Contacts of the helix formed by residues 348 - 365 (chain B) in PDB entry 1K7E
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 ALA 348 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347B PRO* 1.3 72.1 - - - +
349B LEU* 1.4 58.7 + - - +
350B GLU* 3.2 19.1 - - - +
351B SER* 3.3 18.6 + - - +
352B SER* 2.7 31.1 + - - -
378B GLY* 3.1 19.6 + - - -
379B ARG 3.4 14.6 - - - +
380B GLY* 3.3 7.3 - - - +
382B LYS* 4.0 4.5 - - - +
383B ASP* 3.4 7.2 - - - -
402B PLP 4.0 5.6 - - + -
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Residues in contact with LEU 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B ILE* 4.1 28.9 - - + +
301B SER* 3.5 17.9 - - - -
332B ALA* 4.4 4.2 - - + +
333B LEU* 3.9 25.1 - - + +
336B PHE* 4.1 20.9 - - + -
347B PRO 3.7 0.4 + - - -
348B ALA* 1.4 71.8 - - - +
350B GLU* 1.3 59.0 + - - +
352B SER* 3.1 14.3 - - - -
353B HIS* 2.8 23.6 + - - -
383B ASP* 2.7 44.3 + - + +
386B THR* 4.2 19.5 - - + -
387B VAL* 4.2 3.8 - - + -
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Residues in contact with GLU 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ALA* 5.0 3.1 - - - +
230B CYS* 3.3 13.8 - - - +
301B SER* 3.2 19.5 + - - +
303B GLY* 3.4 28.9 + - - -
304B LEU* 4.0 11.2 - - + -
348B ALA* 3.2 7.8 - - - +
349B LEU* 1.3 76.7 + - - +
351B SER* 1.3 58.8 + - - +
353B HIS* 3.0 28.4 + - - +
382B LYS* 2.6 39.9 + - - -
402B PLP 3.3 42.8 + - + +
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Residues in contact with SER 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B CYS* 4.0 6.7 - - - -
348B ALA* 3.6 14.9 - - - +
350B GLU* 1.3 76.5 - - - +
352B SER* 1.3 63.9 + - - +
353B HIS 2.9 1.3 + - - -
354B ALA* 3.1 12.2 + - - +
355B LEU* 3.2 11.6 + - - +
374B VAL* 5.0 0.5 - - - +
375B ASN 4.3 4.3 - - - -
376B LEU* 3.9 24.2 - - - +
377B SER* 2.7 35.5 + - - -
378B GLY 3.0 19.3 + - - -
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Residues in contact with SER 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B ALA* 3.5 23.9 - - - -
335B ALA* 3.5 4.1 - - - +
336B PHE* 3.9 11.2 + - - +
347B PRO* 3.4 22.0 - - - +
348B ALA 2.7 18.3 + - - -
349B LEU* 3.1 21.8 - - - -
350B GLU 3.0 0.2 - - - -
351B SER* 1.3 77.1 - - - +
353B HIS* 1.3 58.7 + - - +
355B LEU* 4.5 6.5 - - - -
356B ALA* 3.0 25.1 + - - +
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Residues in contact with HIS 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B CYS* 4.4 3.6 - - + -
255B VAL* 3.8 15.5 - - + +
257B PRO* 3.8 15.5 - - + +
259B GLY 5.4 0.2 + - - -
299B SER* 3.6 24.7 + - - -
300B ILE* 4.3 5.1 - - + +
301B SER* 4.1 7.6 - - - -
304B LEU* 3.5 15.0 - - + +
327B ILE* 3.3 53.1 + - + +
328B THR 4.3 4.6 + - - -
329B ASP* 4.6 1.8 + - - -
332B ALA* 3.4 18.0 - - + +
349B LEU 2.8 27.7 + - - -
350B GLU 3.0 12.0 + - - +
351B SER 2.9 0.2 + - - -
352B SER* 1.3 78.2 - - - +
354B ALA* 1.3 57.1 + - - +
356B ALA* 3.4 1.4 - - - +
357B HIS* 3.0 22.2 + - - +
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Residues in contact with ALA 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B ILE* 3.7 22.7 - - + +
229B ALA* 3.8 12.3 - - - -
230B CYS* 3.7 23.7 - - - +
255B VAL* 4.0 7.8 - - - +
350B GLU 4.2 0.6 + - - -
351B SER* 3.1 10.9 + - - +
353B HIS* 1.3 76.1 - - - +
355B LEU* 1.3 68.3 + - - +
357B HIS* 2.9 14.0 + - - +
358B ALA* 3.1 10.2 + - - +
374B VAL* 4.0 11.7 - - + -
375B ASN 4.4 3.4 - - - +
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Residues in contact with LEU 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ILE* 5.6 2.0 - - + -
73B LEU* 4.1 26.2 - - + -
75B LEU* 4.6 12.8 - - + -
335B ALA* 3.7 29.4 - - + +
338B THR* 5.7 1.1 - - + -
339B LEU* 3.9 35.4 - - + +
347B PRO* 5.3 3.4 - - + -
351B SER 3.2 8.7 + - - +
352B SER* 3.8 9.0 - - - +
354B ALA* 1.3 79.9 - - - +
356B ALA* 1.3 57.3 + - - +
358B ALA* 3.0 5.4 + - + +
359B LEU* 2.9 40.6 + - + +
374B VAL* 4.0 15.2 - - + +
376B LEU* 5.5 3.4 - - + -
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Residues in contact with ALA 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B ILE* 3.8 20.2 - - + +
