Contacts of the strand formed by residues 435 - 440 (chain C) in PDB entry 1KHU
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 TRP 435 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317B VAL* 3.6 23.1 - - + -
276C TYR* 3.8 1.1 - - - -
277C TYR* 2.9 86.9 + + + +
279C LEU 2.7 21.8 + - - -
413C ARG* 3.8 28.9 - - + -
414C MET 3.3 12.1 - - - +
415C SER* 3.7 3.1 - - - -
416C PHE* 4.9 0.7 - - - -
429C VAL* 3.0 52.1 + - + -
430C THR* 4.0 5.2 - - + -
432C THR* 3.3 22.0 - - - +
434C CYS* 1.3 75.0 - - - +
436C ILE* 1.3 85.3 + - - +
437C GLU* 4.1 5.2 - - + -
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Residues in contact with ILE 436 (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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274C ILE* 4.0 21.5 - - + -
275C VAL 3.0 16.8 - - - +
276C TYR* 3.8 22.4 - - + -
277C TYR* 4.8 0.2 - - - -
296C VAL* 4.4 26.2 - - + -
309C PHE* 5.0 0.9 - - + -
311C LEU* 5.0 0.9 - - + -
334C VAL* 4.8 2.0 - - + -
336C LEU* 5.1 0.2 - - + -
413C ARG* 3.2 4.3 - - - -
414C MET* 2.9 58.4 + - + +
416C PHE* 4.4 15.9 - - + -
435C TRP* 1.3 87.0 - - - +
437C GLU* 1.3 61.7 + - - +
438C ILE* 4.3 12.6 - - + -
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Residues in contact with GLU 437 (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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315B SER* 3.5 30.8 + - - -
317B VAL* 5.7 0.3 - - - +
273C SER 3.9 0.7 - - - +
274C ILE* 3.5 4.2 - - - +
275C VAL* 3.0 31.4 + - + +
277C TYR* 3.8 21.0 + - + -
411C THR* 4.0 14.2 + - - -
412C ILE 3.1 8.5 - - - +
413C ARG* 2.7 38.3 + - + +
435C TRP* 4.1 10.2 - - + -
436C ILE* 1.3 77.4 - - - +
438C ILE* 1.3 63.5 + - - +
439C HIS* 3.8 21.8 + - + +
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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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271C TRP* 5.2 1.3 - - + -
272C CYS* 3.8 27.6 - - + -
273C SER 3.6 5.8 - - - +
274C ILE* 4.0 18.8 - - + -
336C LEU* 3.3 31.4 - - + -
382C ILE* 5.2 2.0 - - + -
410C CYS 3.6 1.2 - - - +
411C THR* 3.1 5.5 - - - -
412C ILE* 2.4 61.2 + - + +
414C MET* 3.9 24.9 - - + -
436C ILE* 4.3 9.4 - - + -
437C GLU* 1.3 77.4 - - - +
439C HIS* 1.3 64.6 + - - +
440C LEU* 4.0 12.7 - - + +
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Residues in contact with HIS 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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313B LEU* 2.9 36.3 + - + -
314B LEU* 4.9 1.0 - - - -
315B SER* 3.8 14.5 + - - -
272C CYS* 3.2 24.3 - - - -
273C SER* 3.1 26.5 + - - +
275C VAL* 6.0 4.8 - - + +
410C CYS 3.6 2.7 - - - -
411C THR* 3.2 29.0 - - + +
437C GLU* 3.8 23.9 + - + +
438C ILE* 1.3 74.9 - - - +
440C LEU* 1.3 62.6 + - - +
441C HIS* 3.4 6.6 + - + +
444C LEU* 3.9 22.2 - - + -
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Residues in contact with LEU 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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271C TRP* 3.9 33.7 - - + +
272C CYS* 3.9 10.1 - - + -
343C VAL* 4.6 8.7 - - + -
383C PHE* 4.5 17.3 - - + -
409C MET 4.9 2.5 - - - +
410C CYS* 2.8 33.8 + - - +
412C ILE* 3.6 34.1 - - + -
438C ILE* 4.0 11.7 - - + +
439C HIS* 1.3 69.8 - - - +
441C HIS* 1.3 60.7 + - - +
442C GLY 3.5 1.6 - - - -
443C PRO* 3.4 20.9 - - + +
444C LEU* 3.0 31.5 + - - +
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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