Contacts of the strand formed by residues 416 - 421 (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 GLN 416 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410C TRP* 3.5 11.5 - - + -
411C ASP* 3.0 23.9 - - - +
412C ASN* 3.1 32.5 + - - +
414C SER 3.6 0.8 - - - -
415C ASN* 1.3 76.1 - - - +
417C VAL* 1.3 63.8 + - - +
429C PHE 3.4 5.4 - - - -
430C ASN* 2.8 27.6 + - - +
432C ASP* 3.2 14.8 - - - +
434C TRP* 3.5 14.1 + - - +
435C GLN 3.4 8.9 + - - +
436C LEU* 3.2 47.6 - - + +
437C SER 4.9 1.0 + - - -
438C SER* 5.2 1.6 + - - -
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Residues in contact with VAL 417 (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* 3.5 29.5 - - + +
275C SER* 3.5 34.5 - - - +
327C PHE* 5.6 2.2 - - + -
409C TRP* 2.9 39.7 - - + -
410C TRP* 3.3 10.5 - - - +
411C ASP* 4.0 2.0 - - + -
415C ASN 4.0 1.4 + - - -
416C GLN* 1.3 81.5 - - - +
418C ALA* 1.3 75.3 + - - +
419C PHE* 4.9 3.4 - - + -
428C VAL* 3.4 1.6 - - - +
429C PHE* 2.7 41.7 + - + +
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Residues in contact with ALA 418 (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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408C ASN 4.1 0.7 - - - -
409C TRP* 3.3 5.2 - - - -
410C TRP* 2.8 34.4 + - + +
417C VAL* 1.3 80.7 - - - +
419C PHE* 1.3 70.0 + - - +
426C PHE* 3.6 18.4 - - + -
427C ILE 3.2 14.1 - - - +
428C VAL* 3.8 6.1 - - + -
429C PHE* 5.1 0.7 - - - -
440C LEU* 3.8 20.4 - - + -
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Residues in contact with PHE 419 (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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327C PHE* 3.5 31.4 - + - -
330C ALA* 3.4 45.3 - - + -
331C HIS* 3.9 10.1 - + + -
397C PHE* 6.0 0.6 - + - -
406C PHE* 3.6 25.4 - + + -
407C ALA 3.6 7.4 - - - +
408C ASN 3.4 11.7 - - - -
409C TRP* 3.9 25.4 - + + -
417C VAL* 4.9 1.1 - - + -
418C ALA* 1.3 80.4 - - - +
420C GLY* 1.3 73.0 + - - +
421C ARG* 4.6 3.8 - - + -
426C PHE* 3.3 8.2 - - - -
427C ILE* 2.9 44.9 + - + +
429C PHE* 4.3 2.2 - + - -
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Residues in contact with GLY 420 (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* 6.1 0.4 - - - -
406C PHE* 3.5 3.6 - - - -
407C ALA* 2.7 38.3 + - - -
408C ASN* 5.5 0.4 - - - -
419C PHE* 1.3 79.7 - - - +
421C ARG* 1.3 69.3 + - - +
422C GLY 4.0 1.8 - - - -
425C GLY 3.0 15.0 - - - -
426C PHE* 3.7 9.6 - - - -
442C THR 4.8 3.1 - - - -
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Residues in contact with ARG 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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329C LEU 4.4 0.4 + - - -
330C ALA 2.8 25.6 + - - +
332C PRO* 3.7 33.2 - - - +
397C PHE* 4.7 5.8 - - + -
398C ARG* 3.6 32.9 + - - +
401C VAL* 3.2 60.7 + - + +
402C ASP* 5.2 2.0 + - - +
403C GLY 4.3 4.4 - - - +
404C GLN* 2.9 38.7 + - + +
405C PRO 3.1 5.4 - - - -
406C PHE* 4.4 4.7 - - - +
419C PHE* 4.6 3.6 - - + -
420C GLY* 1.3 79.7 - - - +
422C GLY* 1.3 66.9 + - - +
424C ARG* 3.3 13.0 + - - +
425C GLY 2.9 13.1 + - - +
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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