Contacts of the helix formed by residues 599 - 610 (chain A) in PDB entry 2PMF
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 SER 599 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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598A GLY* 1.3 76.1 - - - -
600A ILE* 1.3 65.7 + - - +
601A GLY* 3.1 9.6 + - - -
602A ARG* 4.0 31.9 - - - +
603A ARG* 3.1 27.7 + - - +
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Residues in contact with ILE 600 (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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565A LEU* 4.2 15.2 - - + +
567A LEU* 4.3 24.5 - - + -
598A GLY 3.9 0.4 + - - -
599A SER* 1.3 78.8 + - - +
601A GLY* 1.3 62.7 + - - +
603A ARG* 4.1 15.9 - - - +
604A TYR* 3.4 27.8 + - + -
617A THR* 4.0 29.8 - - + +
619A ASP* 6.4 0.9 - - + -
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Residues in contact with GLY 601 (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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548A ARG* 4.1 12.7 + - - -
599A SER* 3.1 6.4 + - - -
600A ILE* 1.3 84.8 - - - +
602A ARG* 1.3 63.2 + - - +
603A ARG 3.3 0.2 - - - -
604A TYR* 3.6 5.9 + - - +
605A ALA* 3.2 21.5 + - - +
633A ARG* 5.5 0.9 + - - -
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Residues in contact with ARG 602 (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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548A ARG* 3.8 21.6 - - - +
598A GLY* 5.1 4.8 - - - -
599A SER* 3.3 34.6 + - - +
601A GLY* 1.3 74.7 - - - +
603A ARG* 1.3 64.7 + - - +
605A ALA* 3.4 4.6 + - - +
606A ARG* 3.2 38.1 + - - +
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Residues in contact with ARG 603 (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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565A LEU* 4.0 24.7 + - + +
566A PRO* 2.8 33.3 + - - +
567A LEU* 3.9 15.3 - - - +
568A SER* 4.7 2.6 - - - +
569A GLN* 4.3 4.6 - - - +
594A ASP* 3.2 46.2 + - - +
596A SER* 3.4 28.4 + - - +
598A GLY 4.0 16.2 + - - +
599A SER 3.1 20.7 + - - +
600A ILE* 4.3 11.2 - - - +
601A GLY 3.3 0.4 - - - -
602A ARG* 1.3 76.9 - - - +
604A TYR* 1.3 62.5 + - - +
606A ARG* 3.3 24.7 + - - +
607A THR* 3.3 24.9 + - - +
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Residues in contact with TYR 604 (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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563A SER* 4.5 3.1 - - - -
565A LEU* 3.5 27.2 - - + +
600A ILE* 3.4 24.3 + - + +
601A GLY* 3.6 6.8 + - - +
603A ARG* 1.3 75.4 - - - +
605A ALA* 1.3 56.5 + - - +
607A THR* 2.8 15.9 + - - -
608A ASP* 2.8 40.7 + - - -
614A PHE 5.2 0.4 - - - -
615A GLY* 3.2 38.7 + - - -
616A VAL 3.3 3.6 + - - -
617A THR* 2.9 38.4 + - + +
633A ARG* 3.6 48.9 - - + +
640A GLN* 5.1 2.5 - - - -
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Residues in contact with ALA 605 (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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542A ARG* 6.2 1.3 - - - +
548A ARG* 3.7 37.5 - - + +
549A THR 4.1 3.6 - - - +
601A GLY 3.2 14.3 + - - +
602A ARG* 3.5 10.8 - - - +
604A TYR* 1.3 76.8 - - - +
606A ARG* 1.3 58.2 + - - +
608A ASP* 3.5 9.6 + - - +
609A GLU* 3.1 28.1 + - - +
633A ARG* 5.3 0.4 - - - +
638A MET* 6.3 2.7 - - + -
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Residues in contact with ARG 606 (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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77A ARG* 2.6 41.9 + - - +
594A ASP* 4.7 1.2 + - - -
596A SER* 2.8 28.7 + - - -
597A SER 3.4 22.6 + - - -
598A GLY* 4.4 3.0 - - - -
602A ARG* 3.2 29.4 + - - +
603A ARG* 3.5 33.8 + - - +
604A TYR 3.1 0.8 - - - -
605A ALA* 1.3 79.7 - - - +
607A THR* 1.3 61.0 + - + +
609A GLU* 3.3 19.0 + - - +
610A ILE* 3.6 3.3 + - - +
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Residues in contact with THR 607 (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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77A ARG* 5.9 0.2 - - - +
560A PHE* 5.3 4.9 - - + -
563A SER* 3.6 25.7 - - - +
565A LEU* 5.1 1.1 - - + -
594A ASP* 4.8 12.6 - - - +
603A ARG 3.3 11.2 + - - +
604A TYR* 2.8 35.5 + - - -
606A ARG* 1.3 75.2 - - + +
608A ASP* 1.3 67.1 + - - +
609A GLU 3.2 0.4 - - - -
610A ILE* 3.3 13.7 - - + +
611A GLY 3.2 4.2 + - - -
612A VAL* 3.1 39.5 + - + -
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Residues in contact with ASP 608 (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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542A ARG* 3.6 21.4 + - - +
549A THR 4.3 1.8 - - - +
550A PHE* 3.2 32.5 - - + +
551A PHE 3.2 3.8 + - - +
604A TYR* 2.8 21.3 + - - +
605A ALA* 3.6 8.9 - - - +
607A THR* 1.3 79.9 + - - +
609A GLU* 1.3 60.0 + - - +
611A GLY* 2.9 16.9 + - - +
612A VAL 4.5 2.8 - - - +
633A ARG* 2.3 39.7 + - - -
635A ARG* 3.8 17.9 - - + +
638A MET* 4.4 1.6 - - - +
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Residues in contact with GLU 609 (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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73A THR* 3.6 18.2 - - + +
76A ARG* 2.6 43.8 + - - -
77A ARG* 3.0 27.6 + - + +
79A PHE* 4.2 0.9 - - - -
549A THR* 3.5 24.8 + - + +
550A PHE* 4.2 1.6 - - - +
551A PHE* 3.1 25.8 - - - -
605A ALA 3.1 13.8 + - - +
606A ARG* 3.3 17.8 - - - +
607A THR 3.2 0.2 - - - -
608A ASP* 1.3 78.0 - - - +
610A ILE* 1.3 58.0 + - - +
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Residues in contact with ILE 610 (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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77A ARG* 3.4 52.5 - - + +
79A PHE* 3.7 12.3 - - + -
99A VAL* 4.0 25.1 - - + -
553A PHE* 3.3 14.1 - - - -
559A PRO* 3.3 23.5 - - + +
560A PHE* 4.1 20.2 - - + -
606A ARG 3.8 5.8 - - - +
607A THR* 3.3 19.7 - - + +
609A GLU* 1.3 75.4 - - - +
611A GLY* 1.3 57.9 + - - +
612A VAL* 3.8 17.5 - - + -
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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