Contacts of the helix formed by residues 416 - 434 (chain M) in PDB entry 5KZ5
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 GLU 416 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321M ARG* 3.5 30.8 + - - +
324M LYS* 3.3 26.1 + - - +
325M LEU* 3.3 22.6 - - - +
328M ARG* 3.1 40.6 + - - +
415M THR* 1.4 76.8 - - - +
417M GLU* 1.4 63.1 + - - +
419M VAL* 3.7 1.0 + - - -
420M ASP* 3.2 26.9 + - + +
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Residues in contact with GLU 417 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76L MET* 5.2 20.5 - - + +
78L LEU* 3.5 17.0 - - - +
321M ARG* 4.5 2.3 + - - -
415M THR* 3.2 27.5 - - - +
416M GLU* 1.4 82.3 - - - +
418M GLU* 1.4 62.3 + - - +
420M ASP* 3.4 6.3 + - - +
421M TYR* 3.0 39.7 + - + -
53l ASP* 6.0 6.3 - - - +
86l VAL* 4.7 13.4 - - + +
87l ASP* 4.7 0.2 - - - -
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Residues in contact with GLU 418 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78L LEU* 5.1 2.9 - - + +
329M LEU* 5.8 2.2 - - + +
413M PHE* 2.7 25.2 - - - +
414M THR* 3.1 27.3 + - + +
415M THR* 3.1 19.1 + - - +
417M GLU* 1.4 77.7 - - - +
419M VAL* 1.4 59.3 + - - +
421M TYR 3.5 1.2 + - - -
422M THR* 2.9 24.7 + - - +
85l ILE 4.9 1.6 - - - +
86l VAL* 3.1 23.1 - - + +
87l ASP* 3.1 33.5 - - - +
110l LYS* 3.5 29.8 + - - +
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Residues in contact with VAL 419 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325M LEU* 3.8 24.7 - - + +
328M ARG* 3.6 31.2 - - + +
329M LEU* 3.9 17.5 - - + +
332M ASN* 3.2 29.0 + - - +
414M THR* 3.5 20.2 - - + -
415M THR 3.2 13.7 + - - +
416M GLU* 3.9 5.8 - - - +
418M GLU* 1.4 71.4 - - - +
420M ASP* 1.4 60.4 + - - +
422M THR* 3.1 26.0 + - - -
423M VAL 3.6 1.7 + - - -
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Residues in contact with ASP 420 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328M ARG* 3.2 27.8 + - - +
416M GLU 3.2 18.9 + - - +
417M GLU* 3.5 9.9 - - - +
418M GLU 3.4 0.2 - - - -
419M VAL* 1.4 74.1 - - - +
421M TYR* 1.4 61.3 + - + +
422M THR 3.5 0.3 + - - -
423M VAL* 3.6 17.7 + - - +
424M GLU* 4.2 2.8 + - - +
51l SER* 3.3 24.8 + - - -
53l ASP* 5.8 0.3 - - - +
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Residues in contact with TYR 421 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417M GLU* 3.0 32.6 + - + -
418M GLU 3.6 0.9 - - - +
419M VAL 3.3 0.2 - - - -
420M ASP* 1.4 80.8 - - + +
422M THR* 1.4 56.1 + - - +
424M GLU 3.2 2.8 + - - -
425M LYS* 3.0 25.4 + - + +
50l GLY* 3.3 28.0 - - - -
51l SER* 3.5 23.3 - - - +
52l LEU* 3.4 37.6 + - - -
53l ASP* 3.7 17.6 - - + +
55l THR* 4.6 3.1 + - - -
78l GLN* 3.6 34.5 + - + -
86l VAL* 4.4 8.4 - - + +
87l ASP* 3.1 39.9 - - + +
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Residues in contact with THR 422 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329M LEU* 3.6 30.0 - - + +
332M ASN* 5.0 4.0 - - + -
333M ILE* 3.8 24.2 - - + -
418M GLU* 2.9 17.5 + - - +
419M VAL 3.1 11.2 + - - -
421M TYR* 1.4 73.6 - - - +
423M VAL* 1.4 65.1 + - - +
425M LYS* 3.6 26.2 + - - +
426M CYS* 3.3 24.8 + - - -
87l ASP* 4.2 4.3 + - - -
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Residues in contact with VAL 423 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328M ARG* 3.9 14.6 - - - +
332M ASN* 3.6 39.2 - - + +
336M SER* 3.9 11.2 + - - +
419M VAL 3.8 2.2 - - - +
420M ASP 3.6 14.6 - - - +
421M TYR 3.2 0.2 - - - -
422M THR* 1.4 79.4 - - - +
424M GLU* 1.3 71.4 + - - +
426M CYS* 3.4 12.8 + - - +
427M ILE* 3.6 14.2 + - + +
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Residues in contact with GLU 424 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420M ASP 4.2 3.8 - - - +
421M TYR 3.2 7.4 + - - +
423M VAL* 1.3 84.5 - - - +
425M LYS* 1.3 62.8 + - - +
427M ILE* 3.2 39.1 - - - +
428M GLN* 3.1 21.5 + - - +
50l GLY 3.5 18.2 - - - +
51l SER* 3.5 28.9 - - - +
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Residues in contact with LYS 425 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333M ILE* 6.2 0.2 - - - +
