Contacts of the helix formed by residues 53 - 71 (chain D) in PDB entry 3G33
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 LYS 53 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45D PHE* 3.5 6.3 - - - -
49D GLN 5.3 7.2 - - - -
50D ARG 5.6 3.6 - - - -
51D GLU* 3.7 9.2 + - - +
52D ILE* 1.3 89.7 - - - +
54D PRO* 1.3 68.4 - - + +
55D HIS* 3.1 35.0 - - + +
56D MET* 2.7 32.7 + - - +
57D ARG 3.1 8.5 + - - -
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Residues in contact with PRO 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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45D PHE* 3.3 44.3 - - + -
53D LYS* 1.3 90.4 - - + +
55D HIS* 1.3 62.6 + - - +
57D ARG* 3.2 3.8 + - - +
58D LYS* 3.2 43.8 + - - +
193D TYR* 5.6 3.4 - - + -
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Residues in contact with HIS 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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53D LYS* 2.9 37.9 + - + +
54D PRO* 1.3 80.5 - - - +
56D MET* 1.3 88.6 + - + +
58D LYS* 3.4 10.8 + - - +
59D MET* 2.8 38.6 + - + +
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Residues in contact with MET 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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51D GLU 3.3 24.5 - - - +
52D ILE* 5.0 2.9 - - + -
53D LYS* 2.7 24.2 + - - +
55D HIS* 1.3 94.9 - - + +
57D ARG* 1.3 60.5 + - - +
59D MET* 3.7 7.8 - - - +
60D LEU* 2.9 30.8 + - - +
96D LYS* 3.7 38.8 - - + +
99D LEU* 3.9 28.9 - - + +
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Residues in contact with ARG 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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44D TYR* 3.4 18.7 + - - +
45D PHE* 3.8 17.0 - - + -
52D ILE* 5.5 3.3 - - + +
53D LYS 3.1 5.7 + - - +
54D PRO 3.2 8.5 + - - +
56D MET* 1.3 77.2 - - - +
58D LYS* 1.3 62.2 + - - +
60D LEU* 3.8 6.5 + - - +
61D ALA* 3.2 19.8 + - - +
82D MET* 3.4 26.8 - - - +
85D LEU* 4.4 12.0 - - + +
86D ASP* 2.7 39.3 + - - -
89D LEU* 4.9 4.5 - - + -
99D LEU* 5.0 4.5 - - - +
189D CYS 5.6 0.2 + - - -
190D ALA* 3.3 22.0 + - - +
191D THR 3.3 17.4 + - - -
192D ASP 3.7 0.8 + - - -
193D TYR* 3.6 30.9 - - - +
196D ALA* 4.2 8.9 - - - +
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Residues in contact with LYS 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 PRO* 3.2 28.2 + - - +
55D HIS* 3.8 9.3 - - - +
57D ARG* 1.3 78.1 - - - +
59D MET* 1.3 65.2 + - - +
60D LEU 3.1 1.6 - - - -
61D ALA* 3.0 16.5 + - - +
62D TYR* 3.1 30.4 + - + -
191D THR 3.3 18.6 - - - +
192D ASP* 4.3 11.9 + - - +
193D TYR* 3.9 30.2 - - - +
194D THR* 5.6 3.0 - - - +
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Residues in contact with MET 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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173B ASP* 4.3 35.4 - - + +
174B ARG* 6.5 0.2 - - - -
55D HIS* 2.8 30.9 + - + +
56D MET* 3.7 9.0 - - - +
58D LYS* 1.3 76.7 - - - +
60D LEU* 1.3 61.4 + - - +
62D TYR* 3.7 7.5 + - - +
63D TRP* 3.6 16.3 + - - +
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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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56D MET 2.9 18.4 + - - +
57D ARG* 3.9 5.4 - - - +
59D MET* 1.3 75.3 - - - +
61D ALA* 1.3 65.7 + - - +
63D TRP* 3.2 29.8 + - + +
64D MET* 3.0 51.5 + - + +
85D LEU* 4.1 15.7 - - + -
99D LEU* 3.7 40.6 - - + +
100D GLN* 4.2 22.0 - - + -
103D GLY* 4.6 0.2 - - - -
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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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57D ARG 3.2 13.4 + - - +
58D LYS* 3.0 12.2 + - - +
60D LEU* 1.3 80.4 - - - +
62D TYR* 1.3 57.5 + - - +
64D MET* 3.2 1.1 + - - -
65D LEU* 3.0 22.9 + - - +
78D PHE* 3.2 14.6 - - + -
82D MET* 4.0 25.4 - - + -
191D THR* 3.8 31.4 - - + +
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Residues in contact with TYR 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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173B ASP 3.8 24.5 - - - +
174B ARG* 4.5 17.7 - - + -
176B ALA* 4.0 18.5 - - + +
177B LEU* 3.3 42.7 - - + +
58D LYS* 3.1 36.2 + - + +
59D MET* 4.1 8.3 - - - +
60D LEU 3.3 0.2 - - - -
61D ALA* 1.3 77.3 - - - +
63D TRP* 1.3 58.3 + - - +
65D LEU* 3.4 9.0 + - + +
66D GLU* 3.0 32.7 + - + +
188D LEU* 5.5 0.3 - - - +
