Contacts of the helix formed by residues 63 - 67 (chain D) in PDB entry 5IRC
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 GLN 63 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1283B TYR 4.2 8.3 - - - +
1284B ARG* 2.8 35.0 + - - +
1286B SER* 4.5 2.5 - - - -
1322B LYS* 4.5 1.1 - - - +
1398B ILE* 5.6 0.2 - - - +
1399B CYS* 4.1 21.4 - - + -
14D GLY* 3.5 5.3 - - - -
36D PRO* 4.7 2.1 - - - +
37D THR 4.4 3.1 - - - +
61D ALA* 3.4 11.3 - - - +
62D GLY* 1.3 85.2 + - - +
64D GLU* 1.3 64.4 + - - +
65D ASP* 3.0 19.5 - - + +
66D TYR* 3.0 28.4 + - + +
70D ARG* 2.9 18.2 + - - -
203D MGF 2.9 30.2 - - - -
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Residues in contact with GLU 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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1286B SER* 4.6 12.1 + - - -
1287B GLY 5.4 3.0 + - - -
1292B MET* 3.8 25.2 - - + +
1319B GLY* 4.1 9.0 - - - +
1322B LYS* 3.9 31.0 + - + +
1323B SER* 5.5 0.8 + - - +
1326B SER* 6.5 0.4 - - - -
1403B THR* 5.6 0.9 - - - +
62D GLY 3.7 1.8 + - - -
63D GLN* 1.3 75.8 - - - +
65D ASP* 1.3 68.9 + - - +
66D TYR 3.1 1.3 + - - -
67D ASP* 3.2 37.9 + - - +
98D LYS* 4.2 8.7 - - - +
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Residues in contact with ASP 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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1322B LYS* 2.7 29.9 + - - +
1399B CYS 3.7 7.6 - - - +
1400B PHE* 3.5 15.4 - - - -
1402B PRO* 3.3 35.3 - - + +
1403B THR* 2.6 36.9 + - - +
1407B PRO* 5.2 0.3 - - - +
1409B PHE* 4.2 6.6 - - - -
63D GLN* 3.0 7.6 - - + +
64D GLU* 1.3 79.5 + - - +
66D TYR* 1.3 69.2 + - + +
67D ASP 3.4 1.2 + - - -
68D ARG* 4.9 1.7 + - - +
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Residues in contact with TYR 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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1398B ILE* 2.6 43.8 + - + +
1401B TRP* 3.6 18.5 + + - -
1402B PRO* 3.8 15.4 - - + +
1409B PHE* 3.8 17.7 - + - -
1422B GLN* 5.0 0.2 + - - -
37D THR 5.0 0.4 - - - -
38D VAL* 3.8 25.6 - - + +
61D ALA* 3.5 34.1 - - + +
63D GLN* 3.0 21.7 + - + +
65D ASP* 1.3 86.1 - - + +
67D ASP* 1.3 65.0 + - - +
68D ARG 3.2 2.9 - - - -
69D LEU* 2.9 36.0 + - + -
70D ARG* 3.0 19.9 + - + +
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Residues in contact with ASP 67 (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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64D GLU* 3.2 26.5 + - - +
65D ASP 3.4 1.0 - - - -
66D TYR* 1.3 76.5 - - - +
68D ARG* 1.3 59.8 + - + +
70D ARG* 3.0 24.2 + - - +
71D PRO* 3.1 23.6 - - - +
98D LYS* 2.8 33.6 + - - +
102D GLU* 4.6 6.3 - - - +
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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