Contacts of the helix formed by residues 61 - 66 (chain D) in PDB entry 3A4Y
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 ALA 61 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D HIS* 3.1 33.9 - - + +
60D ALA* 1.3 82.9 - - - +
62D LEU* 1.3 65.1 + - - +
63D ASP* 3.2 15.9 - - - +
64D HIS* 3.1 3.8 + - + +
65D VAL* 3.1 18.5 + - - +
93D VAL* 4.9 2.0 - - - -
141D HIS* 5.2 2.9 - - - +
142D LEU* 4.1 10.5 - - + +
225D VAL* 5.5 6.3 - - - -
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Residues in contact with LEU 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D MET* 3.3 32.9 - - + +
34D GLN* 3.9 21.8 - - - +
60D ALA 3.4 0.8 + - - -
61D ALA* 1.3 74.3 - - - +
63D ASP* 1.3 55.3 + - - +
64D HIS 3.2 0.7 - - - -
65D VAL 5.0 0.2 - - - -
66D GLY* 2.6 38.8 + - - +
93D VAL* 3.9 23.9 - - + +
94D LEU* 5.3 4.3 - - + -
96D ASP* 5.3 4.3 - - - +
97D ALA* 3.5 34.1 - - + -
101D MET* 5.4 1.8 - - + -
225D VAL* 6.2 0.4 - - - +
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Residues in contact with ASP 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D VAL* 3.5 18.7 - - - +
13D THR* 4.5 5.8 - - + +
14D GLY 4.4 2.9 - - - +
15D SER* 3.5 15.2 + - - -
31D GLY* 3.2 13.4 - - - -
32D MET 3.6 19.3 - - - +
34D GLN* 3.7 20.8 + - + +
61D ALA* 3.6 13.9 - - - +
62D LEU* 1.3 77.3 + - - +
64D HIS* 1.3 60.6 + - - +
400D HIS* 3.7 0.9 + - - -
441D ZN 3.0 29.8 - - - -
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Residues in contact with HIS 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D SER* 3.5 14.6 + - - -
29D ASP* 2.7 40.5 + - - +
30D CYS 3.1 19.7 + - - +
31D GLY* 3.3 10.8 - - - +
57D LEU* 4.1 2.9 - - - +
58D THR* 3.3 6.5 + - - -
59D HIS* 3.3 34.8 - + - +
61D ALA 3.1 8.0 + - - +
63D ASP* 1.3 86.8 - - - +
65D VAL* 1.3 65.6 + - - +
159D TYR* 3.5 13.0 - - - -
161D GLY* 4.4 2.9 - - - -
162D ASP* 3.3 14.0 + - - -
400D HIS* 3.8 0.4 - + - -
441D ZN 2.7 34.9 - - - -
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Residues in contact with VAL 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D CYS* 3.3 5.8 - - - +
57D LEU* 4.0 14.8 - - + -
59D HIS 3.2 24.5 - - - +
60D ALA* 3.7 11.4 - - - +
61D ALA 3.1 11.8 + - - +
62D LEU* 5.0 0.7 - - - -
64D HIS* 1.3 87.9 - - - +
66D GLY* 1.3 63.6 + - - +
67D ARG 3.3 2.5 - - - -
68D LEU* 3.0 27.0 + - + +
69D PRO* 3.6 4.5 - - - +
90D MET* 3.5 21.5 - - + -
94D LEU* 3.5 29.5 - - + +
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Residues in contact with GLY 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D GLY* 3.5 1.8 - - - -
32D MET* 3.5 35.4 - - - +
62D LEU* 2.6 33.9 + - - -
65D VAL* 1.3 73.3 - - - +
67D ARG* 1.3 58.2 + - - +
69D PRO* 3.7 3.0 - - - +
94D LEU* 5.9 0.7 - - - -
105D PHE* 3.5 9.0 - - - -
106D PHE* 3.6 10.9 - - - -
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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