331B GLU* 3.6 17.0 - - + +
334B GLU* 5.9 0.4 - - - +
335B ALA* 3.5 17.9 - - + +
352B SER 3.0 17.2 + - - +
353B HIS 3.4 6.1 - - - +
355B LEU* 1.3 79.6 - - - +
357B HIS* 1.3 63.7 + - - +
359B LEU* 3.2 7.4 + - - +
360B LYS* 3.1 21.0 + - - +
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Residues in contact with HIS 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B ILE* 4.6 4.0 - - + -
253B ILE* 3.8 28.6 - - + +
255B VAL* 3.7 18.6 - - + -
325B VAL* 3.7 31.4 - - + +
326B SER 5.2 1.0 + - - -
327B ILE* 3.7 15.9 - - + +
353B HIS 3.0 5.9 + - - +
354B ALA 2.9 12.4 + - - +
356B ALA* 1.3 74.7 - - - +
358B ALA* 1.3 64.3 + - - +
360B LYS* 3.2 19.3 + - + +
361B MET* 3.0 60.0 + - + +
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Residues in contact with ALA 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B THR* 5.6 0.3 - - - +
73B LEU* 4.1 17.3 - - + -
228B ILE* 4.6 3.9 - - + +
354B ALA 3.1 4.9 + - - -
355B LEU* 3.0 11.3 + - + +
357B HIS* 1.3 77.4 - - - +
359B LEU* 1.3 63.5 + - - +
361B MET* 3.0 22.8 + - - +
362B MET* 3.2 13.5 + - - +
372B LEU* 4.2 13.4 - - + +
374B VAL* 3.6 28.3 - - + -
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Residues in contact with LEU 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ILE* 3.5 32.5 - - + -
73B LEU* 5.1 2.0 - - + -
334B GLU* 3.9 4.9 - - - +
335B ALA* 3.9 34.8 - - + -
338B THR* 4.5 11.2 - - + -
355B LEU* 2.9 29.0 + - + +
356B ALA* 3.6 6.7 - - - +
357B HIS 3.1 0.2 - - - -
358B ALA* 1.3 78.4 - - - +
360B LYS* 1.3 58.3 + - - +
362B MET* 3.3 13.2 + - + -
363B ARG* 2.6 69.4 + - - +
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Residues in contact with LYS 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326B SER 4.2 7.9 + - - -
327B ILE* 3.8 17.5 - - - +
331B GLU* 2.7 36.3 + - - -
356B ALA 3.1 11.2 + - - +
357B HIS* 3.5 24.1 + - + +
359B LEU* 1.3 78.7 - - - +
361B MET* 1.3 57.2 + - - +
363B ARG* 4.6 6.0 - - - +
364B GLU* 2.8 68.1 + - + +
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Residues in contact with MET 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B ALA* 4.4 6.1 - - + -
228B ILE* 4.1 12.8 - - + -
253B ILE* 3.6 23.6 - - + -
357B HIS* 3.0 50.4 + - + +
358B ALA* 3.0 9.6 + - - +
360B LYS* 1.3 78.2 - - - +
362B MET* 1.3 61.8 + - - +
364B GLU* 4.6 2.6 - - - +
365B GLN* 3.6 15.1 + - - +
368B LYS* 6.1 1.1 - - - +
370B GLN* 3.2 32.5 + - - +
372B LEU* 4.1 22.9 - - + -
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Residues in contact with MET 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ILE* 3.6 27.8 - - + +
66B THR* 3.7 37.7 - - - -
69B THR* 3.7 24.9 - - + +
71B THR* 3.3 28.9 - - + +
73B LEU* 6.0 0.9 - - - -
358B ALA 3.2 8.4 + - - +
359B LEU* 3.4 15.9 - - + +
361B MET* 1.3 77.6 - - - +
363B ARG* 1.3 88.7 + - + +
365B GLN 3.1 3.2 - - - -
366B PRO* 3.1 26.2 - - - +
370B GLN* 3.9 1.8 - - - +
372B LEU* 5.2 0.2 - - - +
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Residues in contact with ARG 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B THR* 6.0 0.9 - - - -
334B GLU* 2.7 45.6 + - - -
338B THR* 3.9 10.1 + - - +
359B LEU* 2.6 51.7 + - - +
360B LYS* 4.2 4.4 - - - +
362B MET* 1.3 93.7 - - + +
364B GLU* 1.4 61.4 + - + +
366B PRO* 3.2 16.2 - - - +
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Residues in contact with GLU 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B LYS* 2.8 52.6 + - + +
361B MET* 4.6 2.1 - - - +
363B ARG* 1.4 73.0 - - + +
365B GLN* 1.3 75.6 + - + +
366B PRO* 3.4 4.7 - - - +
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Residues in contact with GLN 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B THR* 5.2 0.2 + - - -
361B MET 3.6 9.3 + - - +
362B MET* 3.1 7.5 + - - +
364B GLU* 1.3 100.5 - - + +
366B PRO* 1.3 60.7 - - - +
367B GLU 3.2 2.9 - - - +
368B LYS* 2.9 57.7 + - + +
370B GLN* 4.1 5.4 + - - -
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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
------------------------------------------------------------
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