Contacts of the helix formed by residues 64 - 78 (chain B) in PDB entry 2I6A
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 GLY 64 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ASN 3.3 24.9 - - - -
16B LEU* 3.9 5.0 + - - +
63B GLY* 1.3 71.8 - - - -
65B SER* 1.3 68.2 + - - -
66B THR 3.5 2.0 - - - -
67B GLN* 3.1 4.7 + - - -
68B ASN* 2.9 26.0 + - - -
500B 5I5 3.1 24.4 + - - -
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Residues in contact with SER 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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64B GLY* 1.3 72.2 - - - +
66B THR* 1.3 65.6 + - - +
68B ASN* 3.0 9.9 + - - +
69B SER* 3.1 12.6 + - - -
166B TYR* 4.7 5.1 + - - -
168B ALA* 4.2 8.2 - - - +
170B PHE* 3.7 35.3 - - - -
196B ASN* 5.4 2.6 + - - -
198B SER* 5.2 0.9 + - - -
300B ASP* 2.5 38.3 + - - +
500B 5I5 3.2 16.6 + - - -
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Residues in contact with THR 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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12B MET 3.5 27.2 + - - +
13B GLY* 4.3 6.9 - - - -
14B ASN 5.4 1.0 - - - +
64B GLY 3.5 0.6 - - - -
65B SER* 1.3 76.8 - - - +
67B GLN* 1.3 64.7 + - - +
69B SER* 3.2 1.9 + - - -
70B ILE* 3.0 29.2 + - + +
86B PHE* 3.8 17.0 - - + -
166B TYR* 3.8 31.0 - - + +
168B ALA* 2.9 34.1 + - - +
500B 5I5 5.7 0.6 - - - -
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Residues in contact with GLN 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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14B ASN 5.6 0.2 + - - -
15B PRO* 3.6 19.5 - - + +
16B LEU 4.1 4.2 + - - +
63B GLY 2.7 25.2 + - - +
64B GLY* 3.1 11.5 + - - +
66B THR* 1.3 78.1 - - - +
68B ASN* 1.3 58.4 + - - +
70B ILE* 3.5 2.3 + - - +
71B LYS* 3.0 59.8 + - + +
86B PHE* 3.4 39.5 - - + -
99B LEU* 4.3 13.6 - - - +
103B ALA* 4.8 1.4 - - - +
108B VAL* 6.6 0.2 - - + -
112B TYR* 2.6 30.7 + - - -
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Residues in contact with ASN 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ALA 3.7 6.9 - - - +
63B GLY* 3.4 18.2 - - - +
64B GLY 2.9 15.5 + - - +
65B SER 3.0 6.9 + - - +
67B GLN* 1.3 79.0 - - - +
69B SER* 1.3 61.2 + - - +
71B LYS* 3.2 12.7 + - - +
72B VAL* 3.0 31.4 + - + +
297B GLY* 5.8 2.6 - - - -
300B ASP* 3.5 23.9 + - + +
332B ARG* 4.5 7.0 - - - +
500B 5I5 2.9 29.3 + - - +
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Residues in contact with SER 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 SER 3.1 8.6 + - - -
66B THR 3.7 6.5 - - - -
68B ASN* 1.3 73.0 - - - +
70B ILE* 1.3 62.6 + - - +
72B VAL* 4.4 0.7 - - - -
73B ALA* 2.9 25.6 + - - +
166B TYR* 4.0 21.7 + - - -
300B ASP* 2.3 41.6 + - - +
303B VAL* 3.4 13.3 - - - +
304B GLY* 3.1 19.7 - - - -
307B LEU* 4.7 1.8 - - - -
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Residues in contact with ILE 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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9B LEU* 3.5 31.9 - - + -
10B PHE 4.3 0.7 - - - +
11B GLY* 4.1 15.5 - - - +
66B THR* 3.0 34.3 + - + +
67B GLN* 3.9 6.1 - - - +
69B SER* 1.3 74.1 - - - +
71B LYS* 1.3 64.8 + - - +
73B ALA* 3.5 3.5 - - - +
74B GLN* 3.1 22.3 + - - +
84B ALA* 3.7 11.5 - - + +
85B THR 3.7 20.6 - - - +
86B PHE* 4.2 5.4 - - + -
108B VAL* 3.6 28.7 - - + -
166B TYR* 5.1 4.3 - - + +
307B LEU* 4.9 5.8 - - + -
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Residues in contact with LYS 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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62B ALA* 3.3 34.4 + - - +
67B GLN* 3.0 43.4 + - + +
68B ASN* 3.5 12.2 + - - +
70B ILE* 1.3 77.8 - - - +
72B VAL* 1.3 52.7 + - + +
74B GLN* 3.2 6.1 + - - +
75B TRP* 2.8 33.3 + - - +
99B LEU 4.9 1.4 + - - -
102B LYS* 3.6 29.7 - - - +
103B ALA* 4.0 8.9 - - - +
