Contacts of the helix formed by residues 508 - 526 (chain C) in PDB entry 4Z2C
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 508 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ARG* 4.8 12.0 + - - -
120A TYR* 5.8 1.6 - - - -
78B HIS* 6.6 0.4 - - + -
506C ASP* 3.2 23.5 - - - +
507C ALA* 1.3 82.9 + - - +
509C VAL* 1.3 68.5 + - + +
510C ASP* 3.4 17.4 + - - +
511C GLY* 3.2 23.2 + - - -
512C ALA* 3.3 16.8 + - - +
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Residues in contact with VAL 509 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ASP* 4.4 14.4 - - + +
22B TYR* 3.4 22.7 - - + +
25B SER* 3.7 32.8 - - - -
26B VAL* 5.8 0.2 - - + -
30B ARG* 5.0 7.6 - - - +
78B HIS* 6.5 0.7 - - + -
508C ASP* 1.3 74.8 - - + +
510C ASP* 1.3 76.0 + - - +
511C GLY 3.1 1.8 - - - -
512C ALA* 3.0 11.4 + - - +
513C HIS 3.0 22.0 + - - -
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Residues in contact with ASP 510 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B TYR* 3.9 4.5 + - + -
30B ARG* 2.9 39.9 + - - -
78B HIS* 4.7 9.9 - - - -
508C ASP* 3.4 15.3 - - - +
509C VAL* 1.3 83.8 + - - +
511C GLY* 1.3 59.1 + - - +
513C HIS* 3.2 11.2 + - + +
514C ILE* 2.9 38.2 + - + +
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Residues in contact with GLY 511 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505C THR* 3.3 14.8 + - - +
506C ASP* 3.4 34.8 - - - -
508C ASP* 3.2 13.5 + - - -
509C VAL 3.1 1.0 - - - -
510C ASP* 1.3 75.3 - - - +
512C ALA* 1.3 58.4 + - - +
514C ILE* 3.3 7.0 + - - -
515C ARG* 2.9 24.0 + - - -
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Residues in contact with ALA 512 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B SER* 3.9 34.8 - - - +
21B ASP* 4.9 4.9 - - + -
22B TYR* 4.9 0.4 - - + -
506C ASP 4.4 0.2 + - - -
508C ASP 3.3 9.0 + - - +
509C VAL* 3.0 15.8 + - - +
511C GLY* 1.3 75.4 - - - +
513C HIS* 1.3 57.9 + - - +
515C ARG* 3.4 16.8 + - - +
516C THR* 2.9 32.9 + - - -
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Residues in contact with HIS 513 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B PHE* 5.5 8.5 - + - -
22B TYR* 3.3 64.4 + + + +
458C LYS* 5.0 9.7 - - + +
509C VAL 3.0 5.5 + - - -
510C ASP* 3.2 10.0 + - - +
512C ALA* 1.3 76.9 - - - +
514C ILE* 1.3 57.2 + - + +
516C THR* 3.1 14.3 + - + -
517C LEU* 2.9 57.2 + - + +
626C MET* 5.6 3.1 - - + +
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Residues in contact with ILE 514 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433C GLU* 4.0 26.7 - - + -
455C ILE* 5.8 7.6 - - + +
457C GLY* 4.0 26.7 - - - +
458C LYS* 4.8 8.7 - - + -
459C ILE* 5.3 6.7 - - + +
505C THR* 3.7 14.6 - - + -
506C ASP* 6.2 0.2 - - + -
510C ASP* 2.9 25.8 + - + +
511C GLY* 3.7 9.2 - - - +
513C HIS* 1.3 75.9 - - + +
515C ARG* 1.3 58.0 + - - +
517C LEU* 3.3 9.0 + - + +
518C LEU* 2.9 42.1 + - + +
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Residues in contact with ARG 515 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B GLU* 4.1 21.1 - - - +
18B SER* 3.6 26.7 + - - -
503C LEU* 4.6 8.2 + - + +
505C THR* 3.5 29.6 + - + +
506C ASP 4.7 8.5 + - - -
507C ALA* 5.9 1.6 - - - +
511C GLY 2.9 15.9 + - - +
512C ALA* 3.4 14.4 - - - +
513C HIS 3.2 0.2 - - - -
514C ILE* 1.3 76.1 - - - +
516C THR* 1.3 57.5 + - - +
518C LEU* 3.4 5.6 + - - +
519C LEU* 2.9 45.7 + - + +
537C ILE* 4.3 27.6 - - + +
538C ALA 5.1 5.1 + - - -
539C GLN* 5.9 3.0 - - - -
540C PRO* 6.1 2.0 - - - +
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Residues in contact with THR 516 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B MET* 3.6 24.4 + - + -
18B SER* 3.8 15.4 - - - -
19B PHE* 4.2 19.9 + - + -
512C ALA 2.9 18.5 + - - -
513C HIS* 3.1 15.7 + - + -
515C ARG* 1.3 76.1 - - - +
517C LEU* 1.3 63.6 + - - +
519C LEU* 3.1 5.8 + - - +
520C THR* 2.9 24.8 + - - +
626C MET* 3.5 32.8 - - + -
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Residues in contact with LEU 517 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458C LYS* 4.1 13.7 - - + -
459C ILE* 3.4 47.1 - - + +
460C LEU 4.9 3.6 - - - +
461C ASN* 3.9 26.5 - - + -
513C HIS* 2.9 44.3 + - + +
514C ILE* 3.7 13.5 - - - +
516C THR* 1.3 73.9 - - - +
518C LEU* 1.3 58.0 + - - +
520C THR* 2.3 29.3 + - - -
521C LEU* 2.9 13.4 + - - +
626C MET* 4.1 12.1 - - + -
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Residues in contact with LEU 518 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431C ILE* 3.8 40.8 - - + +
