Contacts of the helix formed by residues 64 - 72 (chain D) in PDB entry 2R2N
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49D LYS 4.3 1.3 - - - -
50D THR* 4.5 3.1 - - - -
62D GLN* 3.8 5.7 + - - +
63D PHE* 1.3 73.9 - - - +
65D GLU* 1.3 74.8 + - - -
66D GLU 3.3 2.9 + - - -
67D MET* 3.5 8.3 + - - +
68D MET* 2.9 20.6 + - - +
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Residues in contact with GLU 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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49D LYS* 3.6 18.6 - - + +
50D THR* 3.3 21.1 - - - +
64D GLY* 1.3 80.3 - - - +
66D GLU* 1.3 63.6 + - + +
68D MET* 3.6 2.4 + - - +
69D LYS* 3.2 38.0 + - - +
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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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64D GLY 3.3 0.4 - - - -
65D GLU* 1.3 77.8 - - + +
67D MET* 1.3 65.4 + - - +
69D LYS* 3.0 38.4 + - - +
70D ARG* 3.2 19.9 + - - +
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Residues in contact with MET 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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62D GLN 4.9 2.0 - - - +
63D PHE* 3.7 28.5 - - + -
64D GLY 3.5 14.9 + - - +
66D GLU* 1.3 74.0 - - - +
68D MET* 1.3 60.7 + - - +
70D ARG* 3.2 22.0 + - - +
71D ALA* 2.8 26.6 + - - +
82D GLU* 5.9 0.4 - - - +
301D LEU* 4.0 23.1 - - + -
305D GLN* 3.5 24.2 - - - +
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Residues in contact with MET 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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53C ILE* 3.7 9.6 - - + -
302C MET* 4.7 0.4 - - + -
48D PHE* 3.4 39.5 - - + +
49D LYS* 3.3 30.7 - - - +
50D THR 3.7 25.4 - - - +
51D ALA* 4.1 1.8 - - + -
63D PHE* 3.9 15.3 - - + +
64D GLY 2.9 13.8 + - - +
65D GLU 3.7 1.8 - - - +
67D MET* 1.3 74.0 - - - +
69D LYS* 1.3 67.3 + - + +
71D ALA* 3.0 4.0 + - - +
72D LEU* 2.9 32.6 + - + +
298D PHE* 3.7 33.0 - - + -
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Residues in contact with LYS 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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43D PRO* 4.0 38.7 - - + +
44D ASN* 3.0 31.4 + - - +
49D LYS* 6.0 2.9 - - + +
65D GLU* 3.2 19.8 + - - +
66D GLU* 3.0 44.7 + - - +
68D MET* 1.3 80.3 - - + +
70D ARG* 1.3 61.6 + - - +
72D LEU* 3.4 7.6 + - + +
73D GLN* 3.3 23.0 + - - +
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Residues in contact with ARG 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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66D GLU 3.2 12.1 + - - +
67D MET* 3.4 22.5 - - - +
68D MET 3.2 0.2 - - - -
69D LYS* 1.3 75.6 - - - +
71D ALA* 1.4 62.5 + - - +
73D GLN* 3.2 19.3 + - - +
74D TYR 5.0 1.0 - - - +
75D SER* 5.7 3.2 - - - -
80D ILE* 3.7 21.6 - - - +
81D PRO* 3.9 9.7 - - - +
82D GLU* 2.8 44.0 + - - -
297D THR* 3.1 14.6 + - - +
301D LEU* 3.7 25.4 - - + +
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Residues in contact with ALA 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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268C GLY 4.1 4.5 - - - -
63D PHE* 3.8 20.6 - - + -
67D MET 2.8 14.0 + - - +
68D MET* 3.0 9.8 + - - +
70D ARG* 1.4 75.6 - - - +
72D LEU* 1.3 61.1 + - - +
73D GLN 3.7 0.7 + - - -
297D THR* 3.8 7.5 + - - +
298D PHE* 3.0 50.2 + - + +
301D LEU* 3.7 17.0 - - + +
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Residues in contact with LEU 72 (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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266C SER* 2.7 31.6 + - - +
267C SER 3.2 6.9 + - - -
268C GLY 2.8 15.0 + - - -
269C LEU* 4.0 16.8 - - + -
302C MET* 4.7 0.4 - - + -
43D PRO 5.4 0.2 - - - +
46D PHE* 3.2 37.3 - - + -
48D PHE* 3.3 50.3 - - + +
68D MET* 2.9 24.5 + - + +
69D LYS* 3.8 6.3 - - + +
70D ARG 3.2 0.4 - - - -
71D ALA* 1.3 78.2 - - - +
73D GLN* 1.3 52.2 + - - +
298D PHE* 4.0 20.4 - - + -
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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