Contacts of the helix formed by residues 340 - 362 (chain P) in PDB entry 4G7Z
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 SER 340 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010M THR* 5.9 0.8 - - - -
1011M GLY* 4.2 19.8 + - - -
1013M TYR* 4.6 5.6 - - - -
338P LEU 3.5 3.6 + - - -
339P PRO* 1.3 73.5 - - - +
341P PRO* 1.3 66.7 - - - +
342P VAL* 2.9 13.2 - - - -
343P ASP* 2.8 43.6 + - - -
344P ALA* 2.9 9.2 + - - +
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Residues in contact with PRO 341 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1010M THR* 4.2 16.8 - - + -
1013M TYR* 3.9 28.0 - - + +
1063M ARG* 3.7 18.2 - - + +
1064M ASN* 3.1 42.6 - - - +
1067M TYR* 3.5 20.5 - - + -
339P PRO 4.2 0.7 - - - +
340P SER* 1.3 88.3 - - - +
342P VAL* 1.3 55.9 + - + +
343P ASP 3.4 0.2 - - - -
344P ALA* 3.5 2.9 - - + +
345P ALA* 2.9 28.4 + - - +
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Residues in contact with VAL 342 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1010M THR* 4.2 13.2 - - - +
1067M TYR* 3.8 21.8 - - + +
671N LYS* 6.1 2.7 - - + -
674N ARG* 3.4 50.7 - - - +
340P SER* 2.9 9.1 + - - -
341P PRO* 1.3 76.9 - - + +
343P ASP* 1.3 67.2 + - - +
344P ALA 3.2 0.2 - - - -
345P ALA* 3.5 2.1 + - - +
346P THR* 2.9 38.5 + - - +
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Residues in contact with ASP 343 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339P PRO* 4.0 15.2 - - + +
340P SER* 2.8 36.2 + - - +
342P VAL* 1.3 78.3 - - - +
344P ALA* 1.3 62.0 + - - +
346P THR* 3.3 9.2 + - - +
347P GLN* 3.2 24.3 + - - +
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Residues in contact with ALA 344 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1064M ASN* 4.1 24.7 - - + +
1068M GLU* 4.3 5.9 - - - +
339P PRO* 4.4 9.4 - - + +
340P SER 2.9 10.3 + - - +
341P PRO* 3.5 14.4 - - + +
343P ASP* 1.3 77.3 - - - +
345P ALA* 1.3 63.4 + - - +
346P THR 3.5 0.3 + - - -
347P GLN* 3.8 5.1 + - - +
348P SER* 3.7 18.4 + - - -
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Residues in contact with ALA 345 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1067M TYR* 4.0 20.0 - - + -
1068M GLU* 4.0 23.5 + - + +
1071M ILE* 5.4 4.5 - - + -
1072M LYS* 6.1 0.2 - - - +
341P PRO 2.9 16.5 + - - +
342P VAL 3.9 3.6 - - - +
344P ALA* 1.3 76.6 - - - +
346P THR* 1.3 58.1 + - - +
348P SER* 3.1 7.7 + - - -
349P LEU* 2.9 43.4 + - + +
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Residues in contact with THR 346 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671N LYS* 4.0 29.5 - - - +
342P VAL* 2.9 28.3 + - - +
343P ASP* 3.4 10.7 - - - +
344P ALA 3.2 0.4 - - - -
345P ALA* 1.3 77.6 - - - +
347P GLN* 1.3 59.6 + - - +
349P LEU* 3.3 9.0 + - - +
350P LEU* 2.8 30.7 + - + +
421P PHE* 4.1 14.4 - - + -
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Residues in contact with GLN 347 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
768M THR* 4.2 15.5 - - + +
769M PRO* 5.8 0.6 - - - +
770M GLU* 3.5 28.3 + - - +
343P ASP 3.2 15.3 + - - +
344P ALA* 4.4 4.6 - - - +
345P ALA 3.5 0.2 - - - -
346P THR* 1.3 79.3 - - + +
348P SER* 1.3 59.7 + - - +
350P LEU* 3.0 14.0 + - + +