191D THR* 4.0 21.5 + - + -
254D SER* 3.9 18.2 - - - -
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Residues in contact with TRP 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 MET 3.6 10.2 + - - +
60D LEU* 3.2 29.6 + - + +
62D TYR* 1.3 77.4 - - - +
64D MET* 1.3 66.4 + - + +
66D GLU* 3.4 15.6 + - + +
67D VAL* 3.1 35.5 + - + +
100D GLN* 4.0 32.7 + - + -
103D GLY 4.5 0.9 - - - -
104D ALA* 4.3 11.0 - - + -
107D MET* 3.7 22.9 - - + -
124D LEU* 5.3 2.0 - - + -
127D TYR* 3.7 42.5 + - + +
128D THR* 3.8 21.5 - - + -
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Residues in contact with MET 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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60D LEU* 3.0 36.1 + - + +
61D ALA 3.2 6.7 + - - +
63D TRP* 1.3 80.1 - - + +
65D LEU* 1.3 64.0 + - - +
67D VAL* 3.4 1.7 + - - +
68D CYS* 3.1 30.0 + - - -
78D PHE* 3.6 11.9 - - + -
81D ALA* 4.5 13.9 - - - -
82D MET* 3.5 20.2 - - - +
85D LEU* 4.1 17.0 - - + -
103D GLY* 3.2 39.7 - - - +
106D CYS* 5.1 1.3 - - + -
107D MET* 3.6 31.1 - - + +
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Residues in contact with LEU 65 (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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176B ALA* 3.9 21.8 - - + +
177B LEU* 4.0 30.7 - - + +
180B LYS* 5.2 3.4 - - + +
61D ALA 3.0 14.1 + - - +
62D TYR* 3.5 11.4 - - + +
64D MET* 1.3 75.1 - - - +
66D GLU* 1.3 65.9 + - - +
68D CYS* 3.4 3.3 + - + -
69D GLU* 2.9 49.4 + - + +
78D PHE* 3.6 35.4 - - + -
187D ALA* 4.0 13.5 - - + -
191D THR* 4.5 12.3 - - + -
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Residues in contact with GLU 66 (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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172B ARG* 3.2 31.3 - - - +
175B GLN* 4.9 3.1 - - - +
176B ALA* 3.8 22.0 + - + +
62D TYR 3.0 20.5 + - - +
63D TRP* 3.6 17.7 - - + +
64D MET 3.3 0.2 - - - -
65D LEU* 1.3 76.3 - - - +
67D VAL* 1.3 58.5 + - + +
69D GLU* 3.4 3.7 + - - +
70D GLU* 2.8 44.7 + - - +
127D TYR* 5.7 0.4 - - - -
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Residues in contact with VAL 67 (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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63D TRP* 3.1 37.8 + - + +
64D MET 3.7 4.9 - - - +
66D GLU* 1.3 77.0 - - + +
68D CYS* 1.3 58.9 + - - +
70D GLU* 3.2 6.7 + - - +
71D GLN* 2.8 30.4 + - + +
107D MET* 4.0 17.7 - - + -
119D LEU* 4.7 7.9 - - + -
124D LEU* 4.1 23.8 - - + -
127D TYR* 3.9 38.1 - - + -
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Residues in contact with CYS 68 (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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64D MET 3.1 21.1 + - - +
65D LEU* 4.0 3.6 - - + +
67D VAL* 1.3 74.2 - - - +
69D GLU* 1.3 63.5 + - + +
71D GLN 3.4 0.2 + - - -
72D ARG* 2.8 24.4 + - - -
73D CYS* 2.9 32.8 + - + +
74D GLU 5.7 0.9 - - - +
77D VAL* 4.2 15.7 - - - -
78D PHE* 4.1 30.5 - - + +
107D MET* 3.8 22.0 - - - -
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Residues in contact with GLU 69 (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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75B GLU* 5.4 0.2 - - - +
176B ALA* 5.4 4.0 - - + +
180B LYS* 3.2 48.7 + - + +
183B GLN* 4.6 2.8 - - - +
65D LEU* 2.9 38.0 + - + +
66D GLU* 3.9 4.7 - - - +
68D CYS* 1.3 77.6 - - + +
70D GLU* 1.3 63.3 + - - +
72D ARG* 3.4 52.7 + - - +
75D GLU* 3.9 7.8 - - - +
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Residues in contact with GLU 70 (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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74B GLU* 4.9 4.3 - - - +
179B LYS* 5.0 11.8 + - - -
66D GLU* 2.8 32.4 + - - +
67D VAL* 3.4 4.3 - - - +
68D CYS 3.1 0.2 - - - -
69D GLU* 1.3 77.2 - - - +
71D GLN* 1.3 60.5 + - - +
72D ARG* 3.1 11.4 + - - +
127D TYR* 3.2 30.5 - - + +
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Residues in contact with GLN 71 (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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67D VAL* 2.8 15.8 + - + +
70D GLU* 1.3 75.0 - - - +
72D ARG* 1.3 70.5 + - - +
73D CYS* 3.0 19.2 + - - -
119D LEU* 3.4 24.2 - - + -
123D LYS* 3.1 43.5 - - + +
126D ILE* 6.0 1.2 - - - +
127D TYR* 2.5 45.0 + - - -
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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