Contacts of the helix formed by residues 57 - 73 (chain B) in PDB entry 4C8B
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 ASP 57 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55B LEU* 3.1 9.3 - - + +
56B LEU* 1.3 81.9 - - - +
58B SER* 1.3 63.6 + - - +
60B ARG* 3.7 12.1 - - - +
61B LYS* 3.9 5.9 + - - +
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Residues in contact with SER 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LEU* 3.7 12.8 - - - +
57B ASP* 1.3 76.9 - - - +
59B GLU* 1.3 66.9 + - - +
60B ARG 3.2 1.6 - - - -
61B LYS* 3.2 17.4 + - - +
62B ASP* 3.3 12.1 + - - +
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Residues in contact with GLU 59 (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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55B LEU* 3.2 24.8 + - - +
58B SER* 1.3 76.8 - - - +
60B ARG* 1.3 63.0 + - - +
62B ASP* 3.3 15.5 + - - +
63B VAL* 3.3 14.0 + - - +
91B LEU* 4.4 10.5 - - + +
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Residues in contact with ARG 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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55B LEU 4.3 1.6 + - - -
56B LEU* 3.1 33.9 + - - +
57B ASP 3.7 11.6 + - - +
59B GLU* 1.3 78.2 - - - +
61B LYS* 1.3 52.0 + - - +
63B VAL* 3.0 6.2 + - - +
64B LEU* 2.7 38.2 + - + +
86B ASN* 4.0 25.8 + - - +
91B LEU* 4.1 23.2 - - + +
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Residues in contact with LYS 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ASP 3.9 3.9 + - - +
58B SER* 3.2 18.1 + - - +
60B ARG* 1.3 77.7 - - - +
62B ASP* 1.3 54.2 + - - +
64B LEU* 4.0 6.5 - - - +
65B ARG* 2.7 38.0 + - - +
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Residues in contact with ASP 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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58B SER 3.3 7.3 + - - +
59B GLU* 3.3 12.7 + - - +
60B ARG 3.2 0.6 - - - -
61B LYS* 1.3 77.6 - - - +
63B VAL* 1.3 61.7 + - + +
65B ARG* 4.0 5.2 - - - +
66B GLU* 3.2 23.3 + - - +
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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
----------------------------------------------------------
29B SER* 5.9 2.5 - - - +
47B LYS 5.7 0.9 - - - +
49B LEU* 5.0 13.7 - - + +
59B GLU 3.3 9.0 + - - +
60B ARG 3.0 7.9 + - - +
62B ASP* 1.3 77.9 - - + +
64B LEU* 1.3 62.1 + - + +
66B GLU* 3.1 11.1 + - - +
67B ALA* 2.9 27.0 + - - +
84B ILE* 5.3 6.3 - - + -
91B LEU* 4.1 35.7 - - + -
92B GLY* 4.6 14.4 - - - +
93B ILE* 3.8 21.9 - - + +
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Residues in contact with LEU 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 ARG* 2.7 21.9 + - + +
61B LYS* 4.0 7.6 - - - +
63B VAL* 1.3 76.2 - - + +
65B ARG* 1.3 57.6 + - - +
67B ALA* 4.0 5.6 - - - +
68B GLU* 3.0 29.6 + - - +
84B ILE* 6.0 2.9 - - + -
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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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61B LYS 2.7 23.8 + - - +
62B ASP* 4.0 6.5 - - - +
64B LEU* 1.3 71.9 - - - +
66B GLU* 1.3 61.9 + - - +
68B GLU* 3.4 7.7 + - - +
69B ILE* 3.1 33.1 + - + +
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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
