Contacts of the strand formed by residues 425 - 430 (chain C) in PDB entry 1KXT
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 425 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397C PHE* 4.1 6.3 - - - -
401C VAL* 3.7 15.0 - - - -
420C GLY* 3.0 4.4 - - - -
421C ARG 2.9 29.3 + - - -
424C ARG* 1.3 81.7 - - - +
426C PHE* 1.3 61.5 + - - +
444C LEU* 3.4 12.7 - - - +
490C ILE 3.4 9.9 - - - -
491C HIS* 4.1 0.7 - - - -
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Residues in contact with PHE 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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397C PHE* 3.9 5.2 - - - -
408C ASN* 3.8 9.2 - - + -
410C TRP* 5.7 1.1 - - + -
418C ALA* 3.6 31.0 - - + -
419C PHE* 3.3 28.5 - - - -
420C GLY 3.7 3.1 - - - -
425C GLY* 1.3 74.3 - - - +
427C ILE* 1.3 65.4 + - - +
428C VAL* 4.4 2.9 - - + -
440C LEU* 4.2 10.3 - - + -
441C GLN 3.5 22.2 - - - -
442C THR* 3.4 36.1 - - + +
444C LEU* 4.2 2.7 - - + +
477C PHE* 3.8 37.5 - + - -
489C ALA* 3.5 1.4 - - - -
490C ILE* 2.9 42.5 + - + +
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Residues in contact with ILE 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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326C GLY 5.2 0.2 - - - +
330C ALA* 3.9 15.9 - - + -
394C MET* 4.6 7.4 - - + -
397C PHE* 4.6 4.5 - - + -
418C ALA* 3.2 3.1 - - - +
419C PHE* 2.9 58.0 + - + +
426C PHE* 1.3 77.1 - - - +
428C VAL* 1.3 86.1 + - - +
429C PHE* 3.3 39.3 - - + -
487C PHE* 3.7 15.5 - - + -
488C ILE 3.0 15.9 - - - +
489C ALA* 3.6 15.7 - - + -
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Residues in contact with VAL 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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410C TRP* 4.9 0.7 - - + -
417C VAL 3.4 11.4 - - - +
418C ALA* 3.8 13.2 - - + -
426C PHE* 4.4 5.6 - - + -
427C ILE* 1.3 76.4 - - - +
429C PHE* 1.3 66.1 + - - +
436C LEU* 4.0 26.7 - - + -
440C LEU* 4.4 11.2 - - + -
477C PHE* 3.9 26.0 - - + -
479C ILE* 3.9 7.0 - - + +
487C PHE* 3.2 4.7 - - - +
488C ILE* 2.8 55.2 + - + +
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Residues in contact with PHE 429 (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 MET* 3.3 29.6 - - + -
323C ILE* 3.5 42.2 - - + -
326C GLY 4.1 0.4 - - - -
327C PHE* 3.5 42.0 - + + -
416C GLN* 3.4 0.3 - - - -
417C VAL* 2.7 39.6 + - + +
419C PHE* 4.3 3.6 - + - -
427C ILE* 3.3 42.4 - - + -
428C VAL* 1.3 76.7 - - - +
430C ASN* 1.3 62.2 + - - +
431C ASN 4.1 0.2 - - - -
436C LEU* 3.2 14.8 - - - +
479C ILE* 4.8 0.7 - - - -
486C PRO 3.7 4.7 - - - -
487C PHE* 3.6 18.2 - + + -
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Residues in contact with ASN 430 (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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323C ILE* 6.5 0.2 - - - -
415C ASN 3.8 2.2 - - - -
416C GLN* 2.8 27.0 + - - +
429C PHE* 1.3 75.9 - - - +
431C ASN* 1.3 58.0 + - - +
432C ASP* 3.3 14.8 + - - +
434C TRP 3.4 9.7 + - - +
436C LEU* 3.5 18.8 - - + -
479C ILE* 3.0 28.9 + - + +
480C SER 3.7 1.0 - - - -
481C ASN* 3.4 26.4 - - - +
486C PRO* 2.9 36.8 + - - +
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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