Contacts of the helix formed by residues 64 - 79 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A ASP 3.7 3.1 + - - -
63A LEU* 1.3 74.6 - - - +
65A ARG* 1.3 69.9 + - - +
66A GLU* 2.9 20.4 + - - -
67A GLU* 2.7 33.4 + - - +
68A LEU* 3.1 10.1 + - - -
414A HIS* 3.5 23.1 - - - -
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Residues in contact with ARG 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A SER* 1.3 70.1 - - - +
66A GLU* 1.3 85.5 + - - +
68A LEU* 2.8 2.1 + - - +
69A THR* 2.7 28.8 + - - +
412A ASP* 4.9 4.6 + - - -
414A HIS* 3.3 44.4 + - + +
422A PRO* 4.1 22.4 - - + +
424A THR* 3.9 16.3 + - - +
1743A CU 4.4 3.0 - - - -
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Residues in contact with GLU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A SER* 2.9 25.4 + - - +
65A ARG* 1.3 94.1 - - - +
67A GLU* 1.3 55.0 + - + +
69A THR* 3.2 7.4 + - - -
70A ALA* 2.6 36.6 + - - +
73A ARG* 5.2 0.7 + - - -
147A PRO* 6.5 1.6 - - + -
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Residues in contact with GLU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ASP 4.3 1.6 - - - +
63A LEU* 3.4 21.1 - - + +
64A SER* 2.7 37.6 + - - +
66A GLU* 1.3 72.2 - - + +
68A LEU* 1.3 62.3 + - - +
70A ALA* 3.3 7.0 + - - +
71A VAL* 2.9 30.3 + - - +
122A ARG* 3.3 26.4 + - - +
146A LEU* 3.2 38.8 - - + +
147A PRO* 4.8 15.3 - - + +
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Residues in contact with LEU 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A LEU* 4.0 32.5 - - + +
64A SER 3.1 11.7 + - - +
65A ARG 2.8 8.0 + - - +
67A GLU* 1.3 72.9 - - - +
69A THR* 1.3 67.7 + - - +
71A VAL* 3.0 7.6 + - - +
72A MET* 2.8 24.3 + - - +
99A VAL* 3.0 36.6 - - + +
100A GLU* 5.0 0.4 - - - -
414A HIS* 4.1 2.0 - - + +
415A PHE* 3.7 24.5 - - - +
416A LEU* 3.6 20.0 - - + +
422A PRO* 3.7 28.3 - - + -
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Residues in contact with THR 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ARG* 2.7 23.9 + - - +
66A GLU* 3.3 11.3 + - - -
68A LEU* 1.3 73.0 - - - +
70A ALA* 1.3 56.8 + - - +
72A MET* 2.9 6.9 + - + -
73A ARG* 2.6 62.8 + - + +
422A PRO* 3.7 19.5 - - + +
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Residues in contact with ALA 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A GLU 2.6 21.8 + - - +
67A GLU* 3.4 9.0 - - - +
68A LEU 3.2 0.2 - - - -
69A THR* 1.3 73.5 - - - +
71A VAL* 1.3 56.7 + - - +
73A ARG* 3.6 24.2 - - - +
74A PHE* 3.0 27.4 + - - +
146A LEU* 5.2 0.2 - - + -
147A PRO 3.3 26.2 - - - +
149A PRO* 3.7 13.8 - - + +
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Residues in contact with VAL 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A LEU* 5.1 0.4 - - + -
67A GLU 2.9 18.3 + - - +
68A LEU* 3.5 5.4 - - - +
70A ALA* 1.3 72.8 - - - +
72A MET* 1.3 57.8 + - - +
74A PHE* 3.2 3.6 + - - +
75A LEU* 2.7 44.7 + - + +
99A VAL* 3.8 26.9 - - + -
124A ALA* 4.3 10.3 - - + -
126A ALA* 5.0 0.7 - - + -
143A VAL* 3.4 34.8 - - + -
146A LEU* 3.8 21.3 - - + -
149A PRO* 4.1 10.1 - - + -
