Contacts of the helix formed by residues 332 - 336 (chain D) in PDB entry 7C17
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 LYS 332 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92 T 3.7 21.7 + - - -
102 G 4.5 15.5 - - - +
308D ASP* 3.4 28.5 + - - -
310D GLY* 5.4 3.2 - - - +
328D ALA* 3.4 18.1 - - - +
329D ASP* 4.2 22.0 + - - +
331D ILE* 1.3 79.4 - - - +
333D GLY* 1.3 66.0 + - - +
335D GLN* 3.4 18.5 + - - +
336D GLY* 3.1 18.4 + - - -
338D PHE* 5.8 0.2 - - - -
1328D THR* 4.8 10.5 - - + +
1329D THR* 4.2 19.1 - - + -
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Residues in contact with GLY 333 (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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102 G 5.1 13.1 + - - -
112 A 4.2 15.0 - - - -
332D LYS* 1.3 76.2 + - - +
334D LYS* 1.3 62.1 + - - -
335D GLN* 5.4 0.2 - - - -
336D GLY* 3.3 7.3 + - - -
338D PHE* 5.4 1.4 - - - +
339D ARG* 3.3 27.9 + - - +
1325D PHE 5.4 5.3 + - - -
1326D GLN* 6.1 2.2 - - - +
1328D THR* 5.2 5.3 - - - +
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Residues in contact with LYS 334 (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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112 A 2.5 55.8 + - - +
122 C 3.8 41.8 + - - +
1269C ARG* 5.4 0.8 + - - +
1272C GLU* 4.7 5.8 - - - +
1273C MET* 6.0 4.5 - - - -
333D GLY* 1.3 72.3 - - - -
335D GLN* 1.3 57.0 + - - +
336D GLY 3.3 1.3 - - - -
339D ARG* 3.6 38.5 - - + +
340D GLN* 3.4 24.8 - - - +
795D TYR* 3.8 9.3 - - - +
798D ARG* 5.6 0.4 - - - +
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Residues in contact with GLN 335 (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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325D LYS* 3.7 28.0 + - - +
329D ASP* 4.8 13.6 + - - +
330D MET 4.7 0.5 - - - +
332D LYS* 3.4 17.2 + - - +
334D LYS* 1.3 75.6 - - - +
336D GLY* 1.3 64.6 + - - +
337D ARG* 5.3 2.4 + - - -
340D GLN* 3.4 16.5 - - - +
515F GLU* 4.9 4.5 - - - +
516F ASP 6.1 0.4 - - - +
518F HIS* 3.6 31.8 + - + +
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Residues in contact with GLY 336 (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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329D ASP 4.4 0.4 - - - -
330D MET 3.3 12.8 - - - -
331D ILE* 3.9 0.2 - - - -
332D LYS 3.1 26.9 + - - -
333D GLY 3.3 4.2 + - - -
334D LYS 3.3 3.4 - - - -
335D GLN* 1.3 83.0 - - - +
337D ARG* 1.3 66.3 + - - -
338D PHE* 3.3 3.5 + - - -
339D ARG 4.5 0.7 - - - -
340D GLN* 3.3 21.0 + - - +
341D ASN* 3.8 3.0 - - - +
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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