370M LEU 5.4 2.8 + - - -
371M LYS* 5.5 1.4 - - - +
372M ASP* 4.6 16.4 - - - +
421M TYR* 3.0 13.5 + - + +
422M THR* 3.6 32.0 + - + +
424M GLU* 1.3 73.2 - - - +
426M CYS* 1.4 59.8 - - - +
428M GLN* 3.3 4.2 + - - +
429M HIS* 2.9 52.9 + - + -
50l GLY* 4.1 3.6 - - - -
87l ASP* 3.9 25.1 - - + +
88l ALA 4.1 9.9 - - - -
89l ARG* 3.8 52.5 - - + +
110l LYS* 6.1 1.3 - - - +
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Residues in contact with CYS 426 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332M ASN 4.6 0.2 - - - -
333M ILE* 3.9 35.9 - - - -
336M SER* 3.4 24.9 - - - +
337M LEU* 3.3 35.8 - - + +
370M LEU 6.1 0.4 - - - -
422M THR* 3.3 18.9 + - - -
423M VAL 3.7 3.6 - - - +
424M GLU 3.3 0.6 - - - -
425M LYS* 1.4 80.0 - - - +
427M ILE* 1.4 60.4 + - - +
429M HIS* 3.3 20.5 + - - +
430M VAL* 3.4 7.0 + - - +
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Residues in contact with ILE 427 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336M SER* 3.3 21.3 - - - +
423M VAL* 3.6 6.2 + - + +
424M GLU* 3.2 43.7 - - - +
426M CYS* 1.4 74.9 - - - +
428M GLN* 1.4 63.8 + - + +
430M VAL* 3.6 10.2 + - - +
431M LYS* 3.4 25.6 + - - +
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Residues in contact with GLN 428 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60L ARG* 5.1 7.4 + - - -
424M GLU* 3.1 24.3 + - - +
425M LYS 3.3 3.2 + - - +
427M ILE* 1.4 79.6 - - + +
429M HIS* 1.4 62.1 + - - +
431M LYS* 3.3 40.4 + - - +
432M ARG* 3.3 17.9 + - - +
50l GLY 3.3 25.1 + - - -
76l GLN* 5.2 4.3 + - - +
89l ARG* 3.3 37.1 + - - +
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Residues in contact with HIS 429 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337M LEU* 4.6 6.3 - - + +
369M ALA* 3.6 17.6 + - + +
370M LEU 4.7 4.1 + - - -
371M LYS* 3.4 50.7 + - + +
425M LYS* 2.9 58.2 + - + +
426M CYS* 3.4 16.5 - - - +
428M GLN* 1.4 73.9 - - - +
430M VAL* 1.4 61.1 + - - +
432M ARG* 3.3 17.6 + - + +
433M LEU* 3.5 18.2 + - - +
89l ARG* 3.4 27.1 + - - +
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Residues in contact with VAL 430 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336M SER 4.5 5.4 - - - +
337M LEU* 3.7 18.4 - - + -
338M PRO* 4.2 24.7 - - + -
426M CYS 3.4 14.8 + - - +
427M ILE* 3.7 9.4 - - - +
428M GLN 3.4 0.2 - - - -
429M HIS* 1.4 72.4 - - - +
431M LYS* 1.4 63.6 + - - +
433M LEU* 3.5 21.4 - - + +
434M ARG* 3.3 28.9 + - + +
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Residues in contact with LYS 431 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60L ARG* 5.0 11.5 - - - +
427M ILE* 3.4 13.0 + - - +
428M GLN* 3.3 39.6 + - - +
430M VAL* 1.4 77.6 - - - +
432M ARG* 1.4 65.4 + - + +
434M ARG* 3.3 30.9 - - - +
435M GLU* 3.2 40.4 + - - +
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Residues in contact with ARG 432 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60L ARG* 4.1 21.2 - - - +
371M LYS* 5.7 1.3 - - - +
428M GLN* 3.3 14.8 + - + +
429M HIS* 3.3 11.5 + - + +
431M LYS* 1.4 80.8 - - - +
433M LEU* 1.4 62.6 + - - +
435M GLU* 3.4 26.0 + - - +
436M MET* 4.1 0.9 + - - -
439M LEU* 3.5 44.7 - - - +
63l LEU* 6.2 0.2 - - - +
74l LYS* 4.0 32.5 - - - +
76l GLN* 5.9 0.9 - - - -
89l ARG* 6.1 2.0 - - - +
91l LYS* 3.7 53.7 - - + +
93l PHE* 4.2 12.2 - - + -
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Residues in contact with LEU 433 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365M SER* 4.2 25.8 - - - +
369M ALA* 3.7 30.1 - - + -
371M LYS* 5.9 0.2 - - - +
429M HIS 3.5 14.2 + - - +
430M VAL* 3.5 28.5 - - + +
432M ARG* 1.4 80.5 - - - +
434M ARG* 1.4 74.7 + - + +
435M GLU 3.5 0.5 + - - -
436M MET* 3.6 15.2 + - - +
93l PHE* 4.0 24.0 - - + -
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Residues in contact with ARG 434 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430M VAL* 3.3 21.5 + - + +
431M LYS* 3.3 37.9 - - - +
433M LEU* 1.4 78.4 - - + +
435M GLU* 1.4 87.8 + - - +
436M MET* 3.1 10.9 + - - +
437M SER 4.1 3.6 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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