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Residues in contact with MET 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A LEU 2.8 12.9 + - - +
69A THR* 3.5 9.0 - - - +
71A VAL* 1.3 72.9 - - - +
73A ARG* 1.3 61.7 + - - +
75A LEU* 2.6 31.9 + - - +
76A THR* 2.9 35.1 + - + -
96A VAL* 3.7 32.5 - - + -
99A VAL* 4.4 1.1 - - + -
416A LEU* 3.6 26.0 - - + +
419A SER 3.6 20.4 - - - +
420A GLN* 3.5 33.2 - - + +
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Residues in contact with ARG 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A GLU 5.2 0.6 + - - -
69A THR* 2.6 41.0 + - + +
70A ALA* 3.6 29.5 - - - +
72A MET* 1.3 75.6 - - - +
74A PHE* 1.3 58.7 + - - +
76A THR* 3.1 12.6 + - - -
77A GLN* 3.0 37.9 - - + +
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Residues in contact with PHE 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ALA 3.0 19.6 + - - +
71A VAL 3.4 3.8 - - - +
72A MET 3.0 0.6 - - - -
73A ARG* 1.3 79.2 - - - +
75A LEU* 1.3 60.8 + - + +
77A GLN* 3.5 14.2 + - + +
78A ARG* 3.1 58.4 + - + +
143A VAL* 4.0 20.4 - - + -
149A PRO* 3.8 23.8 - - + -
150A SER* 3.7 27.1 - - - -
151A TYR* 3.6 22.2 - - - -
152A MET* 4.3 12.1 - - + -
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Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A VAL* 2.7 24.6 + - + +
72A MET* 2.6 19.4 + - - +
74A PHE* 1.3 71.8 - - + +
76A THR* 1.3 54.0 + - - +
77A GLN 2.9 4.3 - - - -
78A ARG* 5.2 1.1 - - - -
79A LEU* 2.7 61.8 + - + +
96A VAL* 3.8 22.0 - - + -
99A VAL* 3.7 29.2 - - + -
126A ALA* 4.0 12.3 - - + -
128A VAL* 5.5 0.4 - - + -
141A LEU* 5.1 6.7 - - + -
143A VAL* 4.1 18.2 - - + -
152A MET* 4.9 13.2 - - - -
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Residues in contact with THR 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A MET* 2.9 29.7 + - + -
73A ARG* 3.1 18.4 + - - -
75A LEU* 1.3 75.6 - - - +
77A GLN* 1.3 61.8 + - - +
79A LEU 4.3 0.4 - - - -
80A GLY 3.5 19.5 + - - +
83A LEU* 3.2 29.6 - - + +
420A GLN* 4.1 13.0 - - - +
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Residues in contact with GLN 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ARG* 3.0 34.2 + - + +
74A PHE* 3.5 20.0 - - + +
75A LEU 2.9 1.6 - - - -
76A THR* 1.3 80.4 - - - +
78A ARG* 1.3 66.7 + - + +
79A LEU 3.3 0.6 + - - -
80A GLY* 3.6 10.2 + - - -
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Residues in contact with ARG 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A PHE* 3.1 48.2 + - + +
75A LEU* 4.6 1.3 - - - +
77A GLN* 1.3 78.9 - - + +
79A LEU* 1.3 63.2 + - + +
80A GLY* 3.3 0.6 + - - -
151A TYR* 6.0 0.8 - - - +
152A MET* 3.5 45.8 + - - +
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Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LEU* 2.7 54.3 + - + +
78A ARG* 1.3 74.6 - - - +
80A GLY* 1.3 60.6 + - - +
81A PRO* 4.7 0.3 - - - +
82A GLY 5.4 3.5 + - - +
83A LEU* 3.8 32.7 - - + +
96A VAL* 4.0 8.7 - - + -
128A VAL* 4.2 7.6 - - + -
130A PHE* 4.1 31.9 - - + -
141A LEU* 4.8 9.2 - - + -
152A MET* 5.1 7.9 - - + -
2E NAG 5.0 8.3 - - + -
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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