351P SER* 3.0 27.2 + - - -
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Residues in contact with SER 348 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1068M GLU* 3.2 24.5 + - - -
1072M LYS* 4.4 1.4 + - - -
344P ALA 3.7 11.1 + - - -
345P ALA 3.1 9.7 + - - -
347P GLN* 1.3 78.6 - - - +
349P LEU* 1.3 62.2 + - - +
350P LEU 3.1 0.4 - - - -
351P SER* 3.4 7.4 + - - +
352P GLU* 2.9 42.2 + - - +
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Residues in contact with LEU 349 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1071M ILE* 5.0 9.6 - - + -
1072M LYS* 4.6 12.3 - - + +
670N VAL* 4.8 22.7 - - + -
671N LYS* 5.4 11.0 - - + +
345P ALA* 2.9 34.5 + - + +
346P THR* 3.5 8.7 - - - +
348P SER* 1.3 77.5 + - - +
350P LEU* 1.3 58.4 + - - +
352P GLU* 3.5 22.1 - - + +
353P GLU* 3.0 36.8 + - + +
421P PHE* 4.0 10.8 - - + -
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Residues in contact with LEU 350 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
768M THR* 5.7 2.5 - - + -
770M GLU* 3.5 36.6 - - + +
771M GLU* 4.4 8.1 - - + +
774M LEU* 5.1 9.0 - - + -
346P THR* 2.8 16.0 + - + +
347P GLN* 3.0 21.5 + - + +
349P LEU* 1.3 76.2 - - - +
351P SER* 1.3 57.8 + - - +
353P GLU* 3.3 2.0 + - + -
354P LEU* 2.8 55.3 + - + +
418P LEU* 6.1 0.4 - - + -
421P PHE* 3.9 35.4 - - + -
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Residues in contact with SER 351 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
770M GLU* 3.3 31.8 + - - +
347P GLN* 3.0 11.9 + - - +
348P SER* 3.4 8.7 + - - -
350P LEU* 1.3 75.9 - - - +
352P GLU* 1.3 57.2 + - - +
354P LEU* 4.0 6.8 - - - +
355P GLU* 3.0 31.9 + - - +
375P LEU* 5.9 5.6 - - - +
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Residues in contact with GLU 352 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1068M GLU* 4.6 0.5 - - - +
1072M LYS* 3.4 30.4 + - - -
348P SER* 2.9 34.7 + - - +
349P LEU* 3.5 23.9 - - + +
351P SER* 1.3 77.4 - - - +
353P GLU* 1.3 58.3 + - + +
355P GLU* 3.4 5.7 + - - +
356P LYS* 3.0 25.3 + - - +
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Residues in contact with GLU 353 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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669N ASN* 4.2 10.7 + - - +
349P LEU* 3.0 26.4 + - + +
350P LEU* 3.9 3.4 - - + +
352P GLU* 1.3 75.0 - - + +
354P LEU* 1.3 67.6 + - + +
356P LYS* 3.2 33.3 + - - +
357P ALA* 3.2 15.8 + - - +
417P LYS* 3.1 31.2 + - - +
418P LEU* 3.3 33.3 - - + +
421P PHE* 4.0 20.7 - - + -
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Residues in contact with LEU 354 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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770M GLU* 3.6 43.3 - - + +
773M LEU* 3.7 29.8 - - + -
774M LEU* 4.8 4.5 - - + -
777M ILE* 4.5 11.7 - - + -
350P LEU* 2.8 39.9 + - + +
351P SER* 4.1 4.5 - - - +
353P GLU* 1.3 73.2 - - - +
355P GLU* 1.3 60.3 + - - +
357P ALA* 3.9 1.9 + - - +
358P LEU* 3.1 33.8 + - - +
375P LEU* 4.1 13.9 - - + -
418P LEU* 4.2 21.1 - - + -
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Residues in contact with GLU 355 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351P SER 3.0 20.1 + - - +
352P GLU* 3.4 6.5 + - - +
