Contacts of the helix formed by residues 530 - 547 (chain F) in PDB entry 7C97
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 LEU 530 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1248C THR* 4.9 7.6 - - + +
1262C LYS* 5.9 8.3 - - - +
1305C TYR* 5.7 1.3 - - + +
398D LYS* 5.9 4.0 - - + -
529F GLU* 1.3 72.8 - - - +
531F PRO* 1.3 69.8 - - + +
532F LEU* 3.0 43.7 - - + +
533F ASP* 2.4 43.4 + - + +
534F SER 2.8 9.5 + - - -
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Residues in contact with PRO 531 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1248C THR* 3.6 28.9 - - + -
1249C GLY 5.8 0.7 - - - +
1251C TYR* 5.6 7.4 - - + +
1302C THR* 4.2 22.4 - - + +
1305C TYR* 3.7 32.6 - - + -
1306C LYS* 4.6 2.9 - - - -
529F GLU 3.3 7.6 - - - +
530F LEU* 1.3 91.1 - - + +
532F LEU* 1.3 56.4 + - - +
533F ASP 3.3 0.2 - - - -
534F SER* 3.8 11.2 - - - +
535F ALA* 3.0 26.3 + - - +
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Residues in contact with LEU 532 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1305C TYR* 4.3 12.2 - - - +
382D TYR* 4.2 16.2 - - + +
394D ILE* 3.2 47.8 - - + +
395D LYS* 4.8 5.8 - - + +
398D LYS* 3.2 45.8 - - + -
530F LEU* 3.0 25.0 - - + +
531F PRO* 1.3 75.3 - - - +
533F ASP* 1.3 55.0 + - - +
534F SER 3.4 0.4 - - - -
535F ALA* 3.8 3.8 - - + -
536F THR* 2.5 31.9 + - - +
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Residues in contact with ASP 533 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395D LYS* 5.0 10.2 + - - -
529F GLU* 4.5 9.1 - - + +
530F LEU* 2.4 50.0 + - + +
532F LEU* 1.3 70.0 - - - +
534F SER* 1.3 55.6 + - - +
536F THR* 3.9 5.5 + - - -
537F THR* 3.0 27.2 + - - +
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Residues in contact with SER 534 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1302C THR* 5.1 4.5 - - - +
1306C LYS* 2.5 37.8 + - - -
529F GLU* 3.4 29.3 + - - -
530F LEU 2.8 6.6 + - - -
531F PRO* 4.3 6.5 - - - -
533F ASP* 1.3 75.6 - - - +
535F ALA* 1.3 63.9 + - - +
536F THR 3.1 2.0 - - - -
537F THR* 3.5 9.6 + - - -
538F GLU* 3.2 18.5 + - - +
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Residues in contact with ALA 535 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1305C TYR* 4.5 6.5 - - + -
1306C LYS* 3.9 22.2 - - + +
1309C VAL* 5.6 5.4 - - + -
394D ILE* 4.3 22.2 - - + +
531F PRO 3.0 21.5 + - - +
532F LEU* 4.1 8.5 - - - +
533F ASP 3.4 0.4 - - - -
534F SER* 1.3 76.5 - - - +
536F THR* 1.3 58.2 + - - +
538F GLU* 4.3 2.3 - - - +
539F SER* 3.4 22.4 + - - -
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Residues in contact with THR 536 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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899C GLU* 6.0 2.5 - - - +
394D ILE* 4.1 8.7 - - + +
395D LYS* 3.6 36.2 - - + +
532F LEU 2.5 25.9 + - - -
533F ASP* 4.2 8.0 + - - -
534F SER 3.1 1.0 - - - -
535F ALA* 1.3 76.1 - - - +
537F THR* 1.3 55.2 + - - +
538F GLU 3.1 1.8 - - - -
539F SER* 2.7 6.6 + - - -
540F LEU* 2.5 38.9 + - + +
610F PHE* 3.4 32.3 - - + -
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Residues in contact with THR 537 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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896C THR* 6.2 5.2 - - + -
899C GLU* 4.8 12.3 + - - +
533F ASP 3.0 22.4 - - - +
534F SER* 3.5 10.5 + - - -
536F THR* 1.3 74.5 - - - +
538F GLU* 1.3 64.4 + - - +
540F LEU* 3.5 16.0 + - - +
541F ARG* 3.5 26.8 + - - +
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Residues in contact with GLU 538 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1303C LYS* 6.0 3.1 - - - +
1306C LYS* 4.3 22.9 - - + +
534F SER 3.2 14.0 + - - +
535F ALA* 4.3 4.9 - - - +
536F THR 3.1 0.6 - - - -
537F THR* 1.3 81.7 + - - +
539F SER* 1.3 63.0 + - - +
541F ARG* 3.7 24.6 + - - +
542F ALA* 4.1 2.9 + - - +
