Contacts of the helix formed by residues 73 - 80 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A PHE* 4.0 10.3 - - + -
13A ILE 3.8 9.9 - - - +
14A ARG* 3.7 35.2 - - + +
40A PHE* 6.1 0.7 - - + -
41A LEU* 4.2 14.8 - - + -
44A ALA* 3.6 24.2 - - + -
68A GLN* 3.8 39.7 - - + +
69A SER 3.7 8.7 - - - +
70A ILE* 3.1 16.4 + - + +
72A SER* 1.3 77.4 + - - +
74A ILE* 1.3 60.6 + - - +
75A PRO 3.7 0.4 - - - -
76A PRO* 3.5 4.4 - - - +
77A ILE* 3.1 20.6 - - - +
100A HIS* 3.3 23.1 + - + +
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Residues in contact with ILE 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A PHE* 4.8 4.5 - - + -
70A ILE 4.0 4.7 - - - +
71A SER* 3.3 27.1 + - - +
73A MET* 1.3 75.9 - - - +
75A PRO* 1.3 71.1 - - + +
77A ILE* 3.0 7.5 + - - +
78A VAL* 3.0 40.7 + - + +
243A PHE* 3.9 27.8 - - + -
246A ILE* 4.1 20.4 - - + -
248A ILE* 3.9 22.7 - - + -
257A LEU* 5.0 0.4 - - + -
259A VAL* 4.3 8.3 - - + -
268A ILE* 3.8 19.3 - - + -
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Residues in contact with PRO 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A SER 3.5 13.2 - - - +
72A SER* 3.6 13.5 - - - +
74A ILE* 1.3 89.4 - - + +
76A PRO* 1.4 65.4 - - + +
78A VAL* 3.4 1.6 + - - +
79A LEU* 3.0 23.1 + - - +
97A LYS* 4.1 6.3 - - + -
161A LEU* 3.9 15.9 - - + -
208A VAL* 4.2 11.9 - - + +
210A SER* 3.2 39.0 - - - +
266A PHE* 4.0 11.0 - - + -
268A ILE* 4.1 10.1 - - + -
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Residues in contact with PRO 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A SER 3.9 5.2 - - - +
73A MET 3.5 14.1 - - - +
75A PRO* 1.4 93.9 - - + +
77A ILE* 1.3 50.9 + - - +
79A LEU* 4.5 1.3 - - + +
80A ASN* 2.8 29.5 + - - -
81A PRO* 3.5 10.4 - - - +
97A LYS* 3.9 22.4 - - + +
100A HIS* 3.4 36.6 - - + -
101A LEU* 3.8 24.0 - - + -
104A LEU* 3.6 8.0 - - + +
161A LEU* 5.0 2.6 - - + -
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Residues in contact with ILE 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A PHE* 4.3 7.9 - - + -
41A LEU* 3.7 40.2 - - + -
43A TYR* 3.8 14.8 - - - +
73A MET 3.1 20.9 - - - +
74A ILE* 3.0 7.7 + - - +
76A PRO* 1.3 77.0 - - - +
78A VAL* 1.3 62.5 + - - +
80A ASN* 3.3 20.8 - - - +
100A HIS* 3.8 7.0 - - + +
104A LEU* 4.3 8.1 - - + -
242A GLU* 3.5 24.9 - - - +
243A PHE* 4.1 12.1 - - + -
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Residues in contact with VAL 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ILE* 3.0 36.4 + - + +
75A PRO 3.8 3.6 - - - +
77A ILE* 1.3 73.9 - - - +
79A LEU* 1.3 54.7 + - - +
80A ASN* 3.9 2.6 - - - +
208A VAL* 3.8 16.2 - - + -
238A ILE* 3.9 36.6 - - + -
243A PHE* 3.7 18.2 - - + -
257A LEU* 5.1 0.2 - - + -
268A ILE* 4.1 10.1 - - + -
270A LYS* 2.7 43.1 + - + -
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Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A PRO 3.0 15.6 + - - +
76A PRO* 3.9 3.8 - - + +
78A VAL* 1.3 77.3 - - - +
80A ASN* 1.3 71.1 + - - +
81A PRO* 4.6 2.2 - - + -
87A ILE* 4.5 7.2 - - + -
101A LEU* 4.0 21.1 - - + -
159A LYS* 3.1 44.6 + - + +
160A ILE 3.3 37.7 - - - +
161A LEU* 3.7 9.9 - - + +
206A GLU* 3.4 24.2 - - + +
208A VAL* 3.6 23.3 - - + +
270A LYS* 3.5 4.7 + - - +
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Residues in contact with ASN 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A PRO 2.8 12.2 + - - -
77A ILE* 3.3 18.2 - - - +
78A VAL 3.2 4.5 - - - +
79A LEU* 1.3 77.9 - - - +
81A PRO* 1.3 68.9 - - - +
82A ARG* 2.6 36.1 + - - +
104A LEU* 5.2 2.2 - - - +
159A LYS* 3.0 21.1 + - - +
270A LYS* 4.9 2.0 - - - +
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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