Contacts of the helix formed by residues 424 - 429 (chain C) in PDB entry 5D4D
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 GLY 424 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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422C ARG 3.9 3.8 + - - -
423C ALA* 1.3 77.1 - - - +
425C PHE* 1.3 69.5 + - - -
426C ASP* 3.1 6.7 + - - +
427C VAL* 4.0 4.2 + - - +
428C ARG* 3.2 19.9 + - - +
1086D LEU* 4.9 3.1 - - - -
16H C 5.4 4.3 - - - -
17H A 4.9 13.1 + - - -
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Residues in contact with PHE 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424C GLY* 1.3 71.7 - - - -
426C ASP* 1.3 68.0 + - - +
428C ARG* 3.3 5.6 + - - -
429C ASP* 3.0 30.2 + - - +
1079D LYS* 3.5 30.3 - - + +
1082D ALA* 4.3 12.6 - - + -
1083D ASP* 3.0 32.5 - - - -
1086D LEU* 3.4 34.1 - - + -
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Residues in contact with ASP 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325C ILE* 6.2 2.7 - - + -
326C ASP* 3.6 28.6 - - - +
424C GLY* 3.1 4.5 - - - +
425C PHE* 1.3 83.0 - - - +
427C VAL* 1.3 67.9 + - + +
429C ASP* 3.6 17.3 - - - +
1079D LYS* 5.9 0.2 + - - -
17H A 5.0 7.1 + - - -
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Residues in contact with VAL 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325C ILE* 5.9 3.8 - - + -
326C ASP* 3.8 17.7 - - - +
331C ARG* 4.1 28.6 + - - +
412C ALA* 5.9 0.3 - - - +
418C LEU* 3.6 36.1 - - + -
423C ALA* 3.7 23.6 - - + -
424C GLY 4.2 4.2 - - - +
426C ASP* 1.3 78.0 - - + +
428C ARG* 1.3 63.8 + - - +
429C ASP 3.2 7.6 + - - +
434C HIS* 5.7 0.3 - - - -
450C GLY 3.7 10.9 - - - +
451C LEU* 3.9 8.2 - - + +
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Residues in contact with ARG 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420C ARG* 4.5 3.2 - - - +
421C GLU 4.6 7.5 - - - +
423C ALA* 2.8 37.4 + - - +
424C GLY 3.2 20.0 - - - +
425C PHE 3.3 3.9 + - - +
427C VAL* 1.3 75.3 - - + +
429C ASP* 1.3 60.0 + - - +
447C ALA* 2.3 36.0 + - - +
449C ILE* 3.0 30.8 + - - +
450C GLY* 3.5 9.4 - - - -
451C LEU* 3.7 29.0 - - + +
1078D ARG* 2.9 35.2 + - - +
1082D ALA* 4.2 24.0 - - + +
1085D ALA* 5.6 1.6 - - - +
1086D LEU* 4.2 25.6 - - - +
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Residues in contact with ASP 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C ARG* 5.7 0.2 + - - -
425C PHE* 3.0 21.9 + - - +
426C ASP* 3.6 13.8 - - - +
427C VAL 3.2 5.6 - - - +
428C ARG* 1.3 82.8 - - - +
430C VAL* 1.3 68.9 + - - +
431C HIS* 3.5 6.0 + - + +
434C HIS* 3.6 13.7 + - - -
1048D PRO* 3.9 24.2 - - + +
1075D HIS* 4.4 5.4 - - - +
1078D ARG* 3.9 6.1 + - - -
1079D LYS* 3.1 45.3 + - - +
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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