Contacts of the helix formed by residues 61 - 75 (chain B) in PDB entry 2CXU
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 61 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16B TRP* 4.2 7.8 - - - -
24B LEU* 4.5 11.4 - - - +
29B LEU* 4.9 7.6 - - - -
36B ARG* 4.6 2.5 - - - +
40B PHE* 3.8 8.1 - - - -
60B VAL* 1.3 76.6 - - - +
62B LYS* 1.3 65.6 + - - +
63B GLU* 3.5 17.7 + - - +
64B VAL* 3.1 26.4 + - - +
65B MET* 3.0 22.5 + - - +
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Residues in contact with LYS 62 (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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40B PHE* 3.6 19.4 - - + -
61B SER* 1.3 73.3 - - - +
63B GLU* 1.3 70.6 + - - +
65B MET* 3.3 5.6 + - - +
66B GLN* 3.0 55.4 + - + +
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Residues in contact with GLU 63 (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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16B TRP* 4.9 11.4 - - + +
61B SER* 3.1 19.1 + - - +
62B LYS* 1.3 93.0 + - - +
64B VAL* 1.3 56.5 + - - +
66B GLN* 3.4 15.2 + - - +
67B MET* 3.0 41.5 + - + +
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Residues in contact with VAL 64 (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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13B LEU* 4.6 1.3 - - + -
16B TRP* 3.5 38.6 - - + -
24B LEU* 4.8 0.9 - - + -
60B VAL* 3.8 23.1 - - + -
61B SER* 3.1 29.9 + - - +
63B GLU* 1.3 75.3 - - - +
65B MET* 1.3 59.9 + - - +
67B MET* 3.2 9.8 + - + +
68B LEU* 2.9 37.5 + - + +
326B TRP* 3.8 27.8 - - + -
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Residues in contact with MET 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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40B PHE* 3.8 21.3 - - + -
55B TYR* 3.9 20.6 - - + +
60B VAL* 3.8 27.6 - - + -
61B SER 3.0 15.6 + - - +
62B LYS* 3.7 8.3 - - - +
64B VAL* 1.3 75.6 - - - +
66B GLN* 1.3 57.6 + - + +
68B LEU* 3.3 12.8 + - + +
69B VAL* 2.9 36.9 + - + +
319B LEU* 3.9 32.8 - - + +
322B LEU* 5.2 4.3 - - + -
323B LEU* 4.1 15.3 - - + -
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Residues in contact with GLN 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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62B LYS* 3.0 50.2 + - + +
63B GLU* 3.6 18.5 - - - +
64B VAL 3.2 0.2 - - - -
65B MET* 1.3 78.4 - - + +
67B MET* 1.3 57.2 + - + +
69B VAL* 3.4 5.6 + - - +
70B GLU* 2.9 43.6 + - - +
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Residues in contact with MET 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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9B GLN* 4.8 6.2 - - - +
12B LYS* 4.0 40.4 - - + +
13B LEU* 3.8 25.5 - - + +
16B TRP* 3.4 50.7 - - + +
63B GLU* 3.0 26.0 + - + +
64B VAL* 3.2 16.1 + - + +
66B GLN* 1.3 76.1 - - + +
68B LEU* 1.3 57.6 + - - +
70B GLU* 3.4 14.0 + - - +
71B LEU* 3.0 27.4 + - - +
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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
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13B LEU* 3.8 30.7 - - + -
60B VAL* 4.7 1.6 - - + -
64B VAL* 2.9 34.2 + - + +
65B MET* 3.6 22.4 - - + +
66B GLN 3.3 0.2 - - - -
67B MET* 1.3 73.9 - - - +
69B VAL* 1.3 63.9 + - - +
71B LEU* 3.1 7.3 + - + +
72B ALA 3.0 19.2 + - - -
322B LEU* 3.2 59.3 - - + +
323B LEU* 4.7 1.1 - - - +
325B ILE* 4.7 5.6 - - + -
326B TRP* 4.1 19.1 - - + +
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Residues in contact with VAL 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 MET* 2.9 24.5 + - + +
66B GLN* 3.8 5.6 - - - +
68B LEU* 1.3 74.4 - - - +
70B GLU* 1.3 64.8 + - + +
72B ALA* 3.2 5.4 + - - +
73B LYS* 3.1 37.0 + - - +
312B LEU* 4.1 21.3 - - + +
313B GLU* 3.9 34.8 - - + +
319B LEU* 4.4 8.1 - - + -
322B LEU* 3.9 18.8 - - + -
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Residues in contact with GLU 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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9B GLN* 4.0 17.3 - - + +
12B LYS* 4.8 10.6 + - - +
66B GLN* 2.9 30.2 + - - +
67B MET* 3.7 16.5 - - - +
69B VAL* 1.3 77.6 - - + +
71B LEU* 1.3 57.3 + - - +
73B LYS* 3.3 13.0 + - + +
74B SER* 2.9 29.8 + - - -
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Residues in contact with LEU 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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4B LEU* 4.0 6.5 - - + -
7B ASN* 3.3 31.0 - - - +
9B GLN* 3.9 7.5 - - + +
10B PHE* 3.5 38.4 - - + +
13B LEU* 4.2 17.5 - - + -
67B MET 3.0 14.5 + - - +
68B LEU* 3.1 10.5 + - + +
70B GLU* 1.3 73.5 - - - +
72B ALA* 1.3 64.8 + - - +
74B SER* 3.3 4.9 + - - -
75B ARG* 2.9 38.2 + - + +
325B ILE* 4.4 7.0 - - + -
504B MET* 3.6 22.2 - - + -
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Residues in contact with ALA 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 13.2 + - - +
69B VAL 3.2 9.2 + - - +
71B LEU* 1.3 76.3 - - - +
73B LYS* 1.3 63.6 + - - +
75B ARG 3.3 3.5 + - - -
77B VAL* 3.2 43.4 + - + +
312B LEU* 3.9 15.7 - - + -
318B VAL* 4.6 6.3 - - + -
322B LEU* 4.0 19.3 - - + -
504B MET* 3.9 8.9 - - - +
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Residues in contact with LYS 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 VAL* 3.1 32.0 + - + +
70B GLU* 3.6 14.6 - - + +
71B LEU 3.2 0.2 - - - -
72B ALA* 1.3 76.2 - - - +
74B SER* 1.3 57.1 + - - +
76B GLY* 3.0 20.3 + - - -
77B VAL 4.3 1.5 + - - +
78B GLU* 4.2 21.5 + - - +
312B LEU* 3.7 24.9 - - + +
313B GLU* 4.8 8.5 + - - -
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Residues in contact with SER 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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7B ASN* 2.9 27.6 + - - -
9B GLN* 2.7 32.5 + - - +
70B GLU 2.9 17.0 + - - -
71B LEU 3.6 4.2 + - - -
73B LYS* 1.3 75.4 - - - +
75B ARG* 1.3 61.2 + - - +
76B GLY 3.4 0.4 - - - -
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Residues in contact with ARG 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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3B ALA* 3.8 19.0 + - - +
4B LEU* 4.1 14.4 - - + +
7B ASN* 3.6 21.4 - - - +
71B LEU* 2.9 34.6 + - + +
72B ALA 3.3 3.8 + - - +
73B LYS 3.1 0.4 - - - -
74B SER* 1.3 80.7 + - - +
76B GLY* 1.3 60.5 + - - +
77B VAL* 3.5 1.6 - - + -
503B ILE* 2.9 33.7 + - - +
504B MET* 2.8 38.8 + - + +
506B ASP* 2.8 38.0 + - - +
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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