Contacts of the helix formed by residues 49 - 64 (chain D) in PDB entry 2G33
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 49 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47D HIS* 2.3 20.2 + - - +
48D ALA* 1.3 75.0 - - - +
50D PRO* 1.3 69.6 - - - +
51D HIS* 3.2 18.1 + - - +
52D HIS* 2.6 26.7 + - - +
53D THR* 2.8 30.4 + - - -
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Residues in contact with PRO 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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47C HIS* 3.4 35.7 - - + +
49C SER 6.5 0.2 - - - -
50C PRO* 5.9 4.0 - - + -
53C THR* 4.1 23.5 - - + +
8D GLU* 4.4 2.2 - - - +
9D PHE* 4.7 9.2 - - + -
49D SER* 1.3 88.0 - - - +
51D HIS* 1.3 74.6 + - + +
53D THR* 2.9 13.0 + - - +
54D ALA* 2.8 19.3 + - - +
112D ARG* 6.2 0.4 - - - +
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Residues in contact with HIS 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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9D PHE* 3.5 31.6 - + - -
49D SER* 3.5 12.3 - - - +
50D PRO* 1.3 84.6 - - + +
52D HIS* 1.3 65.9 + - - +
54D ALA* 2.8 8.9 + - - +
55D LEU* 2.7 22.3 - - - +
103D PHE* 4.9 5.4 - + - -
104D HIS* 3.1 28.4 + - - +
107D ALA* 4.3 23.5 + - + +
108D LEU* 3.0 30.0 - - + +
112D ARG* 4.0 26.3 + - + +
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Residues in contact with HIS 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D TYR* 5.6 5.8 - + - -
41D ALA* 4.4 18.9 - - + +
42D LEU* 4.7 11.4 - - + -
48D ALA* 3.7 28.9 - - + +
49D SER* 2.6 39.6 + - - +
51D HIS* 1.3 75.9 - - - +
53D THR* 1.3 66.3 + - - +
54D ALA 3.0 0.3 + - - -
55D LEU* 3.2 14.8 + - - +
56D ARG* 3.1 37.0 - - - +
108D LEU* 3.9 29.7 - - + +
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Residues in contact with THR 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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8C GLU* 2.6 37.5 + - - +
9C PHE* 4.4 1.1 - - + -
50C PRO* 4.3 15.2 - - + +
53C THR* 4.9 1.1 - - + -
54C ALA* 3.6 33.4 - - + +
47D HIS* 3.6 6.1 - - - +
49D SER 2.8 20.1 + - - -
50D PRO* 2.9 14.9 + - - +
52D HIS* 1.3 74.4 - - - +
54D ALA* 1.3 68.4 + - - +
56D ARG* 3.6 10.9 - - - +
57D GLN* 3.5 12.9 + - + +
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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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53C THR* 5.0 9.8 - - + +
54C ALA* 5.3 0.9 - - - +
57C GLN* 4.3 23.1 - - - +
9D PHE* 5.1 2.7 - - + -
50D PRO 2.8 10.3 + - - +
51D HIS* 2.8 12.1 + - - +
53D THR* 1.3 80.5 - - - +
55D LEU* 1.3 70.7 + - - +
57D GLN* 2.8 18.0 + - - +
58D ALA* 3.5 2.8 + - - -
100D LEU* 6.5 0.4 - - + -
104D HIS* 3.8 27.1 - - + +
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Residues in contact with LEU 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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34D ALA* 5.8 7.4 - - + -
38D TYR* 6.2 3.6 - - + -
42D LEU* 4.9 17.5 - - + -
51D HIS* 2.7 35.9 - - + +
52D HIS* 3.5 7.2 - - - +
54D ALA* 1.3 68.9 - - - +
56D ARG* 1.3 57.9 + - + +
58D ALA* 2.4 42.4 + - - +
59D ILE* 2.9 19.2 - - + +
100D LEU* 5.8 2.4 - - + +
101D LEU* 5.6 2.2 - - - +
104D HIS* 3.8 35.8 - - + -
105D ILE* 5.0 12.3 - - + -
108D LEU* 5.0 13.7 - - + -
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Residues in contact with ARG 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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3C ILE* 4.8 17.7 - - + -
4C ASP 5.3 8.4 + - - -
5C PRO* 5.5 6.5 - - + -
7C LYS* 5.7 0.2 - - - +
8C GLU* 3.6 37.4 + - - +
41D ALA 3.8 18.8 + - - -
42D LEU* 3.5 32.7 + - + +
44D SER 3.3 22.2 + - - -
46D GLU 3.5 21.6 + - - -
47D HIS* 4.4 0.8 - - - +
52D HIS* 3.1 40.3 + - - +
53D THR 3.6 5.6 - - - +
55D LEU* 1.3 77.2 - - - +
57D GLN* 1.3 69.4 + - - +
59D ILE* 3.1 7.4 + - - +
60D LEU* 2.9 31.4 + - - +
