Contacts of the helix formed by residues 508 - 526 (chain C) in PDB entry 4KPE
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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76A HIS* 5.9 3.3 - - + -
433C GLU* 4.1 2.8 - - - +
506C ASP* 3.0 32.9 - - - +
507C ALA* 1.3 81.6 - - - +
509C THR* 1.3 64.0 + - - +
510C ASP* 3.6 13.7 + - - +
511C GLY* 2.8 30.1 + - - -
512C ALA* 3.1 22.2 + - - +
581C LYS 4.2 12.9 + - - +
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Residues in contact with THR 509 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ARG* 3.8 19.5 - - + +
20A TYR* 3.7 18.0 - - - -
23A TYR* 3.5 51.5 - - + -
508C ASP* 1.3 75.1 - - - +
510C ASP* 1.3 68.6 + - - +
511C GLY 3.0 1.6 - - - -
512C ALA* 2.9 11.7 + - - +
513C HIS 2.8 23.7 + - - -
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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
----------------------------------------------------------
20A TYR* 3.8 3.4 - - - -
28A ARG* 3.0 42.4 + - - -
76A HIS* 4.5 8.3 + - - -
433C GLU* 4.3 7.9 - - - +
458C LYS* 3.3 21.5 + - - +
508C ASP* 3.6 13.0 + - - +
509C THR* 1.3 78.5 + - - +
511C GLY* 1.3 65.0 + - - +
513C HIS* 3.2 8.8 + - - +
514C ILE* 2.9 34.2 + - + +
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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
----------------------------------------------------------
433C GLU* 3.5 18.2 - - - -
505C THR* 3.4 9.5 + - - -
506C ASP 3.4 21.1 - - - -
508C ASP* 2.8 12.6 + - - -
509C THR 3.0 0.2 - - - -
510C ASP* 1.3 77.2 - - - +
512C ALA* 1.3 62.0 + - - +
514C ILE* 3.0 4.5 + - - +
515C GLN* 3.0 25.3 + - - +
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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
----------------------------------------------------------
16A ARG* 3.5 44.1 - - + +
19A ARG* 4.7 8.1 - - + -
20A TYR* 4.8 0.4 - - + -
506C ASP 4.4 0.4 + - - -
508C ASP 3.1 12.7 + - - +
509C THR* 2.9 16.1 + - - +
511C GLY* 1.3 75.7 - - - +
513C HIS* 1.3 59.2 + - - +
515C GLN* 3.2 10.1 + - - +
516C THR* 3.0 22.0 + - - -
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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
----------------------------------------------------------
16A ARG 5.6 0.4 - - - -
17A PHE* 4.8 10.0 - + - +
20A TYR* 3.3 59.2 - + + +
458C LYS* 2.9 30.0 + - + +
509C THR 2.8 8.3 + - - -
510C ASP* 3.5 8.7 - - - +
511C GLY 3.2 0.2 - - - -
512C ALA* 1.3 74.1 - - - +
514C ILE* 1.3 61.6 + - - +
516C THR* 3.2 18.2 - - + +
517C LEU* 3.1 54.8 + - + +
622C MET* 5.3 1.6 - - - +
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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* 4.5 23.6 - - + +
455C LEU* 4.9 5.4 - - + -
457C GLY 4.6 5.6 - - - +
458C LYS* 3.9 31.4 - - + +
459C VAL* 4.3 25.7 - - + +
505C THR* 3.4 22.4 - - + -
510C ASP* 2.9 31.1 + - + +
511C GLY* 3.0 3.3 + - - +
513C HIS* 1.3 72.3 - - - +
515C GLN* 1.3 68.2 + - - +
516C THR 3.0 1.3 - - - -
517C LEU* 3.2 6.2 + - + +
518C LEU* 3.0 38.1 + - + +
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Residues in contact with GLN 515 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ARG* 2.8 40.5 + - + +
503C ILE* 4.3 18.3 - - + +
505C THR* 2.9 28.9 + - + +
506C ASP 5.1 1.2 + - - -
511C GLY 3.0 19.5 + - - +
512C ALA* 3.4 9.0 - - - +
514C ILE* 1.3 76.8 - - - +
516C THR* 1.3 57.0 + - - +
518C LEU* 3.6 1.0 + - - +
519C LEU* 3.0 37.7 + - + +
537C ILE* 3.4 37.8 - - + +
538C ALA 4.6 4.4 + - - -
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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
----------------------------------------------------------
13A MET* 3.5 18.3 + - - +
16A ARG* 3.5 22.1 - - - +
17A PHE* 3.9 16.0 + - + +
512C ALA 3.0 10.4 + - - -
513C HIS* 3.2 24.9 - - + +
514C ILE 3.0 0.2 - - - -
515C GLN* 1.3 78.6 - - - +
517C LEU* 1.3 55.1 + - - +
519C LEU* 4.7 1.1 - - - -
520C THR* 2.8 36.2 + - - +
622C MET* 3.2 34.8 - - + -
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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* 4.9 3.8 - - + -
459C VAL* 3.6 43.0 - - + +
460C ILE 3.9 6.9 - - - +
461C ASN* 3.8 22.2 - - + +
462C THR* 4.6 0.7 + - - -
513C HIS* 3.1 51.9 + - + +
514C ILE* 3.2 10.9 + - + +
516C THR* 1.3 75.4 - - - +
518C LEU* 1.3 66.6 + - - +
520C THR* 3.5 8.4 + - - -
521C PHE* 3.2 21.7 + - - +
622C MET* 3.7 20.9 - - + -
