Contacts of the helix formed by residues 73 - 80 (chain B) in PDB entry 3A4T
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 MET 73 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12B PHE* 3.9 11.7 - - + -
13B ILE 3.7 27.4 - - - +
14B ARG* 3.8 12.8 - - + +
40B PHE* 4.7 2.2 - - + -
41B LEU* 4.0 15.2 - - + +
44B ALA* 3.5 25.8 - - + -
68B GLN* 3.7 45.3 - - + +
69B SER 3.6 9.2 - - - +
70B ILE* 2.9 19.2 + - + +
72B SER* 1.3 79.0 - - - +
74B ILE* 1.3 62.9 + - - +
75B PRO 3.5 0.2 - - - -
76B PRO* 3.5 2.8 - - - +
77B ILE* 3.5 12.3 - - - +
100B HIS* 3.4 25.0 + - - +
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Residues in contact with ILE 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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40B PHE* 4.1 7.0 - - + -
70B ILE 4.0 5.6 - - - +
71B SER* 3.4 16.6 - - - +
73B MET* 1.3 78.7 - - - +
75B PRO* 1.3 70.3 - - + +
77B ILE* 3.3 10.5 - - - +
78B VAL* 3.0 38.1 + - + +
243B PHE* 3.7 23.6 - - + -
246B ILE* 3.9 20.2 - - + -
248B ILE* 3.9 23.8 - - + -
257B LEU* 5.2 0.4 - - + -
259B VAL* 4.2 9.2 - - + -
268B ILE* 3.9 25.8 - - + -
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Residues in contact with PRO 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 SER 3.4 13.5 - - - +
72B SER 3.5 11.9 - - - +
74B ILE* 1.3 94.0 - - + +
76B PRO* 1.4 60.3 - - + +
78B VAL* 3.1 3.3 + - + +
79B LEU* 2.8 30.8 + - - +
97B LYS* 3.9 6.7 - - + -
161B LEU* 4.1 12.1 - - + -
208B VAL* 4.0 21.0 - - + +
210B SER* 3.4 33.4 - - - +
266B PHE* 3.7 11.4 - - + -
268B ILE* 4.5 4.7 - - + -
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Residues in contact with PRO 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 SER 3.8 6.7 - - - +
73B MET 3.5 11.9 - - - +
75B PRO* 1.4 97.8 - - + +
77B ILE* 1.3 55.0 + - - +
79B LEU* 3.5 2.3 + - + +
80B ASN 3.0 22.2 + - - -
81B PRO* 3.4 11.6 - - - +
97B LYS* 4.1 18.2 - - + -
100B HIS* 3.2 37.7 - - + -
101B LEU* 3.7 28.3 - - + +
104B LEU* 3.4 9.1 - - + +
161B LEU* 5.1 2.9 - - + -
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Residues in contact with ILE 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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40B PHE* 4.3 9.4 - - + -
41B LEU* 4.0 17.7 - - + -
43B TYR* 3.0 22.4 - - - +
73B MET 3.5 6.3 - - - +
74B ILE 3.3 13.7 - - - +
76B PRO* 1.3 77.2 - - - +
78B VAL* 1.3 75.6 + - + +
80B ASN* 3.3 16.2 + - - +
100B HIS* 3.0 37.0 - - + +
104B LEU* 4.0 11.2 - - + -
243B PHE* 4.2 16.2 - - + -
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Residues in contact with VAL 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 ILE* 3.0 37.6 + - + +
75B PRO* 3.1 5.8 + - + +
77B ILE* 1.3 78.2 - - + +
79B LEU* 1.3 61.4 + - - +
80B ASN* 3.3 2.8 + - - +
208B VAL* 3.9 9.0 - - + -
238B ILE* 3.8 37.5 - - + -
243B PHE* 3.7 20.0 - - + -
268B ILE* 4.6 3.4 - - + -
270B LYS* 2.8 39.9 + - + -
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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 PRO 2.8 16.2 + - - +
76B PRO* 3.8 5.6 - - + +
78B VAL* 1.3 79.0 - - - +
80B ASN* 1.3 68.7 + - - +
81B PRO* 4.4 3.1 - - + -
87B ILE* 4.4 7.2 - - + -
101B LEU* 4.0 21.8 - - + -
159B LYS* 3.3 48.9 - - + -
160B ILE 3.4 34.3 - - - +
161B LEU* 4.1 11.0 - - + +
206B GLU* 3.6 19.2 - - + +
207B LEU 4.2 0.2 - - - -
208B VAL* 3.6 23.8 - - + +
270B LYS* 4.1 0.9 - - - +
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Residues in contact with ASN 80 (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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76B PRO 3.0 11.4 + - - -
77B ILE* 3.3 15.7 + - - +
78B VAL 3.2 5.0 - - - +
79B LEU* 1.3 81.5 - - - +
81B PRO* 1.3 73.5 - - - +
82B ARG* 3.5 3.6 + - - +
104B LEU* 5.4 1.6 - - - -
159B LYS* 3.4 14.1 + - - +
206B GLU* 5.5 0.2 - - - +
270B LYS* 4.8 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