Contacts of the helix formed by residues 64 - 79 (chain D) in PDB entry 2C11
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 SER 64 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62D ASP 3.3 4.5 + - - -
63D LEU* 1.3 73.6 - - - +
65D ARG* 1.3 65.2 + - - +
66D GLU* 3.5 7.7 + - - +
67D GLU* 3.0 38.2 + - - +
68D LEU* 2.9 28.5 + - - +
414D HIS* 4.6 7.4 - - - -
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Residues in contact with ARG 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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64D SER* 1.3 74.9 - - - +
66D GLU* 1.3 79.1 + - - +
68D LEU* 3.7 3.4 - - - +
69D THR* 2.9 19.9 + - - -
414D HIS* 4.2 36.4 - - + +
422D PRO* 3.4 26.1 - - + +
424D THR* 5.3 3.4 - - - +
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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 SER* 3.2 6.5 + - - +
65D ARG* 1.3 103.2 + - - +
67D GLU* 1.3 58.2 + - - +
68D LEU 3.0 1.8 - - - -
69D THR* 2.6 31.6 + - - -
70D ALA* 3.0 12.9 + - - +
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Residues in contact with GLU 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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63D LEU* 3.9 3.4 - - + -
64D SER* 3.0 30.4 + - - +
66D GLU* 1.3 78.4 - - - +
68D LEU* 1.3 61.6 + - - +
70D ALA* 3.6 3.7 + - - +
71D VAL* 3.0 29.4 + - - +
122D ARG* 2.6 44.0 + - - +
146D LEU* 3.4 44.5 - - + +
147D PRO* 4.3 16.1 - - + +
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Residues in contact with LEU 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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63D LEU* 3.4 30.1 - - + +
64D SER 2.9 28.9 + - - +
65D ARG 3.7 4.3 - - - +
67D GLU* 1.3 74.6 - - - +
69D THR* 1.3 61.0 + - - +
71D VAL* 3.4 6.1 + - - +
72D MET* 2.9 28.9 + - - +
99D VAL* 3.5 27.1 - - + +
100D GLU* 4.6 0.7 - - - -
414D HIS* 4.0 19.7 - - + +
415D PHE* 4.0 18.8 - - - -
416D LEU* 3.6 17.2 - - + +
422D PRO* 3.8 25.4 - - + -
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Residues in contact with THR 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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65D ARG* 2.9 16.3 + - - +
66D GLU* 2.6 18.9 + - - -
68D LEU* 1.3 73.8 - - - +
70D ALA* 1.3 48.8 + - - +
72D MET* 3.0 8.4 + - + +
73D ARG* 2.7 73.1 + - + +
420D GLN 5.9 0.2 - - - -
422D PRO* 3.5 18.6 - - + +
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Residues in contact with ALA 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 3.0 10.1 + - - +
67D GLU* 3.9 9.2 - - - +
69D THR* 1.3 72.9 - - - +
71D VAL* 1.3 60.8 + - - +
73D ARG* 3.2 11.0 + - - +
74D PHE* 2.8 31.2 + - - +
146D LEU* 4.5 0.7 - - + -
147D PRO 3.4 24.9 - - - +
149D PRO* 4.1 10.0 - - + +
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Residues in contact with VAL 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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63D LEU* 4.7 0.9 - - + -
67D GLU 3.0 18.2 + - - +
68D LEU* 3.6 5.6 - - - +
70D ALA* 1.3 74.9 - - - +
72D MET* 1.3 65.3 + - - +
74D PHE* 3.2 7.9 + - - +
75D LEU* 3.0 35.9 + - + +
99D VAL* 3.4 28.3 - - + -
124D ALA* 4.0 19.5 - - + -
126D ALA* 5.2 1.3 - - + -
143D VAL* 4.3 22.4 - - + +
146D LEU* 3.6 19.7 - - + -
149D PRO* 4.5 5.2 - - + -
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Residues in contact with MET 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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68D LEU 2.9 14.6 + - - +
