Contacts of the helix formed by residues 61 - 79 (chain B) in PDB entry 2GB0
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 TYR 61 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B TYR* 3.4 27.4 - + + -
57B GLU* 4.3 7.2 - - + -
58B GLY 3.2 18.1 + - - +
59B ARG 3.1 0.6 + - - -
60B GLU* 1.3 83.9 - - + +
62B VAL* 1.3 64.9 + - - +
63B PRO* 3.5 1.8 - - - -
64B LEU* 3.2 8.3 + - + +
65B ALA* 2.9 18.9 + - - +
324B HIS* 2.6 54.9 + + - +
325B PHE* 3.6 19.6 + + - -
345B HIS* 3.7 16.4 - + - -
349B PHE* 3.6 27.2 - + + -
372B ILE* 4.1 7.9 - - + -
373B PHE* 3.5 31.4 - + - -
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Residues in contact with VAL 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B HIS 3.7 26.2 - - - +
54B ALA* 5.0 0.4 - - - -
55B TYR* 4.3 8.5 - - + +
59B ARG* 2.8 32.8 - - - +
61B TYR* 1.3 77.0 - - - +
63B PRO* 1.3 63.9 - - + +
65B ALA* 2.9 4.7 + - - +
66B LEU* 2.8 45.9 + - + +
107B ALA* 4.4 3.8 - - + +
111B HIS* 3.6 41.3 - - + +
113B LEU* 4.5 6.3 - - + -
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Residues in contact with PRO 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ARG 4.3 1.8 - - - +
60B GLU* 3.7 14.1 - - - +
61B TYR 3.6 3.1 - - - -
62B VAL* 1.3 94.3 - - + +
64B LEU* 1.3 55.8 + - - +
66B LEU* 3.3 9.4 + - + +
67B ARG* 2.9 30.5 + - - +
111B HIS* 4.6 10.3 - - + +
368B HIS* 5.7 3.6 - - + -
369B ASP* 6.6 0.7 - - + -
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Residues in contact with LEU 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B GLU 5.3 0.6 + - - +
61B TYR* 3.2 11.7 + - - +
63B PRO* 1.3 81.2 - - - +
65B ALA* 1.3 58.2 + - - +
67B ARG* 3.5 2.6 + - + -
68B SER* 2.8 35.5 + - - +
325B PHE* 5.0 2.0 - - + -
327B ILE* 5.0 2.5 - - + -
349B PHE* 3.7 28.7 - - + -
352B GLY* 4.2 22.9 - - - +
353B VAL* 4.4 11.2 - - + +
356B VAL* 4.4 7.4 - - + -
368B HIS* 3.8 28.3 - - + +
369B ASP 6.1 0.4 - - - +
370B ILE* 5.9 2.9 - - + -
373B PHE* 4.0 30.3 - - + -
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Residues in contact with ALA 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ILE* 4.1 4.5 - - + +
52B ARG 3.7 22.2 - - - +
53B HIS* 4.0 17.3 - - - +
55B TYR* 5.3 1.3 - - + -
61B TYR 2.9 8.6 + - - +
62B VAL* 3.3 10.5 - - - +
64B LEU* 1.3 78.7 - - - +
66B LEU* 1.3 57.1 + - - +
68B SER* 3.7 3.6 - - - -
69B GLN* 2.9 28.2 + - - +
348B LYS* 5.5 1.1 - - + -
349B PHE* 3.6 25.2 - - + -
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Residues in contact with LEU 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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53B HIS* 3.9 35.4 - - + +
62B VAL* 2.8 36.3 + - + +
63B PRO* 3.9 7.0 - - + +
65B ALA* 1.3 74.3 - - - +
67B ARG* 1.3 66.6 + - - +
69B GLN* 3.3 7.0 + - + +
70B GLU* 3.1 29.3 + - - +
111B HIS* 5.6 3.1 - - + +
113B LEU* 4.4 18.6 - - + -
805B PO4 5.7 0.7 - - - +
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Residues in contact with ARG 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 PRO 2.9 17.2 + - - +
64B LEU* 3.9 4.5 - - + +
66B LEU* 1.3 76.0 - - - +
68B SER* 1.3 67.1 + - - +
70B GLU* 3.0 35.4 + - - +
71B LEU* 3.0 49.1 + - + +
74B GLU* 4.4 10.1 + - - -
352B GLY* 4.9 2.9 - - - -
355B GLU* 2.6 36.3 + - - +
367B GLU* 5.5 2.0 + - - -
368B HIS* 3.4 27.8 - - + +
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Residues in contact with SER 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ILE* 4.7 0.7 - - - -
64B LEU* 2.8 24.0 + - - +
65B ALA* 3.7 6.1 - - - -
67B ARG* 1.3 77.4 - - - +
69B GLN* 1.3 56.1 + - - +
71B LEU* 3.1 2.1 + - - -
72B TRP* 2.8 29.6 + - - -
348B LYS 3.2 19.7 - - - -
349B PHE* 3.3 14.7 + - - +
351B SER* 2.9 23.3 + - - -
352B GLY* 3.1 21.4 + - - +
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Residues in contact with GLN 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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51B ILE* 3.2 23.3 - - + +
53B HIS* 2.8 38.2 + - + +
65B ALA 2.9 14.5 + - - +
66B LEU* 3.5 11.7 - - + +
68B SER* 1.3 76.7 - - - +
70B GLU* 1.3 62.5 + - + +
72B TRP* 3.1 14.0 + - - +
73B TYR* 3.0 54.2 + - + -
84B PHE* 3.5 31.3 - - - -
143B ASN 4.7 1.3 - - - +
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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 LEU* 3.1 18.6 + - - +
