Contacts of the helix formed by residues 532 - 541 (chain f) in PDB entry 5T0J
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 PRO 532 (chain f).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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516f PHE* 4.7 0.4 - - + -
528f ARG* 3.2 17.7 - - + +
529f ARG 3.4 11.2 - - - +
530f ALA 3.7 0.2 - - - -
531f VAL* 1.3 93.0 - - + +
533f LEU* 1.3 61.9 + - - +
534f ALA 3.0 0.7 - - - -
535f LEU* 3.0 32.1 + - + +
551f LEU* 4.5 8.1 - - + -
554f PHE* 4.7 21.8 - - + -
562f VAL* 5.8 2.0 - - - +
565f ASN* 3.7 27.6 - - + +
566f SER* 5.4 0.7 - - - +
569f ALA* 3.5 14.4 - - + +
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Residues in contact with LEU 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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498f ILE* 3.9 14.4 - - + -
502f ALA* 5.3 1.4 - - - +
530f ALA* 3.2 36.6 - - + +
531f VAL 2.9 1.2 + - - -
532f PRO* 1.3 77.4 - - - +
534f ALA* 1.3 60.4 + - - +
535f LEU 3.2 1.7 + - - -
536f ALA* 3.7 15.2 + - - +
537f LEU* 6.1 0.2 - - - +
565f ASN* 4.2 13.9 - - + +
568f PHE* 3.5 36.8 - - + -
678f LEU* 4.5 15.0 - - + -
681f LEU* 3.7 35.9 - - + -
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Residues in contact with ALA 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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498f ILE* 3.5 19.4 - - + +
501f ILE* 4.3 9.4 - - + -
502f ALA* 4.0 23.6 - - + +
516f PHE* 4.0 24.7 - - + -
531f VAL 3.4 1.6 + - - -
532f PRO 3.0 1.6 + - - -
533f LEU* 1.3 74.1 - - - +
535f LEU* 1.3 60.2 + - - +
536f ALA 3.1 7.9 + - - -
537f LEU* 3.5 11.5 + - - +
538f ILE* 3.7 19.8 + - + +
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Residues in contact with LEU 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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516f PHE* 3.5 35.7 - - + -
532f PRO* 3.0 23.8 + - + +
534f ALA* 1.3 78.1 - - - +
536f ALA* 1.3 55.8 + - - +
537f LEU 3.2 2.5 - - - -
538f ILE* 5.0 3.4 - - + -
539f SER* 3.2 33.8 - - - +
546f ASN 5.4 0.4 - - - +
547f ILE* 3.7 22.7 - - + -
550f THR* 4.5 9.0 - - - +
551f LEU* 3.8 22.0 - - + -
569f ALA* 3.6 29.6 - - + +
573f VAL* 3.4 9.2 - - - +
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Residues in contact with ALA 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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532f PRO 4.8 0.2 + - - -
533f LEU 3.7 11.8 + - - +
534f ALA 3.1 2.0 - - - -
535f LEU* 1.3 77.4 - - - +
537f LEU* 1.3 70.6 + - + +
540f VAL* 4.5 5.0 - - - +
568f PHE* 5.2 15.9 - - + +
569f ALA* 4.5 4.4 + - - +
572f MET* 5.9 1.8 - - + +
573f VAL* 4.0 22.6 - - + +
674f PHE* 4.3 21.4 - - + -
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Residues in contact with LEU 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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502f ALA* 3.6 38.6 - - + +
503f MET* 3.8 4.3 - - + +
533f LEU 6.1 0.2 - - - +
534f ALA 3.5 5.7 + - - +
535f LEU 3.2 0.8 - - - -
536f ALA* 1.3 89.8 - - + +
538f ILE* 1.3 64.5 + - + +
539f SER 3.1 5.3 + - - -
540f VAL* 3.3 27.8 - - + +
669f ARG* 3.4 47.4 + - + +
674f PHE* 3.5 31.4 - - + -
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Residues in contact with ILE 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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501f ILE* 4.7 7.9 - - + +
502f ALA* 4.4 10.1 - - - +
505f GLU* 4.1 21.3 - - + +
507f ILE* 6.2 1.6 - - + -
510f GLU* 3.9 26.7 - - + +
512f ALA* 4.1 29.4 - - + -
513f LEU* 5.1 11.7 - - + -
516f PHE* 4.9 21.1 - - + -
534f ALA* 3.7 19.7 - - + +
535f LEU* 5.0 2.7 - - + -
537f LEU* 1.3 74.3 - - + +
539f SER* 1.3 66.8 + - - +
540f VAL* 3.3 2.9 + - - +
541f SER* 3.8 13.5 + - - -
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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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510f GLU* 5.8 0.9 - - - -
535f LEU* 3.2 33.2 + - - +
537f LEU 3.1 1.6 - - - -
538f ILE* 1.3 80.5 - - - +
540f VAL* 1.3 60.0 + - - +
541f SER* 3.0 8.4 + - - -
542f ASN 3.8 3.9 - - - +
543f PRO* 3.4 22.9 - - - +
546f ASN* 5.3 8.0 - - - +
547f ILE* 3.4 30.0 - - - +
573f VAL* 3.8 9.3 - - - +
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Residues in contact with VAL 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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507f ILE 5.9 2.9 - - - +
536f ALA 4.5 6.5 - - - +
537f LEU* 3.3 22.2 - - + +
538f ILE* 3.3 2.4 - - - +
539f SER* 1.3 77.2 - - - +
541f SER* 1.3 64.6 + - - +
543f PRO* 4.3 5.4 - - - +
573f VAL* 3.7 22.0 - - + -
662f LEU* 5.0 18.9 - - + +
667f GLN* 4.7 18.4 - - - +
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Residues in contact with SER 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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508f GLY 3.8 22.0 - - - -
509f ALA* 5.6 0.2 - - - -
510f GLU* 2.3 33.4 + - - -
538f ILE 3.8 8.6 + - - -
539f SER* 4.5 0.9 - - - -
540f VAL* 1.3 85.8 - - - +
542f ASN* 1.3 73.7 + - - +
543f PRO* 3.4 6.1 - - - +
546f ASN* 5.1 0.2 + - - -
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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