +
408D PRO* 3.4 27.5 - - + +
411D ILE* 4.3 11.9 - - + +
412D GLY* 3.3 26.6 - - - +
415D LEU* 5.4 1.8 - - + -
437D ALA* 4.8 3.8 - - + -
440D THR* 3.8 23.8 - - + +
446D ILE* 6.1 0.2 - - + -
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Residues in contact with ALA 54 (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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21D PHE* 3.7 27.0 - - + -
50D VAL 2.9 19.1 + - - +
51D VAL 3.6 4.0 - - - +
53D ILE* 1.3 77.0 - - - +
55D ASP* 1.3 55.9 + - - +
57D TYR* 3.5 0.7 + - - +
58D ALA* 2.9 22.5 + - - +
65D ALA* 3.3 16.2 - - + +
67D ILE* 3.5 33.7 - - + -
92D LEU* 4.1 1.3 - - - -
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Residues in contact with ASP 55 (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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51D VAL* 2.8 22.4 + - + +
52D GLY* 3.4 9.1 - - - +
53D ILE 3.1 0.2 + - - -
54D ALA* 1.3 71.5 - - - +
56D GLY* 1.3 61.2 + - - +
58D ALA* 3.3 1.4 + - - +
59D GLN* 2.9 43.6 + - - +
81D ALA 4.5 3.8 - - - +
84D ASN 4.5 0.9 - - - -
85D ALA* 3.9 23.4 + - - +
88D SER* 4.3 0.9 + - - -
90D SER* 2.5 33.0 + - - -
92D LEU* 4.0 12.1 - - + -
405D PHE* 3.6 19.2 - - + -
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Residues in contact with GLY 56 (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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52D GLY 3.0 11.8 + - - -
53D ILE 3.7 1.1 - - - -
55D ASP* 1.3 75.5 - - - +
57D TYR* 1.3 56.9 + - - +
59D GLN* 4.0 6.8 - - - +
60D ALA* 3.0 33.3 + - - +
396D TYR* 6.2 0.4 - - - -
405D PHE* 5.5 0.7 - - - -
409D ALA* 3.6 27.4 - - - +
413D VAL* 3.4 16.4 - - - +
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Residues in contact with TYR 57 (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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18D ASP* 4.4 5.1 + - - -
19D THR* 3.8 11.2 + - - -
21D PHE* 3.6 26.5 - + + -
40D ARG* 3.1 30.1 + - - -
53D ILE 3.0 11.1 + - - +
54D ALA 3.5 7.4 - - - +
56D GLY* 1.3 75.0 - - - +
58D ALA* 1.3 52.5 + - - +
61D SER* 2.7 51.9 + - - -
64D PRO 5.5 4.9 - - - -
65D ALA* 4.6 7.6 - - + -
412D GLY* 3.3 24.2 - - - +
415D LEU* 3.9 17.5 - - + -
416D ALA* 3.6 28.0 - - + +
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Residues in contact with ALA 58 (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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54D ALA 2.9 18.5 + - - +
55D ASP 3.3 4.4 + - - +
57D TYR* 1.3 74.8 - - - +
59D GLN* 1.3 60.9 + - - +
61D SER* 3.6 0.7 - - - -
62D ARG* 2.9 24.3 + - - -
63D LYS 3.3 26.7 + - - +
65D ALA* 3.7 16.2 - - + +
90D SER* 5.1 2.2 - - - -
91D PRO* 4.1 16.1 - - + +
92D LEU* 3.8 12.6 - - + -
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Residues in contact with GLN 59 (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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55D ASP* 2.9 40.8 + - - +
56D GLY* 4.0 4.2 - - - +
58D ALA* 1.3 76.9 - - - +
60D ALA* 1.3 64.0 + - - +
62D ARG* 3.5 9.6 + - - +
88D SER* 3.8 18.5 + - - +
90D SER* 3.4 21.0 + - - +
91D PRO* 5.9 1.6 - - + -
238D PRO* 4.7 2.3 - - - +
239D ARG* 3.1 51.9 + - - +
396D TYR* 3.5 30.0 - - + -
405D PHE* 3.9 19.1 - - - -
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Residues in contact with ALA 60 (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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56D GLY 3.0 18.7 + - - +
59D GLN* 1.3 79.3 - - - +
61D SER* 1.3 60.9 + - - +
62D ARG* 3.5 17.7 + - - +
371D ILE* 5.7 0.4 - - + -
396D TYR* 3.5 13.2 + - - +
413D VAL* 3.9 24.0 - - + +
416D ALA* 3.7 18.8 - - + -
417D GLU* 4.2 19.9 - - + +
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Residues in contact with SER 61 (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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57D TYR* 2.7 36.8 + - - -
58D ALA* 3.4 2.8 + - - -
60D ALA* 1.3 76.1 - - - +
62D ARG* 1.3 71.3 + - - +
63D LYS* 3.3 37.7 + - - +
64D PRO 5.3 0.2 + - - -
416D ALA* 4.0 11.8 - - - +
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Residues in contact with ARG 62 (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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58D ALA 2.9 12.2 + - - -
59D GLN 3.6 10.8 - - - +
60D ALA 3.3 12.9 + - - -
61D SER* 1.3 79.6 - - - +
63D LYS* 1.3 64.7 + - - +
91D PRO* 5.5 2.5 - - - -
151D GLN* 5.4 7.2 + - - +
212D ASP* 2.9 43.4 + - - -
213D ALA* 3.2 21.9 + - - +
214D ALA 4.7 0.7 - - - -
215D ASN* 3.7 25.2 + - - +
239D ARG* 3.8 9.0 - - - +
392D PRO* 3.8 11.7 - - - +
393D GLY* 3.7 16.3 - - - +
396D TYR* 5.8 0.2 - - - -
417D GLU* 5.3 4.0 + - - -
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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