Contacts of the strand formed by residues 420 - 426 (chain C) in PDB entry 2GD4
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 ILE 420 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55C ASN* 3.8 9.7 + - - +
56C SER* 3.5 32.9 + - - +
59C ALA* 4.4 10.1 - - + -
60C THR* 5.6 0.2 - - + -
80C PRO* 3.3 20.0 - - + +
81C LEU* 4.6 0.3 + - - +
304C LEU* 3.2 34.8 - - + -
411C PHE* 4.1 22.2 - - + -
412C ILE 3.8 3.4 - - - +
413C ARG* 4.3 5.8 - - + -
418C ASN* 4.6 4.7 - - - +
419C THR* 1.3 75.9 - - - +
421C ILE* 1.3 69.4 + - - +
422C PHE 3.7 21.8 - - - +
423C MET* 4.6 6.7 - - + -
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Residues in contact with ILE 421 (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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79C SER* 3.2 14.2 + - - +
80C PRO* 3.0 17.0 - - - +
81C LEU* 4.2 7.8 + - + -
130C LEU* 4.0 40.4 - - + +
134C ALA* 5.6 1.8 - - + -
140C LEU* 5.0 10.1 - - + -
219C ILE* 6.0 0.4 - - + -
221C PHE* 6.0 0.9 - - + -
279C ILE* 4.0 33.0 - - + -
412C ILE* 2.7 14.2 + - + +
413C ARG 4.2 10.1 - - - +
419C THR* 3.1 9.3 + - - +
420C ILE* 1.3 75.9 - - - +
422C PHE* 1.3 92.3 + - + +
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Residues in contact with PHE 422 (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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77C PHE* 3.5 34.8 - + + -
78C LEU 3.5 15.5 - - - +
79C SER* 3.9 17.3 - - - -
140C LEU* 3.5 26.5 - - + -
219C ILE* 3.6 22.2 - - + -
221C PHE* 3.4 31.2 - + + -
371C ALA* 5.6 0.4 - - + -
410C VAL* 6.1 0.2 - - - -
411C PHE* 3.5 3.2 - - - -
412C ILE* 2.7 59.3 + - + +
420C ILE* 3.7 7.3 - - - +
421C ILE* 1.3 104.3 - - + +
423C MET* 1.3 60.6 + - - +
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Residues in contact with MET 423 (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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59C ALA* 3.5 33.2 - - + +
60C THR* 4.4 10.8 - - + +
63C TYR* 3.3 43.7 - - + -
77C PHE* 3.5 7.2 - - - -
78C LEU* 3.2 46.7 + - + +
80C PRO* 4.0 6.5 - - + +
299C LEU* 4.5 7.0 - - + -
410C VAL 3.7 6.7 - - - +
411C PHE* 3.4 34.8 - - + -
420C ILE* 4.6 6.7 - - + -
422C PHE* 1.3 74.6 - - - +
424C GLY* 1.3 61.1 + - - +
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Residues in contact with GLY 424 (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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63C TYR* 4.5 5.9 - - - -
76C ILE* 3.4 17.9 - - - -
77C PHE* 4.1 4.5 - - - -
409C LEU* 3.5 6.4 - - - +
410C VAL* 2.5 46.9 + - - +
423C MET* 1.3 81.2 - - - +
425C ARG* 1.3 57.9 - - - +
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Residues in contact with ARG 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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63C TYR* 3.3 15.2 + - - +
67C ALA* 4.5 16.0 + - - +
70C LYS* 6.0 0.2 - - - +
71C ASN 3.4 9.5 + - - -
72C ASP* 3.2 38.6 + - - +
74C ASP 2.7 29.8 + - - -
75C ASN* 3.4 5.2 - - - +
76C ILE* 2.8 53.6 + - + +
292C LEU* 3.8 25.9 - - + +
296C GLU* 3.2 31.4 + - - -
325C ILE* 3.5 5.0 - - - +
408C PHE 3.8 5.8 - - - +
409C LEU* 4.1 4.0 - - + +
410C VAL* 4.2 1.3 - - - +
424C GLY* 1.3 75.2 - - - +
426C VAL* 1.3 66.1 + - - +
427C ALA* 3.9 16.4 - - - +
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Residues in contact with VAL 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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75C ASN* 3.0 8.1 - - - +
239C PHE* 4.6 5.1 - - + -
321C PRO* 4.8 1.3 - - + -
323C PHE* 3.5 38.4 - - + -
325C ILE* 4.5 0.2 - - + -
407C PRO* 3.8 4.7 - - - +
408C PHE* 2.9 78.0 + - + -
410C VAL* 3.6 8.3 - - + -
425C ARG* 1.3 74.3 - - - +
427C ALA* 1.3 58.4 + - - +
429C PRO* 4.5 21.8 - - + -
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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