Contacts of the helix formed by residues 53 - 71 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45B PHE* 3.5 5.9 - - - -
49B GLN 5.3 7.6 - - - -
50B ARG 5.6 2.9 - - - -
51B GLU 3.7 9.2 + - - +
52B ILE* 1.3 89.7 - - - +
54B PRO* 1.3 68.9 - - + +
55B HIS* 3.0 34.5 - - + +
56B MET* 2.7 33.0 + - - +
57B ARG 3.1 8.5 + - - -
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Residues in contact with PRO 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B PHE* 3.3 44.4 - - + -
52B ILE 4.6 0.2 - - - +
53B LYS* 1.3 90.0 - - + -
55B HIS* 1.3 62.0 + - - +
57B ARG* 3.2 3.6 + - - +
58B LYS* 3.2 44.1 + - - +
193B TYR* 5.6 4.0 - - + -
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Residues in contact with HIS 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LYS* 2.9 38.1 + - + +
54B PRO* 1.3 80.9 - - - +
56B MET* 1.3 88.0 + - + +
58B LYS* 3.4 11.1 + - - +
59B MET* 2.9 38.8 + - + +
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Residues in contact with MET 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B GLU 3.3 24.2 - - - +
52B ILE* 5.0 3.1 - - + -
53B LYS* 2.7 22.8 + - - +
55B HIS* 1.3 94.1 - - + +
57B ARG* 1.3 60.8 + - - +
59B MET* 3.7 8.4 - - + +
60B LEU* 2.9 30.5 + - - +
96B LYS* 3.7 39.7 - - + +
99B LEU* 3.9 29.9 - - + +
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Residues in contact with ARG 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B TYR* 3.4 18.3 + - + +
45B PHE* 3.8 17.3 - - + -
52B ILE* 5.5 3.5 - - + +
53B LYS 3.1 5.3 + - - +
54B PRO 3.2 9.4 + - - +
56B MET* 1.3 77.8 - - - +
58B LYS* 1.3 61.2 + - - +
60B LEU* 3.8 5.7 + - - +
61B ALA* 3.2 21.7 + - - +
82B MET* 3.4 26.3 - - - +
85B LEU* 4.4 12.2 - - + +
86B ASP* 2.7 39.6 + - - -
89B LEU* 4.9 4.0 - - + -
99B LEU* 5.3 4.3 - - - -
189B CYS 5.6 0.2 + - - -
190B ALA* 3.3 21.4 + - - +
191B THR 3.3 16.8 + - - -
192B ASP 3.7 1.2 + - - -
193B TYR* 3.6 30.1 - - - +
196B ALA* 4.2 8.9 - - - +
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Residues in contact with LYS 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B PRO* 3.2 29.3 + - - +
55B HIS* 3.8 9.6 - - - +
56B MET 3.2 0.2 - - - -
57B ARG* 1.3 79.2 - - - +
59B MET* 1.3 66.2 + - - +
60B LEU 3.1 1.3 - - - -
61B ALA* 3.0 16.8 + - - +
62B TYR* 3.1 31.3 + - + -
191B THR 3.3 19.5 - - - +
192B ASP* 4.3 10.8 + - - +
193B TYR* 3.9 30.2 - - - +
194B THR* 5.6 3.4 - - - +
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Residues in contact with MET 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B HIS* 2.9 30.9 + - + +
56B MET* 3.7 9.4 - - + +
58B LYS* 1.3 77.1 - - - +
60B LEU* 1.3 61.4 + - - +
62B TYR* 3.7 6.4 + - - +
63B TRP* 3.6 17.2 + - - +
173D ASP* 2.9 51.6 - - + +
174D ARG* 5.9 2.7 - - - -
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Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B MET 2.9 17.7 + - - +
57B ARG* 3.9 5.4 - - - +
59B MET* 1.3 74.8 - - - +
61B ALA* 1.3 63.9 + - - +
63B TRP* 3.2 29.1 + - + +
64B MET* 3.0 53.4 + - + +
85B LEU* 4.1 15.0 - - + -
99B LEU* 3.7 39.3 - - + +
100B GLN* 4.2 22.2 - - + -
103B GLY* 4.6 0.4 - - - -
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Residues in contact with ALA 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B ARG 3.2 13.6 + - - +
58B LYS* 3.0 11.8 + - - +
60B LEU* 1.3 80.8 - - - +
62B TYR* 1.3 57.7 + - - +
64B MET* 3.2 1.3 + - - -
65B LEU* 3.0 22.9 + - - +
78B PHE* 3.2 14.1 - - + -
82B MET* 4.0 24.5 - - + -
191B THR* 3.8 31.4 - - + +
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Residues in contact with TYR 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B LYS* 3.1 37.9 + - + +
59B MET* 4.1 5.4 - - - +
60B LEU 3.3 0.4 - - - -
61B ALA* 1.3 78.0 - - - +
63B TRP* 1.3 57.7 + - - +
65B LEU* 3.4 6.5 + - + -
66B GLU* 3.0 27.0 + - - +
188B LEU* 5.5 0.3 - - - +
191B THR* 4.0 19.5 + - + -
254B SER* 3.9 19.1 - - - -
172D ARG 5.3 1.1 - - - +
173D ASP* 2.9 30.5 - - - +
174D ARG* 3.6 34.5 - - + +
