Contacts of the helix formed by residues 550 - 561 (chain A) in PDB entry 2PTM
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 550 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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548A GLY 3.8 0.8 + - - -
549A ALA* 1.3 73.6 - - - +
551A SER* 1.3 62.7 + - - +
552A ASN* 2.8 45.3 + - - +
553A PHE* 2.9 29.2 + - + +
554A VAL* 3.1 11.5 + - - +
647A PHE* 4.3 14.1 - - + -
650A MET* 4.3 8.5 - - + +
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Residues in contact with SER 551 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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549A ALA 3.4 4.8 + - - -
550A ASP* 1.3 74.0 + - - +
552A ASN* 1.3 61.5 + - - +
554A VAL* 3.4 9.5 + - - +
555A THR* 2.9 34.4 + - - -
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Residues in contact with ASN 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550A ASP* 2.8 18.1 + - - +
551A SER* 1.3 77.5 - - - +
553A PHE* 1.3 60.4 + - - +
555A THR* 3.9 5.2 - - - -
556A ARG* 3.0 30.1 + - - +
647A PHE* 3.6 19.0 - - + -
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Residues in contact with PHE 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545A PHE* 3.7 24.9 - + - -
546A PHE* 3.8 16.2 - + - -
549A ALA* 4.1 11.9 - - + -
550A ASP* 2.9 11.8 + - + +
552A ASN* 1.3 75.6 - - - +
554A VAL* 1.3 69.2 + - - +
556A ARG* 3.2 3.2 + - + +
557A VAL* 3.0 41.6 + - + +
643A VAL* 4.2 20.4 - - + -
644A LEU* 4.7 3.4 - - + -
647A PHE* 3.4 45.8 - + + -
650A MET* 3.3 48.5 - - + -
654A MET* 5.8 0.2 - - + -
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Residues in contact with VAL 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533A ASN* 4.2 12.1 - - - +
540A VAL* 3.9 35.4 - - + -
546A PHE* 4.3 24.2 - - + +
549A ALA* 4.0 20.9 - - + +
550A ASP 3.1 13.1 + - - +
551A SER* 3.8 8.3 - - - +
553A PHE* 1.3 79.1 - - + +
555A THR* 1.3 63.2 + - - +
557A VAL* 3.3 3.8 + - - +
558A VAL* 3.0 24.2 + - + +
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Residues in contact with THR 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529A GLN* 3.6 45.8 - - + +
533A ASN* 3.2 19.0 + - - +
551A SER* 2.9 19.9 + - - -
552A ASN* 3.9 7.9 - - - -
554A VAL* 1.3 77.6 - - - +
556A ARG* 1.3 62.7 + - - +
558A VAL* 3.3 8.0 - - - +
559A THR* 3.0 31.1 + - + +
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Residues in contact with ARG 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525A GLU* 4.6 12.9 + - - -
529A GLN* 5.7 4.4 - - - +
552A ASN 3.0 18.0 + - - +
553A PHE 3.6 4.7 - - - +
555A THR* 1.3 77.9 - - - +
557A VAL* 1.3 62.2 + - - +
559A THR* 2.8 23.3 + - - -
560A LEU* 3.3 24.3 - - + +
643A VAL* 3.7 24.0 - - + -
646A GLU* 3.0 38.6 + - - +
647A PHE* 4.4 7.3 - - + -
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Residues in contact with VAL 557 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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546A PHE* 4.1 24.0 - - + -
553A PHE* 3.0 48.4 + - + +
554A VAL 3.8 3.6 - - - +
556A ARG* 1.3 76.2 - - - +
558A VAL* 1.3 60.3 + - + +
560A LEU* 2.8 23.1 + - - +
561A LEU* 3.1 33.7 + - + +
584A PHE* 4.7 8.7 - - + -
635A LEU* 4.4 9.1 - - + +
643A VAL* 4.4 18.8 - - + -
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Residues in contact with VAL 558 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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532A ALA* 3.8 13.8 - - + +
533A ASN* 3.7 33.9 - - - +
536A CYS* 3.7 36.4 - - + -
540A VAL* 3.8 21.1 - - + -
546A PHE* 5.6 2.2 - - + -
554A VAL* 3.0 25.5 + - + +
555A THR* 3.3 12.1 - - - +
557A VAL* 1.3 79.3 - - + +
559A THR* 1.3 60.9 + - + +
560A LEU 3.4 0.3 + - - -
561A LEU* 3.6 26.6 + - + +
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Residues in contact with THR 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520A PHE* 6.2 1.6 - - - -
528A ARG* 4.5 4.7 - - + +
529A GLN* 3.9 38.8 - - + +
532A ALA* 4.2 11.2 - - + -
555A THR* 3.0 16.2 + - + +
556A ARG* 2.8 25.5 + - - -
558A VAL* 1.3 78.3 - - + +
560A LEU* 1.3 68.6 + - - +
561A LEU 3.6 2.5 - - - +
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Residues in contact with LEU 560 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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556A ARG* 3.3 25.4 - - + +
557A VAL 2.8 8.0 + - - +
559A THR* 1.3 89.0 - - - +
561A LEU* 1.3 64.7 + - - +
562A GLU* 3.7 9.1 + - - +
634A SER 4.0 3.8 - - - +
635A LEU* 3.8 14.2 - - + +
636A SER 5.5 0.2 + - - -
639A HIS* 3.7 54.4 + - + +
642A GLN* 4.4 8.7 - - - +
643A VAL* 3.8 21.5 - - + -
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Residues in contact with LEU 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536A CYS* 4.3 8.5 - - - -
539A LEU* 4.0 19.5 - - + -
546A PHE* 5.8 1.6 - - + -
557A VAL* 3.1 32.4 + - + +
558A VAL* 3.6 25.8 + - + +
559A THR 3.6 2.4 - - - +
560A LEU* 1.3 80.7 - - - +
562A GLU* 1.3 65.4 + - - +
563A PHE 4.2 1.1 + - - -
584A PHE* 3.8 28.0 - - + -
633A PHE* 3.8 30.8 - - + -
634A SER 3.3 15.9 - - - +
635A LEU* 4.2 6.5 - - + -
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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