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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 LEU* 4.1 9.4 - - + +
455C LEU* 3.6 35.0 - - + -
459C VAL* 4.0 16.6 - - + -
476C ILE* 6.1 0.2 - - + -
479C MET* 3.8 25.4 - - + -
503C ILE* 3.4 43.5 - - + -
514C ILE* 3.0 21.8 + - + +
515C GLN 3.8 3.4 - - - +
517C LEU* 1.3 76.1 - - - +
519C LEU* 1.3 63.7 + - - +
521C PHE* 2.9 19.4 + - + +
522C PHE* 3.0 20.9 + - + -
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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
----------------------------------------------------------
9A LEU* 3.9 25.5 - - + +
12A ILE* 4.3 15.3 - - + -
13A MET* 4.2 15.5 - - + +
16A ARG* 6.4 1.6 - - + -
503C ILE* 3.7 21.1 - - + -
515C GLN* 3.0 24.3 + - + +
516C THR* 3.9 4.5 - - - +
518C LEU* 1.3 76.9 - - - +
520C THR* 1.3 62.0 + - - +
522C PHE* 3.2 6.6 + - + +
523C TYR* 3.0 25.2 + - - +
530C VAL* 6.6 0.2 - - + -
535C VAL* 4.2 16.8 - - + -
537C ILE* 3.8 20.9 - - + -
606C VAL* 4.3 17.0 - - + -
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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
----------------------------------------------------------
13A MET* 3.5 14.1 - - + -
461C ASN* 4.5 3.6 + - - -
462C THR* 3.4 17.6 + - - -
463C ALA* 4.5 6.5 + - - +
516C THR 2.8 26.7 - - - +
517C LEU* 3.6 5.4 + - - +
518C LEU 3.2 1.0 - - - -
519C LEU* 1.3 75.0 - - - +
521C PHE* 1.3 59.6 + - - +
523C TYR* 3.9 4.8 - - - +
524C ARG* 2.8 35.8 + - - +
618C VAL* 4.1 18.4 - - + -
622C MET* 3.4 34.8 - - + +
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Residues in contact with PHE 521 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459C VAL* 5.8 1.8 - - + -
460C ILE 5.8 0.7 - - - +
462C THR* 3.2 37.9 - - + +
476C ILE* 3.3 44.9 - - + -
479C MET* 4.7 12.8 - - + -
480C ILE* 5.4 7.2 - - + -
487C VAL* 5.6 4.7 - - + -
517C LEU 3.2 8.4 + - - +
518C LEU* 2.9 12.6 + - + +
520C THR* 1.3 80.8 + - - +
522C PHE* 1.3 88.2 + + - +
524C ARG* 4.6 0.7 - - - -
525C TYR* 2.9 49.8 + + + +
526C MET* 4.0 13.6 + - + -
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Residues in contact with PHE 522 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431C LEU* 3.7 17.5 - - + -
479C MET* 3.3 28.3 - - + -
483C ILE* 4.5 6.5 - - + -
501C ILE* 4.4 11.0 - - + -
503C ILE* 4.4 13.5 - - + -
518C LEU* 3.0 24.6 + - + -
519C LEU* 3.2 9.2 + - + +
521C PHE* 1.3 102.2 - + - +
523C TYR* 1.3 58.1 + - - +
526C MET* 3.0 63.1 + - + +
527C ARG* 3.3 2.1 + - - -
529C LEU* 5.6 0.2 - - + -
530C VAL* 4.5 8.5 - - + +
535C VAL* 3.9 34.5 - - + -
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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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9A LEU* 3.4 32.5 - - + -
519C LEU 3.0 16.1 + - - +
520C THR* 3.9 4.5 - - - +
522C PHE* 1.3 79.2 - - - +
524C ARG* 1.3 81.8 + - + +
525C TYR 3.4 0.5 + - - -
527C ARG* 3.9 24.2 - - + +
530C VAL* 5.1 9.6 - - + +
608C ILE* 5.6 5.6 - - + -
611C LEU* 3.6 25.4 + - + +
614C ALA* 4.1 13.0 - - + -
615C GLU* 2.7 57.0 + - - +
618C VAL* 4.3 14.1 - - + -
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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 THR* 2.9 29.6 + - - +
463C ALA* 3.7 31.1 + - + +
488C GLY* 5.4 1.7 - - - -
520C THR* 2.8 27.8 + - - +
523C TYR* 1.3 90.6 - - + +
525C TYR* 1.3 99.5 + - + +
526C MET 3.9 0.2 - - - -
615C GLU* 5.0 7.8 + - - -
618C VAL* 5.1 6.7 - - + +
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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 THR* 3.7 24.9 + - + -
465C ALA 5.6 1.6 + - - -
467C MET* 4.2 29.8 - - + +
470C ILE* 5.1 7.0 - - + +
487C VAL* 4.0 10.1 - - + -
488C GLY* 3.1 43.2 + - - +
491C PHE* 4.7 0.5 - - - -
521C PHE* 2.9 34.7 + + + +
524C ARG* 1.3 129.0 + - + +
526C MET* 1.3 70.5 + - - +
527C ARG 4.0 0.2 - - - -
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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
----------------------------------------------------------
479C MET 6.0 0.2 - - - -
480C ILE* 5.6 7.9 - - - -
483C ILE* 3.9 20.6 - - + -
486C GLY 4.5 3.4 - - - +
487C VAL* 5.2 2.9 - - + -
488C GLY 5.1 0.9 - - - -
491C PHE* 3.8 31.6 - - + -
521C PHE* 4.2 13.0 - - + -
522C PHE* 3.0 46.1 + - + +
525C TYR* 1.3 89.5 - - + +
527C ARG* 1.3 69.2 + - - +
528C PRO* 3.2 8.7 - - - -
529C LEU* 2.7 56.8 + - + +
530C VAL 3.7 0.7 + - - -
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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