Contacts of the strand formed by residues 437 - 440 (chain C) in PDB entry 3KHU
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 437 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321C SER* 3.5 30.1 - - - -
322C LEU* 3.8 22.4 - - + -
323C PHE* 6.1 1.1 - + - -
409C HIS 3.2 15.8 + - - +
410C ALA* 3.3 3.0 - - + -
411C VAL 2.8 24.4 + - - -
432C MET* 3.9 4.4 - - - +
435C PRO* 3.6 42.4 - - + -
436C ALA* 1.3 74.0 - - - +
438C ILE* 1.3 66.3 + - - +
439C PHE* 3.4 35.7 - + + -
457C PHE* 4.6 0.4 - - - -
458C GLN* 3.4 32.5 - - + -
460C GLU* 4.7 6.1 - - - -
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Residues in contact with ILE 438 (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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411C VAL* 3.3 20.2 - - + +
413C ILE* 4.5 8.1 - - + -
425C TYR* 4.0 22.4 - - + -
437C PHE* 1.3 77.5 - - - +
439C PHE* 1.3 72.5 + - - +
440C ASP 4.4 0.4 - - - +
445C LEU* 3.9 13.5 - - + -
452C LEU* 4.1 18.2 - - + -
457C PHE* 3.6 43.5 - - + -
458C GLN 2.9 9.1 + - - +
459C ILE* 3.6 19.7 - - + -
460C GLU* 2.9 27.5 + - - +
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Residues in contact with PHE 439 (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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314C PHE* 3.9 21.0 - + + -
317C ARG* 4.3 8.3 - - + -
318C ILE* 3.7 43.3 - - + -
321C SER* 3.6 29.6 - - - -
322C LEU* 5.4 0.9 - - + -
410C ALA* 4.1 13.9 - - + -
411C VAL 2.8 12.4 + - - +
412C VAL* 3.4 6.1 - - + -
413C ILE* 2.9 30.7 + - - +
437C PHE* 3.4 30.5 - + + -
438C ILE* 1.3 73.5 - - - +
440C ASP* 1.3 56.7 + - - +
441C GLY 3.7 1.5 + - - -
460C GLU* 3.4 41.1 - - + +
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Residues in contact with ASP 440 (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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314C PHE* 4.2 2.5 - - - -
413C ILE* 4.3 8.4 - - - +
438C ILE 3.9 0.4 - - - -
439C PHE* 1.3 69.3 - - - +
441C GLY* 1.3 57.7 + - - +
442C ARG* 3.0 6.6 + - - +
443C ARG* 2.9 22.8 + - - -
444C VAL* 2.9 20.7 + - - +
445C LEU* 2.9 39.8 + - + +
446C ASP* 4.3 0.5 + - - +
449C HIS* 5.1 0.9 + - - -
459C ILE* 4.4 13.0 - - + -
460C GLU 2.8 13.1 + - - +
461C THR* 2.7 41.0 + - - +
462C ILE 3.4 4.3 + - - -
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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