Contacts of the helix formed by residues 64 - 79 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62B ASP 3.3 3.0 + - - -
63B LEU* 1.3 73.5 - - - +
65B ARG* 1.3 67.2 + - - +
66B GLU* 3.6 7.3 + - - +
67B GLU* 2.9 39.6 + - - +
68B LEU* 2.9 26.7 + - - +
122B ARG* 5.5 0.2 - - - -
414B HIS* 4.8 5.4 - - - -
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Residues in contact with ARG 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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64B SER* 1.3 76.5 - - - +
66B GLU* 1.3 77.9 + - - +
68B LEU* 3.7 3.6 + - - +
69B THR* 3.1 20.6 + - - +
414B HIS* 4.1 40.1 - - + +
422B PRO* 3.5 26.9 + - + +
424B THR* 5.3 4.2 + - - +
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Residues in contact with GLU 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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64B SER* 3.1 6.1 + - - +
65B ARG* 1.3 102.8 + - - +
67B GLU* 1.3 58.7 + - - +
68B LEU 3.1 1.6 - - - -
69B THR* 2.7 36.0 + - - -
70B ALA* 3.0 7.7 + - - +
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Residues in contact with GLU 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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63B LEU* 3.8 3.7 - - + -
64B SER* 2.9 36.4 + - - +
66B GLU* 1.3 73.5 - - - +
68B LEU* 1.3 63.2 + - - +
70B ALA* 3.2 6.9 + - - +
71B VAL* 3.1 27.5 + - - +
122B ARG* 2.6 43.6 + - - +
146B LEU* 3.4 43.3 - - + +
147B PRO* 4.4 15.4 - - + +
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Residues in contact with LEU 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LEU* 3.5 29.6 - - + +
64B SER 2.9 20.9 + - - +
65B ARG 3.7 3.8 - - - +
67B GLU* 1.3 76.6 - - - +
69B THR* 1.3 57.2 + - - +
71B VAL* 3.3 6.3 + - - +
72B MET* 3.0 24.6 + - - +
99B VAL* 3.5 27.4 - - + +
100B GLU* 4.5 0.9 - - + -
414B HIS* 4.0 21.5 - - + +
415B PHE* 3.9 19.1 - - - -
416B LEU* 3.5 27.4 - - + +
422B PRO* 3.9 22.7 - - + -
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Residues in contact with THR 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 ARG* 3.1 14.4 + - - +
66B GLU* 2.7 21.2 + - - -
68B LEU* 1.3 73.8 - - - +
70B ALA* 1.3 54.6 + - - +
72B MET* 3.4 6.5 + - - +
73B ARG* 2.9 69.6 + - + +
422B PRO* 3.4 20.2 - - + +
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Residues in contact with ALA 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 GLU 3.0 9.2 + - - +
67B GLU* 3.2 8.3 + - - +
69B THR* 1.3 74.4 - - - +
71B VAL* 1.3 61.8 + - - +
73B ARG* 3.9 9.8 - - - +
74B PHE* 2.9 28.9 + - - +
146B LEU* 4.6 1.3 - - + -
147B PRO 3.4 25.8 - - - +
148B HIS* 6.0 0.2 - - - +
149B PRO* 4.0 11.1 - - + +
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Residues in contact with VAL 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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63B LEU* 4.8 0.7 - - + -
67B GLU 3.1 16.9 + - - +
68B LEU* 3.3 7.6 + - - +
70B ALA* 1.3 73.5 - - - +
72B MET* 1.3 66.0 + - - +
74B PHE* 3.3 6.2 + - - +
75B LEU* 3.0 34.7 + - + +
99B VAL* 3.4 28.0 - - + -
124B ALA* 4.0 18.6 - - + -
126B ALA* 5.1 1.1 - - + -
143B VAL* 4.0 27.8 - - + +
146B LEU* 3.6 20.9 - - + -
149B PRO* 4.5 2.9 - - + -
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Residues in contact with MET 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 LEU 3.0 17.3 + - - +