69D THR* 3.2 11.2 - - - +
71D VAL* 1.3 78.1 - - - +
73D ARG* 1.3 63.8 + - + +
75D LEU* 3.0 21.8 + - - -
76D THR* 3.0 29.9 + - + +
83D LEU* 5.5 0.2 - - - -
96D VAL* 3.9 30.5 - - + -
99D VAL* 4.7 1.1 - - + -
416D LEU* 4.0 17.7 - - + +
419D SER 3.7 14.8 - - - +
420D GLN* 3.1 51.6 - - + +
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Residues in contact with ARG 73 (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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69D THR* 2.7 48.9 + - + +
70D ALA* 3.2 9.2 + - - +
72D MET* 1.3 73.2 - - + +
74D PHE* 1.3 59.3 + - - +
76D THR* 3.1 13.9 + - - -
77D GLN* 2.7 37.7 + - - +
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Residues in contact with PHE 74 (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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70D ALA 2.8 21.0 + - - +
71D VAL* 3.4 5.8 - - - +
73D ARG* 1.3 72.6 - - - +
75D LEU* 1.3 64.1 + - + +
77D GLN* 3.4 10.7 - - - +
78D ARG* 3.2 69.7 + - + +
143D VAL* 3.5 14.6 - - + -
149D PRO* 3.9 23.8 - - + -
150D SER* 3.0 39.3 - - - -
151D TYR 3.1 20.6 - - - -
152D MET* 3.6 16.6 - - + -
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Residues in contact with LEU 75 (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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71D VAL* 3.0 28.2 + - + +
72D MET* 3.0 13.8 + - - +
74D PHE* 1.3 76.4 - - + +
76D THR* 1.3 64.7 + - - +
77D GLN 2.8 6.6 + - - -
78D ARG 3.0 1.2 + - - +
79D LEU* 2.9 48.1 + - + +
83D LEU* 4.6 0.7 - - - -
96D VAL* 4.2 22.2 - - + -
99D VAL* 4.3 2.5 - - + -
126D ALA* 4.0 25.8 - - + -
128D VAL* 5.4 0.9 - - + -
141D LEU* 5.0 5.4 - - + -
143D VAL* 4.3 11.4 - - + -
152D MET* 3.8 29.2 - - - -
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Residues in contact with THR 76 (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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72D MET* 3.0 32.8 + - + +
73D ARG* 3.1 13.7 + - - -
75D LEU* 1.3 73.7 - - - +
77D GLN* 1.3 65.0 + - - +
80D GLY 3.0 24.7 - - - +
81D PRO* 4.8 2.4 - - - +
83D LEU* 4.0 18.8 - - + +
420D GLN* 5.0 9.2 - - - +
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Residues in contact with GLN 77 (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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73D ARG* 2.7 34.7 + - - +
74D PHE* 3.4 6.7 - - - +
75D LEU 2.8 1.0 + - - -
76D THR* 1.3 87.4 + - - +
78D ARG* 1.3 90.4 + - - +
80D GLY* 3.7 8.1 + - - -
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Residues in contact with ARG 78 (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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74D PHE* 3.2 56.7 + - + +
75D LEU* 3.0 3.2 + - - +
77D GLN* 1.3 116.8 + - - +
79D LEU* 1.3 58.9 + - - +
80D GLY* 3.0 10.3 + - - -
150D SER 4.9 2.6 + - - -
152D MET* 4.0 27.1 - - + +
2K NAG 5.3 2.6 - - - +
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Residues in contact with LEU 79 (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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75D LEU* 2.9 37.7 + - + +
78D ARG* 1.3 70.1 - - + +
80D GLY* 1.3 62.3 + - - +
82D GLY* 4.7 2.6 + - - -
83D LEU* 3.7 39.8 + - + +
94D ASN* 5.4 6.4 + - - +
96D VAL* 4.0 11.2 - - + -
128D VAL* 3.8 19.5 - - + -
130D PHE* 3.6 30.0 - - + -
141D LEU* 4.3 12.6 - - + -
152D MET* 4.7 4.7 - - + -
2K NAG 4.1 16.4 - - - +
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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