Contacts of the helix formed by residues 348 - 363 (chain A) in PDB entry 5K9S
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 LYS 348 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A LEU* 3.8 33.5 - - + +
311A THR* 5.3 3.4 - - - -
346A ASN* 2.9 19.6 + - - +
347A PRO* 1.3 77.2 - - - +
349A THR* 1.3 66.2 + - - +
350A ASN* 4.1 26.9 - - + +
351A ILE* 3.0 34.9 + - + +
352A GLN 3.3 8.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A PRO 3.3 6.5 + - - -
348A LYS* 1.3 72.6 - - - +
350A ASN* 1.3 63.4 + - - +
352A GLN* 3.3 11.9 + - - +
353A LYS* 3.0 27.2 + - + +
390A ASP* 3.2 38.7 + - - +
393A THR* 4.1 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A THR* 4.1 17.4 - - - +
315A ARG* 5.3 4.7 + - - +
348A LYS* 3.2 25.0 - - + +
349A THR* 1.3 80.1 - - - +
351A ILE* 1.3 73.5 + - - +
353A LYS* 3.6 16.3 + - - +
354A GLU* 3.0 41.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A LEU* 3.8 23.1 - - + -
310A VAL* 4.4 4.5 - - + -
311A THR* 3.7 34.8 - - - +
314A LEU* 3.8 14.3 - - + +
343A LEU* 3.9 28.5 - - + +
346A ASN* 3.7 26.7 - - + +
348A LYS* 3.0 18.0 + - + +
350A ASN* 1.3 84.2 - - - +
352A GLN* 1.3 60.4 + - - +
354A GLU* 3.3 2.0 + - + +
355A ALA* 2.8 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A LEU 3.7 12.3 - - - +
344A LEU* 3.5 23.1 + - - +
345A THR* 3.6 13.3 + - - +
346A ASN 2.6 30.2 + - - +
347A PRO* 4.8 1.6 + - - +
348A LYS 3.3 4.7 + - - +
349A THR* 3.3 11.3 + - - +
351A ILE* 1.3 76.5 - - - +
353A LYS* 1.3 57.9 + - - +
355A ALA* 3.2 2.3 + - - +
356A THR* 2.8 35.5 + - - +
385A VAL* 5.2 1.6 - - + +
389A ALA* 4.0 22.5 - - - +
390A ASP* 4.7 4.9 - - - +
393A THR* 4.2 10.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A THR* 3.0 18.3 + - + +
350A ASN* 3.9 15.6 + - - +
352A GLN* 1.3 76.0 - - - +
354A GLU* 1.3 58.2 + - - +
356A THR* 3.4 1.8 + - - -
357A TRP* 3.0 29.0 + - + +
390A ASP* 5.3 1.1 - - - +
392A LYS* 4.0 37.0 - - + +
393A THR* 3.4 21.2 + - - +
396A GLU* 4.1 20.3 - - + +
15C ARG* 5.9 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A THR* 5.7 1.2 - - - +
314A LEU* 3.6 33.2 - - + +
315A ARG* 3.5 28.1 + - - +
350A ASN* 3.0 33.7 + - - +
351A ILE* 3.7 0.4 - - - +
353A LYS* 1.3 79.8 + - - +
355A ALA* 1.3 58.9 + - - +
357A TRP* 3.5 15.8 + - + +
358A THR* 2.9 31.4 + - - -
15C ARG* 3.0 37.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A LEU* 4.0 8.0 - - + +
340A PHE* 3.5 18.4 - - + -
343A LEU* 3.7 30.5 - - + -
344A LEU* 4.0 11.7 - - + -
351A ILE 2.8 17.2 + - - +
352A GLN 3.8 2.9 - - - +
354A GLU* 1.3 74.5 - - - +
356A THR* 1.3 60.8 + - - +
358A THR* 3.4 1.8 + - - -
359A MET* 3.0 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A LEU* 3.3 17.8 - - - +
352A GLN 2.8 17.5 + - - -
353A LYS 3.8 3.6 - - - -
355A ALA* 1.3 75.2 - - - +
357A TRP* 1.3 65.7 + - - +
359A MET* 3.0 13.5 + - - +
360A SER* 3.0 13.3 + - - -
382A LEU* 4.5 8.7 - - + -
385A VAL* 3.7 5.7 - - + +