106B ALA* 3.7 20.4 - - + +
108B VAL* 3.8 13.2 - - + -
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Residues in contact with VAL 72 (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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68B ASN* 3.0 19.4 + - + +
69B SER 3.8 4.3 - - - +
71B LYS* 1.3 73.3 - - + +
73B ALA* 1.3 66.0 + - - +
75B TRP* 3.3 9.5 + - + +
76B MET* 2.9 26.3 + - + +
301B ALA* 3.7 40.4 - - + +
304B GLY* 4.2 2.5 - - - -
305B GLY* 3.9 6.7 - - - +
326B ALA* 3.9 16.6 - - + -
330B ILE* 4.5 26.7 - - + -
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Residues in contact with ALA 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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9B LEU* 3.5 30.3 - - + -
69B SER 2.9 19.5 + - - +
70B ILE 3.5 5.8 - - - +
72B VAL* 1.3 76.7 - - - +
74B GLN* 1.3 54.1 + - - +
76B MET* 3.1 2.9 + - - -
77B ILE* 2.7 41.4 + - + +
84B ALA* 5.0 0.2 - - + -
304B GLY* 3.4 21.3 - - - +
307B LEU* 4.5 1.3 - - + -
308B SER* 3.7 9.5 - - - +
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Residues in contact with GLN 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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70B ILE 3.1 10.2 + - - +
71B LYS 3.2 9.2 - - - +
73B ALA* 1.3 79.9 - - - +
75B TRP* 1.3 54.4 + - - +
77B ILE* 3.0 7.5 + - - +
78B GLN* 2.6 61.6 + - - +
80B PRO 3.1 11.9 + - - -
81B HIS* 3.9 2.6 - - - +
82B LYS 3.7 3.5 + - - +
83B ALA* 2.9 29.3 + - - +
84B ALA* 3.0 17.1 + - + +
106B ALA 3.1 26.7 - - - +
107B HIS* 3.7 19.1 + - + +
108B VAL* 4.3 6.1 - - + +
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Residues in contact with TRP 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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71B LYS 2.8 13.6 + - - +
72B VAL* 3.5 12.8 - - + +
73B ALA 3.2 0.2 - - - -
74B GLN* 1.3 77.4 - - - +
76B MET* 1.3 89.6 + - + +
78B GLN* 3.1 25.1 - - - +
106B ALA 5.1 1.3 + - - -
325B TYR* 3.5 26.0 - + - -
326B ALA* 5.3 2.5 - - - -
329B ILE* 3.8 14.8 - - + -
330B ILE* 4.1 29.4 - - + -
338C PHE* 4.5 8.1 - + + +
339C PRO* 2.8 42.5 + - + -
340C GLU 3.7 12.6 + - - -
341C LYS 3.8 2.0 - - - -
342C PRO* 3.4 28.2 - - + +
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Residues in contact with MET 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 VAL* 2.9 21.8 + - + +
75B TRP* 1.3 87.1 - - + +
77B ILE* 1.3 69.4 + - - +
78B GLN* 4.1 0.2 - - - +
305B GLY* 4.3 8.3 - - - -
308B SER* 3.4 24.7 - - - +
309B GLN* 4.5 5.3 + - - +
322B ALA* 3.5 36.6 - - + +
325B TYR* 3.5 40.8 - - + -
326B ALA* 5.0 2.2 - - + -
342C PRO* 3.9 18.1 - - - +
344C PHE* 3.7 20.8 - - + +
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Residues in contact with ILE 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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4B VAL* 4.2 14.6 - - + -
8B ILE* 4.8 3.6 - - + -
9B LEU* 5.2 4.5 - - + -
73B ALA* 2.7 32.1 + - + +
74B GLN* 3.3 10.5 - - - +
76B MET* 1.3 72.7 - - - +
78B GLN* 1.3 71.6 + - - +
79B GLN 3.2 22.7 + - - +
80B PRO 4.4 1.1 - - - +
83B ALA* 3.6 36.3 - - + -
84B ALA* 5.2 1.1 - - + +
308B SER* 4.3 19.9 - - - +
311B VAL* 4.4 21.8 - - + -
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Residues in contact with GLN 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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74B GLN* 2.6 28.3 + - - +
75B TRP* 3.1 12.8 - - - +
76B MET 3.3 4.8 - - - +
77B ILE* 1.3 80.8 - - - +
79B GLN* 1.3 76.0 + - + +
80B PRO 2.6 24.8 - - - +
81B HIS* 3.7 12.7 + - - -
107B HIS* 5.3 6.5 - - - -
340C GLU 3.7 11.8 + - - +
341C LYS* 3.8 30.4 - - + +
342C PRO* 2.8 34.9 - - + +
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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
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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