176D ALA* 3.6 24.6 - - + +
177D LEU* 3.5 37.1 - - + +
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Residues in contact with TRP 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B MET 3.6 10.8 + - - +
60B LEU* 3.2 28.6 + - + +
62B TYR* 1.3 77.6 - - - +
64B MET* 1.3 68.5 + - + +
66B GLU* 3.4 16.9 + - + +
67B VAL* 3.1 34.4 + - + +
100B GLN* 4.0 32.3 + - + -
103B GLY 4.5 0.7 - - - -
104B ALA* 4.3 11.0 - - + -
107B MET* 3.7 22.7 - - + -
124B LEU* 5.3 2.0 - - + -
127B TYR* 3.7 39.3 + - + +
128B THR* 3.8 26.5 - - + -
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Residues in contact with MET 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B LEU* 3.0 36.4 + - + +
61B ALA 3.2 6.7 + - - +
63B TRP* 1.3 79.7 - - + +
65B LEU* 1.3 64.0 + - - +
67B VAL* 3.4 1.6 + - - +
68B CYS* 3.1 30.7 + - - -
78B PHE* 3.6 12.1 - - + -
81B ALA* 4.5 13.9 - - - -
82B MET* 3.6 19.5 - - - +
85B LEU* 4.1 17.0 - - + -
103B GLY* 3.2 39.7 - - - +
106B CYS* 5.1 1.6 - - + -
107B MET* 3.6 28.9 - - + +
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Residues in contact with LEU 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ALA 3.0 13.7 + - - +
62B TYR* 3.6 10.8 - - + +
63B TRP 3.2 0.2 - - - -
64B MET* 1.3 75.7 - - - +
66B GLU* 1.3 64.8 + - - +
68B CYS* 3.4 2.8 + - + +
69B GLU* 2.9 50.1 + - + +
78B PHE* 3.6 33.8 - - + -
187B ALA* 4.0 12.1 - - + -
191B THR* 4.5 9.9 - - + -
176D ALA* 3.3 24.2 - - + +
177D LEU* 3.7 32.5 - - + +
180D LYS* 5.2 2.7 - - + +
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Residues in contact with GLU 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B TYR 3.0 18.9 + - - +
63B TRP* 3.6 17.8 - - + +
64B MET 3.3 0.2 - - - -
65B LEU* 1.3 77.7 - - - +
67B VAL* 1.3 58.8 + - + +
69B GLU* 3.4 4.0 + - - +
70B GLU* 2.8 43.3 + - - +
127B TYR* 5.7 0.7 - - - -
172D ARG* 3.4 35.8 - - - +
175D GLN* 4.4 8.8 - - - +
176D ALA* 4.1 17.7 - - + +
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Residues in contact with VAL 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B TRP* 3.1 37.8 + - + +
64B MET 3.7 4.9 - - - +
65B LEU 3.3 0.2 - - - -
66B GLU* 1.3 77.2 - - + +
68B CYS* 1.3 59.0 + - - +
70B GLU* 3.2 6.7 + - - +
71B GLN* 2.8 30.9 + - + +
107B MET* 4.0 16.8 - - + -
119B LEU* 4.8 7.4 - - + -
124B LEU* 4.1 23.6 - - + -
127B TYR* 3.9 37.7 - - + -
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Residues in contact with CYS 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B MET 3.1 24.7 + - - +
65B LEU* 4.0 3.6 - - + +
67B VAL* 1.3 74.8 - - - +
69B GLU* 1.3 63.1 + - + +
71B GLN 3.4 0.2 + - - -
72B ARG* 2.8 24.9 + - - -
73B CYS* 2.9 33.1 + - + +
74B GLU 5.7 0.4 - - - +
77B VAL* 4.2 15.3 - - - -
78B PHE* 4.1 31.9 - - + +
107B MET* 3.8 21.3 - - - -
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Residues in contact with GLU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B LEU* 2.9 38.1 + - + +
66B GLU* 3.9 4.5 - - - +
68B CYS* 1.3 76.8 - - + +
70B GLU* 1.3 63.7 + - - +
72B ARG* 3.4 53.5 + - - +
75B GLU* 3.9 7.6 - - - +
176D ALA* 5.3 4.3 - - + +
179D LYS* 6.0 8.2 + - + +
180D LYS* 3.2 47.5 + - + +
183D GLN* 4.3 4.3 - - - +
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Residues in contact with GLU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B GLU* 2.8 32.4 + - - +
67B VAL* 3.4 4.5 - - - +
69B GLU* 1.3 77.5 - - - +
71B GLN* 1.3 60.8 + - - +
72B ARG* 3.1 7.1 + - - +
127B TYR* 3.1 29.4 - - + +
74D GLU* 4.5 10.9 - - - +
179D LYS* 4.4 17.8 + - - +
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Residues in contact with GLN 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B VAL* 2.8 14.7 + - + +
70B GLU* 1.3 75.1 - - - +
72B ARG* 1.3 71.3 + - - +
73B CYS* 3.0 19.2 + - - -
119B LEU* 3.4 23.6 - - + -
123B LYS* 3.1 42.4 - - + +
126B ILE* 6.0 1.4 - - - +
127B TYR* 2.5 45.4 + - - -
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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