Contacts of the helix formed by residues 59 - 68 (chain B) in PDB entry 4C48
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 HIS 59 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B ALA 3.8 12.5 + - - -
23B ARG 4.1 5.6 - - - -
24B ALA 4.6 0.9 - - - -
25B GLY* 3.7 30.3 - - - -
27B ASP* 4.7 4.7 - - - +
54B ALA* 3.2 9.8 + - + +
57B TRP* 3.5 37.8 + + + +
58B GLY* 1.3 76.8 - - - +
60B LEU* 1.3 64.5 + - - +
61B GLU 3.4 0.7 - - - +
62B ILE* 3.8 24.2 - - + +
63B VAL* 2.9 23.0 + - - +
95B ILE* 3.5 2.4 - - - +
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Residues in contact with LEU 60 (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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58B GLY 3.8 6.4 + - - +
59B HIS* 1.3 69.2 - - - +
61B GLU* 1.3 64.2 + - + +
63B VAL* 2.7 31.6 + - - +
64B GLU* 2.9 22.5 + - - +
94B GLU* 3.3 52.9 - - + +
95B ILE* 3.6 15.0 - - + +
98B VAL* 4.4 13.9 - - + -
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Residues in contact with GLU 61 (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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27B ASP* 3.0 32.1 + - + +
59B HIS* 3.4 1.0 - - - +
60B LEU* 1.3 84.5 - - + +
62B ILE* 1.3 62.4 + - - +
64B GLU* 3.1 15.0 + - + +
65B VAL* 3.0 31.7 + - + +
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Residues in contact with ILE 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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21B ALA 3.8 0.7 - - - +
22B ALA* 3.7 36.8 - - + +
25B GLY* 3.1 32.5 - - - +
27B ASP* 2.9 27.3 + - - +
30B VAL* 4.1 18.6 - - + +
50B PRO* 4.8 1.8 - - + +
54B ALA* 3.8 15.3 - - + -
59B HIS* 3.6 20.4 + - + +
61B GLU* 1.3 78.4 - - - +
63B VAL* 1.3 61.6 + - - +
65B VAL* 3.3 7.7 + - - +
66B LEU* 3.1 27.4 + - + +
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Residues in contact with VAL 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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51B LEU* 3.5 16.6 - - + +
54B ALA* 3.8 17.7 - - + -
55B ALA* 4.7 1.1 - - + +
59B HIS 2.9 19.3 - - - +
60B LEU* 2.7 17.4 + - - +
62B ILE* 1.3 72.9 - - - +
64B GLU* 1.3 55.3 + - + +
66B LEU* 3.1 5.7 + - - +
67B LEU* 2.7 48.1 + - + +
95B ILE* 3.9 22.4 - - + -
98B VAL* 4.9 3.8 - - + -
99B LEU* 3.3 29.8 - - + -
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Residues in contact with GLU 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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60B LEU* 2.9 24.6 + - - +
61B GLU* 3.5 17.7 - - + +
63B VAL* 1.3 77.3 - - - +
65B VAL* 1.3 66.0 + - + +
66B LEU 2.9 1.2 + - - -
67B LEU* 3.1 4.9 + - - -
68B LYS* 3.0 31.3 + - + +
98B VAL* 3.1 40.1 - - - +
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Residues in contact with VAL 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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27B ASP* 5.1 9.0 - - + +
30B VAL* 4.3 12.8 - - + -
31B ARG* 4.6 15.0 - - + -
34B MET* 3.2 37.9 - - + +
61B GLU* 3.0 21.9 + - + +
62B ILE* 3.3 6.5 + - - +
64B GLU* 1.3 78.5 - - + +
66B LEU* 1.3 59.7 + - - +
68B LYS* 4.9 14.8 - - - +
69B ASN* 3.6 10.6 + - - +
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Residues in contact with LEU 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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18B LEU* 4.4 9.4 - - + -
30B VAL* 5.7 2.7 - - + +
34B MET* 3.7 15.9 - - + -
40B VAL* 3.5 32.5 - - + +
50B PRO* 3.5 15.3 - - + +
51B LEU* 3.2 45.5 - - + +
62B ILE* 3.1 22.1 + - + +
63B VAL* 3.4 4.3 - - - +
64B GLU 2.9 0.2 - - - -
65B VAL* 1.3 79.0 - - - +
67B LEU* 1.3 61.3 + - - +
69B ASN* 3.5 8.3 + - - +
70B GLY 3.5 0.2 + - - -
71B ALA* 3.0 37.5 + - + +
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Residues in contact with LEU 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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51B LEU* 3.8 24.7 - - + -
63B VAL* 2.7 41.5 + - + +
64B GLU* 4.0 4.0 - - - +
66B LEU* 1.3 68.0 - - - +
68B LYS* 1.3 61.8 + - - +
69B ASN 3.1 1.8 - - - -
70B GLY* 2.9 19.9 + - - -
71B ALA* 4.0 5.6 + - + +
73B VAL* 3.4 36.1 - - + +
98B VAL* 3.7 17.7 - - + +
99B LEU* 4.3 5.2 - - + -
102B ASN* 3.2 42.2 + - + +
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Residues in contact with LYS 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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64B GLU* 3.0 16.5 + - + +
65B VAL* 4.9 14.4 - - - +
67B LEU* 1.3 78.5 - - - +
69B ASN* 1.3 61.8 + - - +
70B GLY* 3.1 3.0 + - - -
102B ASN* 5.3 2.9 - - - +
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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