393A THR* 3.6 14.9 - - - +
396A GLU* 3.4 8.5 - - + +
397A ALA* 3.2 45.5 - - + +
400A ALA* 4.6 0.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A ARG 5.2 1.1 - - - -
318A GLY* 3.7 37.5 - - - -
319A ASN* 4.2 4.7 - - - -
322A THR* 3.9 9.0 - - + -
353A LYS* 3.0 18.2 + - + +
354A GLU* 3.7 16.8 - - - +
356A THR* 1.3 75.7 - - - +
358A THR* 1.3 77.4 + - - +
360A SER* 2.6 30.3 + - - -
361A ASN* 3.3 26.8 + - - +
396A GLU* 3.7 29.5 - - - +
12C LYS* 3.7 27.7 + - - +
13C MET 4.2 6.7 - - - -
15C ARG* 3.4 62.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A LEU* 4.2 7.0 + - + +
317A ILE* 4.4 8.5 - - + -
318A GLY* 3.4 22.2 + - - -
321A VAL* 3.8 24.9 - - + +
340A PHE* 3.6 27.8 - - + -
354A GLU* 2.9 19.1 + - - +
355A ALA* 3.5 6.3 - - - -
356A THR 3.2 0.2 - - - -
357A TRP* 1.3 83.3 - - - +
359A MET* 1.3 61.1 + - - +
361A ASN* 3.5 1.7 + - - -
362A ILE* 3.3 26.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A LEU* 4.4 8.3 - - + -
340A PHE* 3.5 31.2 - - + -
344A LEU* 4.4 6.7 - - + -
355A ALA 3.0 20.5 + - - +
356A THR 3.0 8.2 + - - +
358A THR* 1.3 73.9 - - - +
360A SER* 1.3 60.1 + - - +
362A ILE* 3.2 8.0 + - + +
363A THR* 2.9 34.0 + - + +
373A VAL* 3.8 29.2 - - + -
378A LEU* 3.6 28.0 - - + -
382A LEU* 4.0 36.1 - - + -
400A ALA* 4.3 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A THR 3.0 9.0 + - - -
357A TRP* 2.6 30.0 + - - -
359A MET* 1.3 77.5 - - - +
361A ASN* 1.3 59.9 + - - +
363A THR* 3.1 15.3 + - - -
364A ALA 3.2 6.6 + - - -
396A GLU* 4.2 5.9 + - - -
399A TRP* 4.1 7.0 - - - +
400A ALA* 3.6 29.8 - - - +
403A ASN* 2.8 28.2 + - - -
12C LYS* 5.4 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A VAL* 3.6 26.7 - - + +
322A THR* 3.8 8.1 - - - +
357A TRP* 3.3 33.1 + - - +
358A THR 4.0 1.6 - - - +
359A MET 3.3 0.6 - - - -
360A SER* 1.3 81.6 + - - +
362A ILE* 1.3 65.6 + - - +
364A ALA* 3.5 8.5 + - - +
403A ASN* 5.2 1.4 + - - -
10C ASN 4.7 0.5 - - - +
11C LYS* 3.2 39.4 + - + -
12C LYS* 3.0 44.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A VAL* 4.2 13.0 - - + -
328A THR* 4.1 20.8 - - + +
331A VAL* 5.2 5.8 - - + -
332A ILE* 4.3 22.7 - - + -
336A ALA* 6.2 0.2 - - + -
337A LEU* 3.9 22.4 - - + -
340A PHE* 5.1 3.8 - - + -
358A THR* 3.3 26.1 + - + +
359A MET* 3.2 16.2 + - + +
361A ASN* 1.3 73.5 - - - +
363A THR* 1.3 58.8 + - - +
364A ALA 3.0 4.0 - - - -
365A GLY* 2.9 23.2 + - - -
369A GLN* 4.7 10.3 - - + +
370A ILE* 4.8 1.7 + - - +
373A VAL* 3.7 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A MET* 2.9 23.8 + - + +
360A SER* 3.1 15.8 + - - -
362A ILE* 1.3 73.6 - - - +
364A ALA* 1.3 55.9 + - - +
365A GLY 3.2 2.5 + - - -
370A ILE* 3.6 23.3 - - + +
373A VAL* 4.5 22.7 - - + -
382A LEU* 4.8 8.3 - - + -
400A ALA* 3.1 27.4 + - + +
403A ASN* 3.4 20.5 - - - +
404A TYR* 4.1 22.0 - - + -
407A GLY* 5.4 0.3 - - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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