69B THR* 3.6 6.1 - - - +
71B VAL* 1.3 79.3 - - - +
73B ARG* 1.3 64.1 + - + +
75B LEU* 3.1 6.9 + - + -
76B THR* 3.0 42.5 + - + +
83B LEU* 5.2 0.9 - - - -
96B VAL* 3.9 40.4 - - + -
99B VAL* 4.7 1.6 - - + -
416B LEU* 4.0 19.3 - - + -
419B SER 4.1 5.2 - - - +
420B GLN* 3.2 55.0 - - + +
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Residues in contact with ARG 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 THR* 2.9 49.2 + - + +
70B ALA* 3.9 7.4 - - - +
72B MET* 1.3 76.3 - - + +
74B PHE* 1.3 55.0 + - - +
76B THR* 3.0 12.4 + - - -
77B GLN* 2.6 42.7 + - - +
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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 ALA 2.9 19.5 + - - +
71B VAL* 3.4 5.8 - - - +
72B MET 3.1 0.2 - - - -
73B ARG* 1.3 78.6 - - - +
75B LEU* 1.3 62.7 + - + +
77B GLN* 3.1 28.5 - - - +
78B ARG* 3.1 56.0 + - + +
143B VAL* 3.6 15.0 - - + -
149B PRO* 3.7 21.1 - - + -
150B SER* 2.9 39.5 - - - -
151B TYR 3.2 19.7 - - - -
152B MET* 3.7 16.2 - - + -
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Residues in contact with LEU 75 (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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71B VAL* 3.0 29.0 + - + +
72B MET* 3.5 10.8 - - - +
74B PHE* 1.3 75.1 - - + +
76B THR* 1.3 64.6 + - - +
77B GLN 2.8 6.6 + - - -
78B ARG* 2.9 1.5 + - - +
79B LEU* 2.8 49.9 + - + +
83B LEU* 4.6 0.4 - - - -
96B VAL* 4.2 22.0 - - + -
99B VAL* 4.4 2.9 - - + -
126B ALA* 4.0 25.6 - - + -
128B VAL* 5.5 1.1 - - + -
141B LEU* 5.0 6.3 - - + -
143B VAL* 4.2 14.8 - - + -
152B MET* 3.8 27.1 - - - -
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Residues in contact with THR 76 (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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72B MET* 3.0 39.4 + - + +
73B ARG* 3.0 15.5 + - - -
75B LEU* 1.3 72.5 - - - +
77B GLN* 1.3 64.9 + - - +
80B GLY 3.1 24.0 - - - +
81B PRO* 4.9 2.6 - - - +
83B LEU* 4.0 18.1 - - + +
420B GLN* 5.1 7.9 - - - +
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Residues in contact with GLN 77 (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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73B ARG* 2.6 37.3 + - - +
74B PHE* 3.1 8.3 - - - +
75B LEU 2.8 1.0 - - - -
76B THR* 1.3 87.0 + - - +
78B ARG* 1.3 92.1 + - - +
80B GLY* 4.2 5.0 + - - -
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Residues in contact with ARG 78 (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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74B PHE* 3.1 53.4 + - + +
75B LEU* 2.9 4.2 + - - +
77B GLN* 1.3 125.5 + - - +
79B LEU* 1.3 59.5 + - - +
80B GLY* 3.0 9.8 + - - -
150B SER 5.2 1.0 + - - -
152B MET* 3.9 25.4 - - + +
2G NAG 4.9 7.1 - - - +
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Residues in contact with LEU 79 (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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75B LEU* 2.8 37.8 + - + +
78B ARG* 1.3 70.6 - - - +
80B GLY* 1.3 61.8 + - - +
82B GLY 4.8 2.1 + - - -
83B LEU* 3.8 30.9 + - + +
94B ASN* 5.4 6.1 + - - +
96B VAL* 3.9 11.9 - - + -
128B VAL* 3.6 29.2 - - + -
130B PHE* 3.6 30.5 - - + -
141B LEU* 4.4 12.1 - - + -
152B MET* 4.7 4.7 - - + -
2G NAG 4.1 18.2 - - + -
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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