----------------------------------------------------------
29B SER* 4.4 7.1 - - - -
47B LYS* 2.8 36.2 + - - -
62B ASP 3.2 12.9 + - - +
63B VAL* 3.1 13.0 + - - +
65B ARG* 1.3 76.5 - - - +
67B ALA* 1.3 65.7 + - - +
69B ILE* 3.2 13.2 + - + +
70B LEU* 3.0 23.1 + - + +
93B ILE* 3.7 17.8 - - + +
1000B 0LI 3.0 42.1 + - + +
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Residues in contact with ALA 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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10B LEU* 4.4 6.2 - - + +
63B VAL 2.9 15.4 + - - +
64B LEU* 4.0 5.8 - - - +
66B GLU* 1.3 73.8 - - - +
68B GLU* 1.3 66.1 + - - +
71B HIS* 2.9 27.1 + - - +
81B ILE* 3.8 21.8 - - + +
84B ILE* 3.6 31.2 - - + -
93B ILE* 3.9 6.7 - - + +
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Residues in contact with GLU 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 LEU 3.0 18.1 + - - +
65B ARG* 3.5 8.5 - - - +
67B ALA* 1.3 77.3 - - - +
69B ILE* 1.3 56.2 + - + +
71B HIS* 3.7 7.4 - - - +
72B LYS* 2.8 32.3 + - - +
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Residues in contact with ILE 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 23.2 + - + +
66B GLU* 3.5 14.6 - - - +
67B ALA 3.2 0.2 - - - -
68B GLU* 1.3 76.3 - - + +
70B LEU* 1.3 66.4 + - - +
72B LYS* 3.0 8.1 + - - +
73B ALA* 2.9 21.5 + - - +
142B LEU* 3.6 32.4 - - + +
1000B 0LI 4.1 42.6 - - + -
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Residues in contact with LEU 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 15.0 + - + +
67B ALA 4.0 2.9 - - - +
69B ILE* 1.3 81.1 - - - +
71B HIS* 1.3 61.0 + - - +
73B ALA* 3.3 19.6 + - - +
74B ARG* 3.7 4.2 + - - +
78B ILE* 4.0 14.3 - - + +
79B LEU* 3.2 28.6 - - + +
81B ILE* 4.1 32.0 - - + +
93B ILE* 4.6 2.0 - - + -
95B THR* 4.2 11.2 - - + -
1000B 0LI 3.8 61.7 - - + +
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Residues in contact with HIS 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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9A ALA* 4.0 23.4 - - + +
71A HIS* 3.9 28.0 + + - -
74A ARG* 5.2 1.6 - - + -
9B ALA* 4.2 29.1 - - + +
10B LEU* 3.7 26.8 - - + +
67B ALA 2.9 19.1 + - - +
68B GLU* 3.7 6.5 - - - +
70B LEU* 1.3 75.7 - - - +
72B LYS* 1.3 64.6 + - + +
73B ALA 3.1 0.2 - - - -
74B ARG* 3.1 37.5 + - - +
81B ILE* 3.9 11.6 - - + +
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Residues in contact with LYS 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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9A ALA* 4.4 26.7 - - + +
68B GLU 2.8 21.5 + - - +
69B ILE* 3.6 6.5 - - - +
71B HIS* 1.3 74.5 - - + +
73B ALA* 1.3 57.7 + - - +
74B ARG* 3.5 3.3 + - - +
134B TYR* 4.5 6.6 + - - -
138B MET* 3.5 21.6 - - + +
142B LEU* 5.7 0.7 - - + -
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Residues in contact with ALA 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 ILE 2.9 15.9 + - - +
70B LEU* 3.3 10.1 + - - +
71B HIS 3.1 0.8 - - - -
72B LYS* 1.3 77.5 - - - +
74B ARG* 1.3 63.9 + - - +
75B PHE* 3.3 3.3 + - - +
78B ILE* 3.6 26.0 - - + +
134B TYR* 4.0 4.9 - - - -
135B LEU* 4.0 25.6 - - + -
138B MET* 3.8 15.0 - - + -
142B LEU* 4.2 4.5 - - + -
1000B 0LI 4.8 3.4 - - - -
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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