Contacts of the helix formed by residues 63 - 74 (chain B) in PDB entry 1V2E
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 LEU 63 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B GLN* 4.0 20.6 - - - +
58B ALA* 4.0 25.8 - - + -
59B PRO* 4.3 4.9 - - + +
62B GLY* 1.3 70.2 - - - -
64B PRO* 1.3 83.3 - - + +
65B ALA* 4.3 8.3 - - + +
66B LEU* 2.8 21.8 + - + +
67B ARG* 3.1 10.0 + - - +
257B THR* 3.8 15.7 - - + +
260B GLN* 3.1 17.9 + - + +
261B ALA* 3.7 37.5 - - + +
264B ALA* 6.1 0.2 - - + -
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Residues in contact with PRO 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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59B PRO* 4.6 10.3 - - + -
62B GLY 3.4 7.5 - - - +
63B LEU* 1.3 90.7 - - + +
65B ALA* 1.3 63.0 + - - +
67B ARG* 3.3 9.4 + - + +
68B GLU* 2.9 39.3 + - + +
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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
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63B LEU* 2.9 12.0 + - + +
64B PRO* 1.3 76.5 - - - +
66B LEU* 1.3 56.1 + - - +
68B GLU* 3.3 7.0 + - - +
69B ALA* 2.8 28.6 + - - +
261B ALA* 6.2 0.9 - - - -
264B ALA* 4.0 15.6 - - + +
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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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63B LEU* 2.8 18.0 + - + +
65B ALA* 1.3 72.1 - - - +
67B ARG* 1.3 65.2 + - - +
69B ALA* 3.0 1.6 + - - -
70B LEU* 2.9 43.0 + - + +
83B VAL* 3.5 25.6 - - + -
231B VAL* 4.0 12.8 - - + -
233B TRP* 5.4 0.7 - - + -
260B GLN* 3.5 50.7 - - + +
263B VAL* 4.3 5.8 - - + -
264B ALA* 3.8 13.6 - - + +
267B LEU* 3.7 20.0 - - + -
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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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59B PRO* 6.2 0.4 - - - +
61B ALA* 3.5 38.1 + - - +
62B GLY* 3.6 22.9 + - - -
63B LEU 3.1 10.2 + - - +
64B PRO* 3.8 10.9 - - + +
66B LEU* 1.3 75.2 - - - +
68B GLU* 1.3 57.0 + - - +
70B LEU* 3.6 2.0 + - - +
71B ALA* 2.8 29.2 + - - +
78B PRO* 3.1 35.6 + - + +
79B GLU* 3.5 17.6 + - - +
81B VAL* 3.1 34.5 + - + +
82B VAL* 5.1 1.6 - - - +
83B VAL* 4.4 6.1 - - + -
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Residues in contact with GLU 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B PRO* 2.9 30.4 + - + +
65B ALA* 3.6 6.5 - - - +
67B ARG* 1.3 76.3 - - + +
69B ALA* 1.3 65.0 + - - +
71B ALA* 3.5 8.2 - - - +
72B GLU* 3.2 29.5 + - - +
78B PRO* 3.9 21.6 - - + +
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Residues in contact with ALA 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 ALA 2.8 17.4 + - - +
66B LEU* 3.0 8.0 + - - +
68B GLU* 1.3 79.7 - - - +
70B LEU* 1.3 62.8 - - - +
72B GLU* 3.3 8.7 + - - +
73B GLU* 3.4 3.5 + - - +
264B ALA* 3.8 22.2 - - + +
267B LEU* 4.2 11.7 - - + -
268B LYS* 3.3 39.8 + - + +
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Residues in contact with LEU 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* 2.9 46.1 + - + +
69B ALA* 1.3 74.9 - - - +
71B ALA* 1.3 66.2 + - - +
72B GLU 3.1 0.3 + - - -
73B GLU* 3.1 8.7 + - - +
74B PHE* 3.1 44.3 + - + +
81B VAL* 3.9 23.6 - - + -
83B VAL* 4.5 4.7 - - + -
233B TRP* 3.7 56.5 - - + -
235B VAL* 5.1 0.4 - - + -
267B LEU* 3.7 17.9 - - + -
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Residues in contact with ALA 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 ARG 2.8 20.7 + - - +
68B GLU* 3.5 11.2 - - - +
69B ALA 3.3 0.4 - - - -
70B LEU* 1.3 76.5 - - - +
72B GLU* 1.3 54.4 + - + +
74B PHE 3.8 0.2 + - - -
75B ALA* 3.2 6.8 + - - -
76B VAL* 3.0 53.9 + - - +
77B GLU 3.9 1.6 - - - +
78B PRO* 3.7 23.6 - - + -
81B VAL* 4.2 1.3 - - - +
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Residues in contact with GLU 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 GLU* 3.2 17.3 + - - +
69B ALA* 3.6 8.5 - - - +
70B LEU 3.1 0.8 - - - -
71B ALA* 1.3 75.9 - - + +
73B GLU* 1.3 66.2 + - - +
74B PHE 3.2 0.6 + - - -
75B ALA* 3.4 10.2 + - - +
268B LYS* 4.1 23.6 + - - +
272B ARG* 5.1 4.0 + - - -
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Residues in contact with GLU 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 ALA 3.4 3.7 + - - +
70B LEU* 3.1 13.8 + - - +
72B GLU* 1.3 80.1 - - - +
74B PHE* 1.3 70.4 + - + +
75B ALA* 3.7 0.9 + - - +
223B ARG* 2.7 38.2 + - - -
267B LEU* 3.7 26.1 - - - +
268B LYS* 3.3 20.4 + - - +
271B ARG* 3.1 38.4 + - + +
276B TYR* 4.3 0.7 + - - -
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Residues in contact with PHE 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 LEU* 3.1 44.2 + - + +
73B GLU* 1.3 91.4 - - + +
75B ALA* 1.3 69.4 + - - +
76B VAL* 3.2 22.0 - - + +
195B ASP* 4.3 2.5 - - - -
205B ARG* 3.6 42.8 - - - -
207B ARG* 3.6 24.1 + - - +
216B THR* 4.5 13.7 - - + -
223B ARG* 4.2 5.8 - - - -
233B TRP* 3.7 21.1 - + - -
235B VAL* 4.2 28.7 - - + -
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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