455C ILE* 5.2 7.4 - - + -
459C ILE* 4.9 13.2 - - + -
479C LEU* 4.8 5.4 - - + -
503C LEU* 4.2 21.3 - - + -
505C THR* 4.1 13.5 - - + -
514C ILE* 2.9 39.4 + - + +
515C ARG* 3.6 5.4 - - - +
517C LEU* 1.3 75.8 - - - +
519C LEU* 1.3 58.9 + - - +
521C LEU* 3.3 21.2 + - + +
522C ILE* 2.9 29.9 + - - +
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Residues in contact with LEU 519 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 3.9 25.0 - - + +
14B GLU* 4.7 10.1 - - + -
15B MET* 3.7 27.6 - - + +
18B SER* 6.6 0.2 - - - -
503C LEU* 3.7 22.9 - - + -
515C ARG* 2.9 32.9 + - + +
516C THR* 3.1 5.6 + - - +
518C LEU* 1.3 73.4 - - - +
520C THR* 1.3 60.3 + - - +
522C ILE* 3.8 6.3 - - + +
523C TYR* 2.9 32.1 + - - +
535C VAL* 4.6 12.8 - - + -
537C ILE* 4.3 15.3 - - + -
610C VAL* 4.6 4.9 - - + -
622C PHE* 3.7 3.1 - - - -
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Residues in contact with THR 520 (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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15B MET* 4.2 1.8 - - + -
460C LEU 4.9 0.5 + - - -
461C ASN* 4.2 12.7 + - - -
462C VAL* 4.3 13.2 + - - +
463C GLU* 5.3 2.7 - - - -
516C THR 2.9 14.9 + - - +
517C LEU* 2.3 28.8 + - - -
519C LEU* 1.3 73.7 - - - +
521C LEU* 1.3 60.9 + - - +
523C TYR* 3.4 1.2 + - - +
524C ARG* 2.9 35.5 + - - +
622C PHE* 3.5 22.5 - - + -
626C MET* 3.5 41.7 - - + -
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Residues in contact with LEU 521 (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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460C LEU 5.4 4.0 - - - +
462C VAL* 3.8 31.6 - - + -
470C ILE* 5.4 3.4 - - + -
476C ILE* 4.3 28.3 - - + -
479C LEU* 3.7 30.5 - - + -
480C PHE* 4.5 15.5 - - + -
517C LEU 2.9 8.2 + - - +
518C LEU* 3.4 19.1 - - + +
520C THR* 1.3 82.8 + - - +
522C ILE* 1.3 56.6 + - - +
525C TYR* 2.9 38.0 + - + +
526C MET* 3.7 3.1 + - - +
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Residues in contact with ILE 522 (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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501C LEU* 5.9 4.9 - - + -
503C LEU* 6.3 1.6 - - + -
518C LEU 2.9 17.0 + - - +
519C LEU* 3.9 12.1 - - + +
520C THR 3.2 0.2 - - - -
521C LEU* 1.3 75.8 - - - +
523C TYR* 1.3 60.3 + - - +
526C MET* 2.9 51.6 + - + +
527C LYS* 3.2 1.2 + - - -
529C ILE* 6.3 0.2 - - + -
530C LEU* 4.9 5.4 - - + +
535C VAL* 4.9 19.7 - - + -
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Residues in contact with TYR 523 (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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11B LEU* 3.7 20.2 - - + -
519C LEU 2.9 16.8 + - - +
520C THR 4.1 1.6 - - - +
522C ILE* 1.3 77.6 - - - +
524C ARG* 1.3 66.5 + - + +
525C TYR 3.6 0.2 - - - -
527C LYS* 3.1 63.6 + - + +
530C LEU* 5.5 8.1 - - + -
612C VAL* 4.5 16.4 - - + -
615C ALA* 3.3 27.4 + - - +
618C ALA* 3.6 17.2 - - + +
619C ASP* 3.9 12.9 + - + +
622C PHE* 3.7 34.5 - + + -
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Residues in contact with ARG 524 (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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462C VAL* 4.1 9.0 - - + -
463C GLU* 5.4 7.4 - - - +
520C THR 2.9 17.9 + - - +
523C TYR* 1.3 83.7 - - + +
525C TYR* 1.3 87.9 + - + +
526C MET 3.9 0.2 - - - -
527C LYS* 5.0 1.8 - - - -
622C PHE* 6.5 0.2 - - + -
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Residues in contact with TYR 525 (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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462C VAL* 3.7 35.6 + - + +
467C MET* 5.0 9.8 - - + +
470C ILE* 3.3 24.3 - - + +
480C PHE* 3.4 26.6 - - + -
487C PHE* 3.6 31.0 - + + -
488C GLY* 4.9 13.3 + - - +
521C LEU* 2.9 16.3 + - + +
524C ARG* 1.3 103.5 - - + +
526C MET* 1.3 67.6 + - - +
527C LYS 3.7 1.8 - - - -
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Residues in contact with MET 526 (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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479C LEU* 4.3 23.3 - - - -
480C PHE* 3.5 29.6 - - + -
483C MET* 3.7 33.0 - - + -
485C THR* 5.2 7.2 - - + +
501C LEU* 4.9 8.5 - - + -
521C LEU* 3.7 3.3 + - - +
522C ILE* 2.9 32.4 + - + +
525C TYR* 1.3 83.4 - - - +
527C LYS* 1.3 65.2 + - - +
528C PRO* 3.3 6.5 - - - -
529C ILE* 2.9 47.9 + - + +
530C LEU 3.6 2.3 + - - -
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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