Contacts of the helix formed by residues 317 - 331 (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 ASP 317 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267C ARG* 3.0 36.1 + - - -
313C LEU* 3.8 16.4 - - + +
314C THR* 3.0 17.2 + - - +
316C TRP* 1.3 81.1 - - - +
318C ALA* 1.3 53.3 + - - +
319C ARG* 3.5 2.0 - - - -
320C LEU* 3.3 12.4 + - + -
321C TYR* 2.7 32.6 + - - +
346C ARG* 5.5 3.2 + - - -
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Residues in contact with ALA 318 (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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315C PHE 3.2 16.9 + - - +
316C TRP 3.3 3.5 + - - +
317C ASP* 1.3 71.9 - - - +
319C ARG* 1.3 69.0 + - - +
321C TYR* 2.7 17.4 + - - +
322C LYS* 2.8 25.0 + - - +
388C TRP* 4.1 18.4 - - + -
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Residues in contact with ARG 319 (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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317C ASP 3.5 0.8 - - - -
318C ALA* 1.3 81.2 - - - +
320C LEU* 1.3 80.2 + - + +
322C LYS* 3.2 22.0 + - - +
323C ILE* 3.2 17.6 + - + +
431C ASN* 5.8 2.4 + - - -
481C ASN 2.7 28.9 + - - -
482C SER* 4.1 2.5 - - - +
483C ALA 2.7 31.5 + - - +
484C GLU* 3.3 17.2 + - - +
485C ASP* 5.1 1.1 - - - +
486C PRO* 3.6 28.5 - - + +
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Residues in contact with LEU 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C VAL* 3.7 30.4 - - + +
267C ARG* 4.2 22.4 - - + +
313C LEU* 3.6 13.2 - - + +
317C ASP* 3.3 12.4 + - + +
319C ARG* 1.3 97.0 - - + +
321C TYR* 1.3 62.7 + - - +
323C ILE* 3.3 13.3 + - + +
324C ALA* 3.0 24.8 + - - +
431C ASN* 5.2 6.3 - - - +
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Residues in contact with TYR 321 (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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296C VAL* 3.5 11.5 - - + +
297C ASP* 2.4 27.9 + - - -
313C LEU* 3.1 30.5 - - + +
314C THR* 3.2 36.8 - - - +
315C PHE 4.3 1.8 - - - -
317C ASP 2.7 18.9 + - - +
318C ALA* 2.7 13.5 + - - +
320C LEU* 1.3 70.3 - - - +
322C LYS* 1.3 59.4 + - - +
324C ALA* 3.1 3.5 + - - +
325C VAL* 2.9 52.3 + - + +
338C VAL* 6.0 0.5 - - - +
339C MET* 3.8 16.6 + - - +
385C GLU* 4.2 23.4 + - + -
388C TRP* 4.1 17.3 - + - -
391C ILE* 4.9 4.7 - - + -
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Residues in contact with LYS 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318C ALA* 2.8 35.5 + - - +
319C ARG* 3.6 11.4 - - - +
321C TYR* 1.3 73.6 - - - +
323C ILE* 1.3 57.6 + - - +
325C VAL* 3.7 5.9 - - - +
326C GLY* 2.7 25.8 + - - -
388C TRP* 3.4 33.7 - - + -
390C GLU* 3.7 39.8 + - + +
391C ILE* 4.3 10.6 - - + +
484C GLU 4.6 3.8 + - - -
485C ASP* 3.1 29.0 + - - +
487C PHE* 3.6 9.4 - - + -
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Residues in contact with ILE 323 (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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266C VAL* 4.8 9.6 - - + -
274C MET* 4.8 10.8 - - - -
319C ARG* 3.2 21.5 + - + +
320C LEU* 3.7 17.3 - - + +
321C TYR 3.1 1.2 - - - -
322C LYS* 1.3 74.0 - - - +
324C ALA* 1.3 59.9 + - - +
326C GLY* 3.0 1.2 + - - -
327C PHE* 2.9 27.0 + - - +
429C PHE* 3.5 32.3 - - + -
430C ASN 6.5 0.2 - - - -
431C ASN* 4.9 15.0 - - + +
485C ASP* 5.6 0.2 - - - -
486C PRO* 3.3 32.1 - - + +
487C PHE* 3.8 25.6 - - + -
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Residues in contact with ALA 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C LEU* 3.5 39.4 - - + +
263C GLY 5.7 0.4 - - - +
266C VAL* 3.8 6.9 - - + +
296C VAL* 4.0 14.4 - - + -
313C LEU* 3.7 18.2 - - + -
320C LEU 3.0 17.0 + - - +
321C TYR 3.6 4.0 - - - +
323C ILE* 1.3 76.2 - - - +
325C VAL* 1.3 63.2 + - - +