67B ARG* 3.0 41.3 + - - +
69B GLN* 1.3 75.3 - - + +
71B LEU* 1.3 59.1 + - - +
73B TYR* 3.2 12.2 + - - +
74B GLU* 3.0 32.3 + - - +
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Residues in contact with LEU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B TYR* 6.2 1.3 - - + -
21B GLN* 4.3 15.0 - - - +
24B LYS* 5.8 2.5 - - - +
67B ARG* 3.0 51.1 + - + +
68B SER 3.1 6.7 + - - +
70B GLU* 1.3 76.0 - - - +
72B TRP* 1.3 59.6 + - - +
74B GLU* 3.2 24.7 + - - +
75B LEU* 2.9 27.0 + - - +
156B TYR* 4.5 5.4 + - - +
351B SER* 3.4 40.4 - - - +
352B GLY* 3.7 10.8 - - - -
355B GLU* 4.2 11.2 - - + +
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Residues in contact with TRP 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ILE* 3.8 14.6 - - + -
68B SER 2.8 26.1 + - - -
69B GLN* 3.1 13.0 + - - +
71B LEU* 1.3 73.5 - - - +
73B TYR* 1.3 62.2 + - - +
75B LEU* 3.2 14.8 + - + +
76B GLU* 2.9 27.9 + - - +
83B ILE* 3.8 8.8 - - + +
84B PHE* 5.0 3.6 - - + -
147B LEU* 3.3 30.5 - - + +
152B CYS* 3.4 33.9 - - + -
156B TYR* 3.8 26.2 - + - -
347B PHE* 3.7 19.1 - + - -
348B LYS 2.9 19.8 + - - -
350B SER* 3.2 28.3 - - - -
351B SER* 3.2 24.5 + - - -
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Residues in contact with TYR 73 (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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69B GLN* 3.0 41.1 + - + -
70B GLU* 3.2 10.7 + - - +
72B TRP* 1.3 76.6 - - - +
74B GLU* 1.3 62.1 + - + +
76B GLU* 3.4 14.0 + - + +
77B LYS* 3.4 34.5 + - - +
84B PHE* 3.2 39.9 - + + -
86B LYS* 4.0 16.5 - - - +
143B ASN* 4.7 2.8 + - - +
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Residues in contact with GLU 74 (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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20B TYR* 5.4 1.2 + - - +
24B LYS* 4.7 10.0 + - - -
67B ARG* 4.4 12.9 + - - -
70B GLU* 3.0 19.1 + - - +
71B LEU* 3.5 30.8 - - + +
72B TRP 3.2 0.2 - - - -
73B TYR* 1.3 77.5 - - + +
75B LEU* 1.3 61.4 + - - +
77B LYS* 3.1 20.3 + - + +
78B GLU* 3.2 33.2 + - - +
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Residues in contact with LEU 75 (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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20B TYR* 5.3 1.3 - - + -
71B LEU 2.9 14.6 + - - +
72B TRP* 3.6 35.7 - - + +
74B GLU* 1.3 77.2 - - - +
76B GLU* 1.3 63.8 + - - +
78B GLU* 2.9 18.6 + - - +
79B THR* 3.2 17.8 + - + +
83B ILE* 3.7 26.7 - - + -
152B CYS* 4.1 14.6 - - - +
155B ALA* 4.1 8.5 - - + -
156B TYR* 3.8 29.4 - - + -
159B LEU* 3.7 30.3 - - + -
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Residues in contact with GLU 76 (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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72B TRP 2.9 13.3 + - - +
73B TYR* 3.4 19.5 - - + +
75B LEU* 1.3 74.8 - - - +
77B LYS* 1.3 63.5 + - + +
79B THR 3.3 17.3 - - - +
81B HIS 3.6 8.7 - - - +
82B LYS* 3.6 14.3 + - - +
83B ILE* 2.9 30.6 + - + +
84B PHE* 2.8 40.2 + - + +
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Residues in contact with LYS 77 (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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73B TYR* 3.4 23.5 + - - +
74B GLU* 3.1 12.6 + - - +
75B LEU 3.1 0.8 - - - -
76B GLU* 1.3 79.8 - - + +
78B GLU* 1.3 62.2 + - + +
79B THR 3.6 1.0 - - - +
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Residues in contact with GLU 78 (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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20B TYR* 2.6 39.7 + - - -
24B LYS* 4.9 3.3 + - - +
74B GLU* 3.3 30.7 - - - +
75B LEU* 2.9 9.6 + - - +
77B LYS* 1.3 81.7 - - + +
79B THR* 1.3 58.4 + - - +
159B LEU* 4.0 28.5 - - + +
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Residues in contact with THR 79 (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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75B LEU* 3.3 16.8 - - + +
76B GLU 3.3 15.3 - - - +
77B LYS 4.7 1.0 - - - +
78B GLU* 1.3 80.2 - - - +
80B HIS* 1.3 70.7 + - - +
81B HIS* 3.2 43.8 + - - +
83B ILE* 4.0 7.9 - - + -
155B ALA* 3.7 25.9 - - + +
158B GLU* 4.6 1.6 + - - -
159B LEU* 4.6 10.9 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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