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Residues in contact with SER 539 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386D GLU* 5.7 1.0 + - - -
393D THR* 4.2 6.1 + - - -
394D ILE* 5.0 6.9 + - - +
535F ALA 3.4 15.5 + - - -
536F THR* 2.7 17.6 + - - -
538F GLU* 1.3 76.0 + - - +
540F LEU* 1.3 58.9 + - - +
542F ALA* 2.9 30.8 + - - +
543F ALA* 3.7 2.1 + - - +
610F PHE* 3.9 16.5 - - - -
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Residues in contact with LEU 540 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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898C GLU* 4.9 10.1 - - + +
899C GLU* 3.3 44.0 - - + +
902C LEU* 4.4 14.6 - - + -
536F THR* 2.5 19.0 + - + +
537F THR* 3.8 10.8 - - - +
538F GLU 3.3 0.2 - - - -
539F SER* 1.3 73.2 - - - +
541F ARG* 1.3 61.8 + - + +
542F ALA 3.2 0.5 + - - -
543F ALA* 3.2 2.8 + - + -
544F THR* 3.2 40.2 + - + +
607F LEU* 4.4 14.8 - - + -
610F PHE* 4.0 27.5 - - + -
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Residues in contact with ARG 541 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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898C GLU* 4.4 27.3 + - + +
537F THR* 3.5 20.2 + - - +
538F GLU* 3.9 17.8 - - - +
539F SER 3.2 0.8 - - - -
540F LEU* 1.3 76.8 - - - +
542F ALA* 1.3 57.9 + - - +
544F THR* 3.8 8.9 + - - -
545F HIS* 2.9 31.6 + - + +
566F ASP* 6.0 1.1 - - - +
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Residues in contact with ALA 542 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538F GLU 4.1 2.5 + - - +
539F SER* 2.9 22.2 + - - +
541F ARG* 1.3 79.5 - - - +
543F ALA* 1.3 51.5 + - - +
545F HIS* 3.6 2.5 - - - +
546F ASP* 2.7 38.4 + - - +
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Residues in contact with ALA 543 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539F SER 3.7 1.0 + - - -
540F LEU 3.2 8.2 + - - +
542F ALA* 1.3 79.1 - - - +
544F THR* 1.3 54.1 + - - +
546F ASP* 2.7 7.8 + - - -
547F VAL* 2.3 41.5 + - + +
606F VAL* 4.6 21.3 - - + -
607F LEU* 4.1 26.0 - - + -
610F PHE* 4.5 15.3 - - + -
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Residues in contact with THR 544 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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898C GLU* 3.7 32.0 - - + +
901C LEU* 5.1 8.1 - - + -
902C LEU* 6.2 1.1 - - + -
540F LEU* 3.2 37.2 + - + -
541F ARG* 3.8 5.0 - - - -
543F ALA* 1.3 74.2 - - - +
545F HIS* 1.3 57.9 + - - +
547F VAL* 4.9 2.9 - - - -
548F LEU* 3.0 33.4 - - - +
560F ARG* 5.0 2.1 + - - -
565F ILE* 4.9 20.1 - - - +
566F ASP* 5.0 2.3 + - - -
607F LEU* 4.5 14.8 - - + -
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Residues in contact with HIS 545 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541F ARG* 2.9 22.8 + - + +
542F ALA* 3.8 2.5 - - - +
543F ALA 3.0 0.6 - - - -
544F THR* 1.3 79.5 + - - +
546F ASP* 1.3 58.7 + - - +
549F ALA* 3.0 24.9 + - + +
560F ARG* 4.4 14.3 + - - +
566F ASP* 3.8 22.9 - - - +
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Residues in contact with ASP 546 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542F ALA 2.7 18.6 + - - +
543F ALA* 2.7 3.3 + - - +
545F HIS* 1.3 78.6 - - - +
547F VAL* 1.3 67.2 + - + +
548F LEU 3.3 0.9 - - - -
549F ALA* 2.9 14.3 + - - +
550F GLY* 3.0 10.9 + - - -
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Residues in contact with VAL 547 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543F ALA* 2.3 33.1 + - - +
544F THR* 5.3 0.9 - - - -
546F ASP* 1.3 71.4 - - + +
548F LEU* 1.3 58.7 + - + +
550F GLY* 3.1 20.1 + - - -
598F LEU* 3.9 27.3 - - + +
603F ARG* 3.5 22.4 - - - +
606F VAL* 3.3 34.1 - - + -
607F LEU* 3.8 28.0 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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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