Contacts of the helix formed by residues 64 - 72 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49C LYS 4.3 3.1 - - - -
50C THR* 4.6 5.8 - - - -
62C GLN* 3.9 4.6 + - - +
63C PHE* 1.3 74.6 - - - +
65C GLU* 1.3 61.5 + - - -
66C GLU 3.4 2.7 - - - -
67C MET* 3.5 7.6 + - - +
68C MET* 2.9 26.7 + - - +
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Residues in contact with GLU 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C LYS* 3.2 26.8 - - - +
50C THR* 3.4 19.3 - - - +
64C GLY* 1.3 71.3 - - - +
66C GLU* 1.3 72.3 + - + +
68C MET* 3.8 1.9 - - - +
69C LYS* 3.2 32.9 + - - +
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Residues in contact with GLU 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C GLY 3.4 0.4 - - - -
65C GLU* 1.3 82.0 - - + +
67C MET* 1.3 67.4 + - - +
69C LYS* 3.0 38.1 + - - +
70C ARG* 3.1 21.8 + - - +
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Residues in contact with MET 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C GLN 4.8 2.2 - - - +
63C PHE* 3.6 28.9 - - + -
64C GLY 3.5 15.7 + - - +
66C GLU* 1.3 79.0 - - - +
68C MET* 1.3 56.9 + - - +
70C ARG* 3.2 23.4 + - - +
71C ALA* 2.9 26.2 + - - +
82C GLU* 5.7 0.7 - - - +
301C LEU* 4.0 22.0 - - + -
305C GLN* 3.6 22.4 - - - +
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Residues in contact with MET 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C PHE* 3.6 18.2 - - - +
49C LYS* 3.3 26.0 - - - +
50C THR 3.4 5.8 - - - +
51C ALA* 3.3 44.4 - - + +
63C PHE* 3.5 15.4 - - + +
64C GLY 2.9 19.7 + - - +
65C GLU 3.8 1.8 - - - +
67C MET* 1.3 76.9 - - - +
69C LYS* 1.3 64.6 + - + +
71C ALA* 3.1 4.0 + - - +
72C LEU* 3.0 38.7 + - + +
298C PHE* 3.7 20.6 - - + -
53D ILE* 5.2 2.7 - - + -
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Residues in contact with LYS 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C PRO* 4.0 35.4 - - + +
44C ASN* 3.1 35.9 + - - +
48C PHE 6.1 0.2 - - - +
49C LYS* 6.1 4.7 - - + +
65C GLU* 3.2 16.3 + - - +
66C GLU* 3.0 43.5 + - - +
68C MET* 1.3 80.0 - - + +
70C ARG* 1.3 60.3 + - - +
72C LEU* 3.5 7.5 + - + +
73C GLN* 3.2 24.8 + - - +
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Residues in contact with ARG 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C GLU 3.1 12.9 + - - +
67C MET* 3.2 25.2 + - - +
69C LYS* 1.3 77.5 - - - +
71C ALA* 1.3 62.4 + - - +
73C GLN* 3.1 19.8 + - - +
74C TYR 5.0 0.9 - - - +
75C SER* 5.6 3.1 - - - -
80C ILE* 3.8 20.8 - - - +
81C PRO* 4.1 10.1 - - - +
82C GLU* 2.7 44.0 + - - -
297C THR* 3.3 11.5 + - - +
301C LEU* 3.7 23.9 - - + +
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Residues in contact with ALA 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C PHE* 3.9 13.2 - - + -
67C MET 2.9 16.3 + - - +
68C MET* 3.4 9.4 - - - +
70C ARG* 1.3 73.6 - - - +
72C LEU* 1.3 60.4 + - - +
73C GLN 3.4 0.4 + - - -
297C THR* 3.9 4.0 - - - +
298C PHE* 3.1 53.5 + - + +
301C LEU* 3.7 19.2 - - + +
268D GLY* 4.0 9.7 - - - -
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Residues in contact with LEU 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C PRO 5.5 0.4 - - - +
46C PHE* 3.3 37.1 - - + -
48C PHE* 3.3 49.6 - - + +
68C MET* 3.0 26.1 + - + +
69C LYS* 3.8 5.4 - - - +
70C ARG 3.2 0.2 - - - -
71C ALA* 1.3 75.1 - - - +
73C GLN* 1.3 54.2 + - - +
298C PHE* 4.0 14.4 - - + -
265D ILE 4.7 0.2 - - - +
266D SER* 2.8 22.0 + - - +
267D SER 3.2 7.1 + - - -
268D GLY 2.8 24.1 + - - -
269D LEU* 3.8 23.1 - - + -
302D MET* 4.8 0.4 - - + -
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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