Contacts of the strand formed by residues 423 - 428 (chain C) in PDB entry 3U1K
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 PHE 423 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419C LYS* 3.5 20.7 - - - +
420C ASP 3.5 11.0 + - - +
421C LYS* 3.1 8.9 - - + +
422C ASN* 1.3 77.6 - - - +
424C MET* 1.3 69.9 + - - +
425C LEU* 4.7 7.2 - - + -
455C GLU* 3.5 39.3 - - + -
458C LEU* 3.8 27.4 - - + -
459C TYR* 3.9 20.3 - + + -
462C ILE* 3.6 39.3 - - + -
470C ILE* 3.5 19.5 - - + -
472C VAL* 4.0 24.0 - - + -
495C LEU* 4.4 0.7 - - + -
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Residues in contact with MET 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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419C LYS* 4.1 19.1 - - + -
423C PHE* 1.3 81.9 - - - +
425C LEU* 1.3 64.7 + - - +
426C HIS* 3.6 21.5 - - + +
455C GLU* 3.4 10.8 - - - +
469C THR* 5.8 2.5 - - + -
470C ILE 3.0 8.0 + - - +
471C ARG* 2.8 53.7 - - + +
472C VAL* 3.0 41.8 + - - +
473C THR* 5.2 3.1 - - + -
115D ASN* 5.5 0.4 - - - +
116D TYR* 4.0 17.0 - - + -
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Residues in contact with LEU 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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423C PHE* 4.7 2.7 - - + -
424C MET* 1.3 79.8 - - - +
426C HIS* 1.3 71.7 + - - +
427C TYR* 4.2 3.8 - - + +
451C GLY* 3.7 30.8 - - - +
454C ALA* 4.0 20.0 - - + -
455C GLU* 2.9 30.3 + - + +
458C LEU* 3.7 26.0 - - + -
472C VAL* 3.2 34.1 - - + +
474C SER* 3.8 17.9 - - - +
487C SER 4.6 2.7 - - - +
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Residues in contact with HIS 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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424C MET* 3.6 17.5 - - + +
425C LEU* 1.3 75.6 - - - +
427C TYR* 1.3 65.5 + - - +
428C GLU* 2.8 42.9 + - + +
447C GLU* 5.9 0.9 - - - -
472C VAL 2.9 8.1 + - - +
473C THR* 3.3 8.0 - - - -
474C SER* 2.8 26.0 + - - +
475C GLU* 6.3 0.4 - - + -
115D ASN* 3.1 40.1 + - - +
116D TYR* 3.8 17.6 + - + +
117D LEU 6.1 0.4 - - - -
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Residues in contact with TYR 427 (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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425C LEU* 4.2 5.4 - - + +
426C HIS* 1.3 82.0 + - - +
428C GLU* 1.3 70.1 + - - +
429C PHE* 3.2 29.6 - + + -
446C ARG* 5.2 0.9 - - + -
447C GLU* 3.5 37.3 + - + +
450C HIS* 3.1 36.3 + + + -
451C GLY* 3.5 25.7 - - - +
474C SER* 3.3 8.3 - - - +
476C VAL* 3.8 11.0 - - + -
483C SER* 2.2 41.1 + - - -
484C SER* 3.9 4.5 - - - -
487C SER* 3.5 28.5 - - - -
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Residues in contact with GLU 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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426C HIS* 2.8 38.6 + - + +
427C TYR* 1.3 76.3 - - - +
429C PHE* 1.3 59.5 + - - +
430C PRO* 3.4 9.4 - - + +
447C GLU* 3.5 13.5 - - - +
474C SER 2.8 10.7 + - - +
475C GLU* 3.4 23.2 - - + +
476C VAL* 3.0 31.6 + - - +
103D ARG* 3.1 37.6 + - - -
115D ASN* 4.1 12.5 - - - +
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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