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Residues in contact with GLN 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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5C PRO* 4.2 31.8 + - - +
8C GLU* 5.1 3.4 + - - -
9C PHE* 5.1 4.4 - - - -
54C ALA* 4.0 35.2 - - - +
55C LEU* 4.4 1.7 + - - -
57C GLN* 3.6 21.1 - - + -
58C ALA* 4.7 11.2 - - - +
61C ALA* 5.4 0.8 - - - +
100C LEU* 4.4 17.5 - - - +
104C HIS* 4.9 5.8 + - - -
53D THR 3.5 12.3 + - - +
54D ALA 2.8 15.5 + - - +
55D LEU 2.8 1.6 + - - -
56D ARG* 1.3 74.4 - - - +
58D ALA* 1.3 58.4 + - - +
60D LEU* 3.7 4.1 + - - +
61D ALA* 3.0 30.3 + - - +
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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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57C GLN* 4.6 10.2 + - - +
61C ALA* 6.0 0.9 - - - -
54D ALA 3.5 1.1 + - - +
55D LEU* 2.4 34.8 + - - +
57D GLN* 1.3 67.9 - - - +
59D ILE* 1.3 68.5 + - + +
61D ALA* 3.3 2.9 + - - -
62D TRP* 2.9 25.0 + - - +
97D PHE* 3.7 18.7 - - + -
100D LEU* 4.2 24.2 - - + -
101D LEU* 5.8 6.1 - - + -
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Residues in contact with ILE 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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1C MET* 5.3 15.3 - - + -
3C ILE* 5.7 3.6 - - + -
31D LEU* 5.2 15.5 - - + -
55D LEU* 2.9 39.0 + - + +
56D ARG* 3.7 7.9 - - - +
58D ALA* 1.3 77.0 - - + +
60D LEU* 1.3 63.7 + - + +
62D TRP* 3.0 14.0 + - + +
63D GLY* 2.3 36.8 + - - +
101D LEU* 5.7 12.6 - - + -
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Residues in contact with LEU 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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1C MET 5.5 5.4 - - - +
3C ILE* 3.2 39.5 - - + +
5C PRO* 3.1 38.1 - - + -
96C LYS* 4.7 13.7 - - - +
56D ARG 2.9 15.7 + - - +
57D GLN* 4.2 3.8 - - - +
59D ILE* 1.3 83.8 - - + +
61D ALA* 1.3 66.5 + - - +
63D GLY* 3.6 5.7 - - - -
64D ASP* 2.9 29.8 + - - +
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Residues in contact with ALA 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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58C ALA* 6.1 0.7 - - - -
61C ALA* 3.6 31.2 - - + +
65C LEU* 6.0 1.4 - - + +
97C PHE* 3.7 22.2 - - + -
57D GLN 3.0 20.4 + - - +
58D ALA 3.9 3.6 - - - +
60D LEU* 1.3 77.2 - - - +
62D TRP* 1.3 58.6 + - - +
64D ASP* 3.4 16.7 - - - +
65D LEU* 3.0 23.7 - - + +
97D PHE* 4.8 2.7 - - + -
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Residues in contact with TRP 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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27D VAL* 3.9 34.1 - - + -
31D LEU* 4.3 21.6 - - + +
58D ALA 2.9 17.9 + - - +
59D ILE* 3.3 11.7 - - + +
61D ALA* 1.3 74.5 - - - +
63D GLY* 1.3 61.4 - - - +
64D ASP 3.0 5.4 - - - -
65D LEU* 2.8 39.3 + - + +
66D MET* 2.9 48.3 + - + -
89D VAL* 5.0 14.8 - - + -
90D ASN* 5.5 7.0 - - - -
93D VAL* 5.7 2.7 - - + -
94D GLY* 4.4 20.4 - - - -
97D PHE* 3.5 34.3 - + + -
101D LEU* 5.8 4.3 - - + -
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Residues in contact with GLY 63 (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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59D ILE* 2.3 26.2 + - - -
60D LEU* 3.1 8.9 + - - -
62D TRP* 1.3 74.8 - - - +
64D ASP* 1.3 54.8 + - - +
65D LEU 3.1 0.9 - - - -
66D MET* 4.0 5.0 - - - +
67D THR* 2.5 37.4 + - - -
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Residues in contact with ASP 64 (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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88C TYR* 4.3 4.3 + - - -
93C VAL* 4.5 14.8 - - + +
96C LYS* 2.7 47.7 + - - +
97C PHE* 4.1 9.3 - - + -
60D LEU* 2.9 16.2 + - - +
61D ALA* 3.4 14.5 - - - +
62D TRP 3.0 0.2 - - - -
63D GLY* 1.3 77.9 - - - +
65D LEU* 1.3 62.8 + - + +
67D THR* 3.8 9.6 - - - +
68D LEU* 3.0 24.4 + - - +
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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