Contacts of the helix formed by residues 63 - 73 (chain B) in PDB entry 4A69
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 63 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B CYS* 4.1 0.4 - - - -
61B PHE 3.9 1.0 + - - -
62B HIS* 1.3 76.9 - - - +
64B GLU* 1.3 64.6 + - - +
65B ASP* 3.3 11.2 + - - -
66B TYR* 3.1 24.8 + - - +
67B ILE* 3.2 21.5 + - - +
88B PHE* 5.0 0.5 - - - -
138B LYS* 3.1 8.8 + - - +
139B PHE* 3.5 35.6 - - - +
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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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334A PRO* 4.3 19.8 - - - +
55B GLN* 3.4 19.4 + - - +
59B CYS* 3.9 16.0 - - + +
62B HIS 3.8 1.2 + - - -
63B SER* 1.3 73.9 - - - +
65B ASP* 1.3 58.9 + - - +
67B ILE 3.3 1.0 + - - -
68B ASP* 2.8 39.9 + - - +
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Residues in contact with ASP 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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63B SER* 3.3 11.3 + - - -
64B GLU* 1.3 77.2 - - - +
66B TYR* 1.3 72.6 + - - +
68B ASP* 3.6 13.2 - - + +
69B PHE* 3.0 23.6 + - - +
88B PHE* 3.7 21.0 - - + -
139B PHE* 5.7 0.7 - - - -
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Residues in contact with TYR 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 HIS* 3.7 19.3 - + + -
63B SER* 3.1 22.7 + - - +
65B ASP* 1.3 78.7 + - - +
67B ILE* 1.3 68.2 + - + +
69B PHE* 3.0 14.8 + - + +
70B LEU* 3.0 38.5 + - + +
88B PHE* 3.6 39.0 - + + -
90B VAL* 5.0 0.4 - - + -
137B LYS 4.1 4.9 - - - -
138B LYS 3.7 15.5 - - - +
139B PHE 3.8 8.3 - - - +
140B GLU* 3.6 1.8 - - - -
141B ALA* 3.1 39.0 + - + +
146B TYR* 2.6 33.2 + - - +
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Residues in contact with ILE 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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55B GLN* 3.8 32.3 - - + +
58B MET* 4.0 15.7 - - + -
59B CYS* 3.7 10.1 - - - -
62B HIS* 3.7 29.6 - - + -
63B SER 3.2 16.8 + - - +
66B TYR* 1.3 74.2 - - + +
68B ASP* 1.3 67.6 + - - +
70B LEU* 3.1 23.6 + - + +
71B GLN* 3.0 23.8 + - - +
101B PHE* 3.7 23.3 - - + -
147B VAL* 4.1 9.2 - - + -
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Residues in contact with ASP 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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345A ARG* 4.9 3.4 + - - +
55B GLN* 3.0 25.0 + - - +
64B GLU* 2.8 36.5 + - - +
65B ASP* 3.6 13.1 - - + +
67B ILE* 1.3 72.7 - - - +
69B PHE* 1.3 60.9 + - - +
71B GLN* 3.5 10.9 + - - +
72B ARG* 3.1 28.2 + - - +
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Residues in contact with PHE 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 ASP 3.0 14.2 + - - +
66B TYR 3.0 8.7 + - - +
68B ASP* 1.3 74.0 - - - +
70B LEU* 1.3 64.3 + - + +
72B ARG* 3.1 14.7 + - - +
73B VAL* 2.9 62.3 + - + +
81B PHE* 4.0 18.4 - + + -
84B SER* 3.5 26.5 - - - -
85B LEU* 3.7 24.7 - - + -
88B PHE* 3.5 29.8 - + + -
90B VAL* 3.8 29.8 - - + -
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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 TYR* 3.0 55.5 + - + +
67B ILE* 3.1 22.2 + - + +
69B PHE* 1.3 78.3 - - + +
71B GLN* 1.3 60.4 + - - +
73B VAL* 4.1 14.7 + - + +
90B VAL* 4.2 15.9 - - + -
100B LEU* 4.3 20.6 - - + +
101B PHE* 3.9 23.4 + - + +
104B CYS* 5.0 1.3 - - - -
146B TYR* 3.9 35.9 - - + -
147B VAL* 4.1 9.4 - - + -
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Residues in contact with GLN 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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341A ASP* 5.6 1.2 - - - +
343A SER 5.0 4.6 + - - -
345A ARG* 3.8 55.1 + - + +
55B GLN* 2.9 45.5 + - - +
67B ILE 3.0 10.4 + - - +
68B ASP* 3.7 18.0 - - - +
70B LEU* 1.3 76.0 - - - +
72B ARG* 1.3 62.4 + - - +
73B VAL 4.5 2.5 - - - +
101B PHE* 3.5 41.0 - - + +
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Residues in contact with ARG 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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345A ARG* 3.5 19.3 - - - +
68B ASP* 3.1 16.9 + - - +
69B PHE* 3.1 17.1 + - + +
71B GLN* 1.3 80.8 - - - +
73B VAL* 1.3 68.0 + - - +
74B SER* 3.4 5.2 + - - -
77B ASN* 3.5 21.3 + - - +
81B PHE* 3.1 39.8 - - + -
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Residues in contact with VAL 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 PHE* 2.9 55.2 + - + +
70B LEU* 4.1 15.4 - - + +
71B GLN 3.6 2.3 - - - +
72B ARG* 1.3 80.3 - - - +
74B SER* 1.3 63.5 + - - +
77B ASN* 3.8 4.9 - - - +
78B MET* 4.0 21.1 - - + -
81B PHE* 5.2 1.8 - - + -
85B LEU* 4.3 1.1 - - + -
90B VAL* 5.0 1.8 - - + -
96B VAL* 4.0 34.1 - - + +
100B LEU* 4.7 12.9 - - + +
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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