327C PHE* 3.2 4.2 + - - +
328C MET* 3.1 17.0 + - - +
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Residues in contact with VAL 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C VAL* 3.5 24.9 - - + -
321C TYR* 2.9 48.0 + - + +
322C LYS 3.9 3.6 - - - +
324C ALA* 1.3 76.3 - - - +
326C GLY* 1.3 61.9 + - - +
328C MET* 3.3 10.0 + - + +
329C LEU* 2.9 51.3 + - + +
338C VAL* 5.0 5.6 - - + -
391C ILE* 3.6 26.7 - - + -
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Residues in contact with GLY 326 (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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322C LYS 2.7 16.4 + - - -
323C ILE 3.0 5.3 + - - -
325C VAL* 1.3 79.1 - - - +
327C PHE* 1.3 62.0 + - - +
330C ALA* 3.2 18.7 + - - +
390C GLU 5.6 0.7 - - - -
394C MET* 3.3 24.9 - - - +
429C PHE* 4.1 5.8 - - - -
487C PHE* 4.1 16.8 - - - -
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Residues in contact with PHE 327 (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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258C TYR* 4.3 2.9 - - - -
262C LEU* 4.7 11.0 - - + -
266C VAL* 6.1 0.9 - - + -
274C MET* 5.6 6.5 - - + -
277C LEU* 3.7 43.5 - - + -
280C TRP* 3.3 37.2 - + + -
323C ILE* 2.9 10.1 + - + +
324C ALA* 3.2 10.3 + - - +
326C GLY* 1.3 75.4 - - - +
328C MET* 1.3 59.9 + - - +
330C ALA* 3.2 3.1 + - - +
331C HIS* 2.8 49.0 + + + +
409C TRP* 4.6 6.7 - + - -
417C VAL* 5.6 1.8 - - + -
419C PHE* 3.5 30.5 - + - -
429C PHE* 3.5 26.2 - + + -
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Residues in contact with MET 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C TYR* 3.8 26.3 + - + +
262C LEU* 4.5 1.6 - - + -
294C VAL* 3.8 15.5 - - + -
295C PHE* 3.7 31.2 - - - -
296C VAL* 3.9 9.0 - - + +
324C ALA 3.1 13.1 + - - +
325C VAL* 3.5 13.5 - - + +
326C GLY 3.2 0.2 - - - -
327C PHE* 1.3 76.5 - - - +
329C LEU* 1.3 83.8 + - + +
330C ALA 3.1 0.7 + - - -
331C HIS* 3.1 21.0 + - - +
333C TYR 5.4 0.5 - - - +
336C THR* 3.8 27.5 - - + +
337C ARG 3.8 20.9 - - - +
338C VAL* 4.6 4.5 - - + -
398C ARG* 3.4 2.8 + - - -
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Residues in contact with LEU 329 (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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12C SER* 3.7 11.7 - - - +
325C VAL* 2.9 49.2 + - + +
328C MET* 1.3 86.8 - - + +
330C ALA* 1.3 57.2 + - - +
336C THR* 3.7 29.6 - - - +
338C VAL* 4.4 9.0 - - + -
391C ILE* 5.1 1.8 - - + +
394C MET* 3.6 46.0 - - + +
395C VAL* 4.2 11.9 - - + -
397C PHE* 4.3 1.6 - - - -
398C ARG* 2.8 39.2 + - - +
421C ARG* 4.4 1.0 + - - -
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Residues in contact with ALA 330 (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 3.2 17.3 + - - +
327C PHE* 3.5 5.2 - - - +
328C MET 3.0 0.6 - - - -
329C LEU* 1.3 79.1 - - - +
331C HIS* 1.3 59.3 + - - +
394C MET* 3.8 10.7 - - + +
397C PHE* 4.0 14.1 - - + -
419C PHE* 3.4 22.3 - - + -
421C ARG* 2.8 30.1 + - - +
427C ILE* 3.9 16.6 - - + -
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Residues in contact with HIS 331 (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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258C TYR* 4.4 4.5 - - - +
277C LEU 5.1 0.4 + - - -
278C LYS 5.2 0.6 + - - -
280C TRP* 3.4 42.8 + + + +
327C PHE* 2.8 44.7 + + + +
328C MET 3.1 8.7 + - - +
330C ALA* 1.3 77.7 - - - +
332C PRO* 1.3 76.7 - - + +
333C TYR* 3.1 35.0 + - + +
398C ARG* 2.7 31.2 + - - -
406C PHE* 3.9 27.8 - + - -
419C PHE* 3.9 3.8 - + + -
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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
------------------------------------------------------------
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