353P GLU 3.2 0.2 - - - -
354P LEU* 1.3 77.2 - - - +
356P LYS* 1.3 61.5 - - - +
358P LEU* 4.0 7.8 - - - +
359P SER* 3.7 20.9 + - - -
370P LYS* 2.5 41.0 + - - +
375P LEU* 3.8 23.8 - - - +
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Residues in contact with LYS 356 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352P GLU 3.0 13.7 + - - +
353P GLU* 3.2 28.7 + - - +
355P GLU* 1.3 80.4 - - - +
357P ALA* 1.3 62.3 + - + +
358P LEU 3.3 0.7 + - - -
359P SER* 4.5 1.4 - - - -
360P LYS* 3.7 35.4 + - - +
416P ARG* 3.0 33.0 - - - +
417P LYS* 3.1 30.1 - - - +
418P LEU* 5.5 2.4 - - + +
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Residues in contact with ALA 357 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353P GLU 3.2 10.7 + - - +
354P LEU* 4.2 1.8 - - + +
356P LYS* 1.3 77.7 - - + +
358P LEU* 1.3 63.1 + - - +
360P LYS* 3.7 27.7 - - + +
361P LEU* 3.8 5.0 - - - +
408P LEU* 3.7 37.6 - - + +
412P GLU* 4.9 3.8 - - + -
416P ARG* 6.6 0.2 - - + -
418P LEU* 4.8 18.6 - - + -
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Residues in contact with LEU 358 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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773M LEU* 4.7 10.3 - - + -
354P LEU 3.1 22.5 + - - +
355P GLU* 4.0 7.6 - - - +
356P LYS 3.3 0.2 - - - -
357P ALA* 1.3 83.1 - - - +
359P SER* 1.3 59.0 + - - +
360P LYS 3.4 0.2 - - - -
361P LEU* 3.1 18.8 - - + +
362P SER 3.2 1.4 - - - +
366P ALA* 3.0 26.7 - - + +
369P LEU* 3.7 30.5 - - + -
370P LYS* 3.4 48.0 - - + +
375P LEU* 3.8 18.6 - - + -
408P LEU* 4.5 7.2 - - + -
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Residues in contact with SER 359 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355P GLU* 3.7 17.5 + - - -
356P LYS 3.9 1.8 + - - -
358P LEU* 1.3 78.6 - - - +
360P LYS* 1.3 64.1 + - - +
361P LEU 3.7 0.2 - - - -
362P SER* 4.4 10.1 + - - +
363P GLU* 5.9 0.7 - - - +
366P ALA* 4.6 4.9 - - - -
370P LYS* 5.5 5.2 - - - -
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Residues in contact with LYS 360 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356P LYS* 3.7 34.4 + - - +
357P ALA* 3.7 23.8 - - + +
359P SER* 1.3 78.3 - - - +
361P LEU* 1.3 72.4 + - + +
411P HIS* 6.0 3.1 - - + +
412P GLU* 4.7 17.0 - - - +
416P ARG* 3.0 43.8 - - - +
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Residues in contact with LEU 361 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357P ALA 3.8 11.7 - - - +
358P LEU* 3.1 30.3 - - + +
360P LYS* 1.3 85.2 - - + +
362P SER* 1.3 75.5 + - - +
365P GLU* 4.2 13.5 - - + -
366P ALA* 4.6 2.5 - - - +
369P LEU* 6.1 0.9 - - + -
404P ALA* 3.3 36.1 - - + +
407P LYS* 5.5 1.1 - - + -
408P LEU* 3.4 25.8 - - + +
412P GLU* 5.1 6.7 - - - +
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Residues in contact with SER 362 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358P LEU 3.2 5.1 - - - +
359P SER 4.7 5.8 - - - -
360P LYS 3.7 1.0 - - - -
361P LEU* 1.3 84.8 - - - +
363P GLU* 1.3 69.6 + - - +
364P ARG* 3.4 14.7 + - - +
365P GLU* 3.5 25.6 + - - +
366P ALA* 3.1 27.0 + - - +
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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