Contacts of the helix formed by residues 594 - 610 (chain A) in PDB entry 1PJR
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 594 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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592A GLU 3.6 7.0 + - - +
593A ASP* 1.3 75.1 + - - +
595A ASP* 1.3 59.9 + - - +
597A MET* 3.1 11.6 + - - +
598A GLU* 2.9 33.9 + - + +
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Residues in contact with ASP 595 (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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258A ARG* 3.5 33.9 + - - +
265A GLN* 5.5 2.6 - - - +
305A ASN* 4.0 17.9 + - - -
593A ASP* 3.4 9.5 + - - +
594A ASP* 1.3 78.5 - - - +
596A GLU* 1.3 61.0 + - - +
598A GLU* 3.5 9.1 + - - +
599A GLU* 3.1 21.7 + - - +
602A ARG* 4.3 4.2 + - - -
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Residues in contact with GLU 596 (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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258A ARG* 2.8 42.2 + - - +
589A ARG* 4.7 25.2 + - + +
590A SER* 3.7 23.8 - - - +
593A ASP* 3.3 24.1 + - + +
595A ASP* 1.3 76.7 - - - +
597A MET* 1.3 58.1 + - - +
599A GLU* 3.2 10.3 + - + +
600A GLU* 2.9 34.4 + - - +
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Residues in contact with MET 597 (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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303A ASN* 5.0 0.4 - - - -
586A PRO* 3.4 25.1 - - + -
590A SER* 3.3 37.6 - - - +
591A LEU* 3.7 12.3 - - + +
593A ASP 2.9 10.5 + - - +
594A ASP* 3.2 17.0 - - - +
596A GLU* 1.3 77.2 - - - +
598A GLU* 1.3 58.0 + - + +
600A GLU* 3.1 4.6 + - - +
601A ARG* 2.9 36.9 + - - +
636A ARG* 3.5 46.4 - - - +
637A PHE* 4.6 5.4 - - - -
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Residues in contact with GLU 598 (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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302A HIS 4.8 0.5 - - - +
303A ASN* 3.3 30.4 - - - +
304A VAL* 2.9 32.2 + - - +
305A ASN* 3.1 39.4 + - - +
594A ASP* 2.9 19.7 + - + +
595A ASP* 3.7 10.1 - - - +
596A GLU 3.4 0.2 - - - -
597A MET* 1.3 75.7 - - + +
599A GLU* 1.3 57.1 + - - +
601A ARG* 3.3 2.1 + - - +
602A ARG* 2.9 46.7 + - - +
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Residues in contact with GLU 599 (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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255A SER* 3.5 15.2 + - - +
256A ILE* 3.0 23.4 - - - +
258A ARG* 3.0 49.1 + - + +
259A TRP* 4.6 3.0 - - + -
565A HIS* 5.4 1.1 + - - +
595A ASP 3.1 13.8 + - - +
596A GLU* 3.2 17.5 + - + +
598A GLU* 1.3 76.4 - - - +
600A GLU* 1.3 59.5 + - - +
602A ARG* 2.8 35.6 + - - +
603A LEU* 3.0 30.0 + - + +
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Residues in contact with GLU 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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359A ARG* 2.8 45.3 + - - -
585A PHE* 3.6 15.6 - - + -
586A PRO* 4.1 14.1 - - + -
587A HIS* 3.0 25.1 + - - +
589A ARG* 5.2 1.4 + - - -
590A SER* 3.6 23.5 - - - +
596A GLU* 2.9 20.9 + - + +
597A MET 3.1 7.2 + - - +
599A GLU* 1.3 79.1 - - - +
601A ARG* 1.3 59.7 + - - +
603A LEU* 3.2 13.8 + - - +
604A ALA* 3.0 18.5 + - - +
637A PHE* 4.0 5.2 - - + -
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Residues in contact with ARG 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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299A VAL* 3.5 36.2 - - + +
300A ILE* 4.4 5.8 - - + +
302A HIS* 3.8 19.3 + - - +
303A ASN* 2.9 30.1 - - - +
597A MET* 2.9 24.6 + - - +
598A GLU* 3.3 9.2 + - - +
600A GLU* 1.3 74.8 - - - +
602A ARG* 1.3 63.5 + - - +
604A ALA* 2.9 14.9 + - - +
605A TYR* 3.0 13.0 + - - +
636A ARG* 4.3 9.7 - - - +
637A PHE* 3.2 29.4 - - + -
640A GLU* 2.5 44.8 + - - -
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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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252A ALA 3.3 23.8 - - - -
253A ASP* 3.5 20.5 - - - +
255A SER* 2.9 28.8 + - - +
256A ILE* 4.0 4.3 - - + -
258A ARG* 4.9 4.0 - - - +
264A ILE* 3.5 30.2 - - - +
300A ILE* 4.2 8.7 - - + -
303A ASN* 3.8 11.7 + - - +
305A ASN* 4.6 5.9 + - - +
595A ASP 4.3 4.8 + - - -
598A GLU* 2.9 43.3 + - - +
599A GLU* 2.8 39.0 + - - +
601A ARG* 1.3 70.1 - - - +
603A LEU* 1.3 61.6 + - - +
605A TYR* 3.3 4.2 + - - +
606A VAL* 3.0 25.3 + - - +
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Residues in contact with LEU 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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256A ILE* 3.9 19.9 - - + +
359A ARG* 3.4 37.7 - - - +
564A LEU* 3.5 32.4 - - + +
565A HIS* 3.9 38.4 - - + +
585A PHE* 4.0 10.8 - - + -
599A GLU* 3.0 14.6 + - + +
600A GLU* 3.2 18.8 + - - +
602A ARG* 1.3 76.0 - - - +
604A ALA* 1.3 56.6 + - - +
606A VAL* 3.3 7.5 + - + +
607A GLY* 3.0 23.2 + - - -
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Residues in contact with ALA 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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299A VAL* 4.7 10.1 - - + -
577A LEU* 4.9 3.4 - - + +
580A MET* 5.7 2.7 - - + -
585A PHE* 3.6 24.4 - - + -
600A GLU 3.0 7.7 + - - +
601A ARG* 2.9 11.7 + - - +
603A LEU* 1.3 73.7 - - - +
605A TYR* 1.4 51.7 + - - +
607A GLY* 3.1 4.2 + - - -
608A ILE* 2.8 42.4 + - + +
637A PHE* 4.1 22.7 - - + -
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Residues in contact with TYR 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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33A ALA* 4.3 4.8 + - + -
251A ASP* 3.7 18.6 + - - -
253A ASP* 3.3 36.1 + - + -
254A GLN* 4.1 11.4 - - + -
296A ALA* 3.7 27.6 - - + -
297A ASN* 4.9 1.8 - - - -
299A VAL* 5.3 3.4 - - + +
300A ILE* 3.6 43.3 - - + +
309A LYS* 3.7 15.8 - - - -
311A ILE* 3.8 22.8 - - + +
601A ARG 3.0 11.2 + - - +
602A ARG 3.3 7.8 + - - +
604A ALA* 1.4 71.4 - - - +
606A VAL* 1.4 56.5 + - - +
608A ILE* 4.5 7.6 - - - +
609A THR* 2.7 44.3 + - + +
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Residues in contact with VAL 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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254A GLN* 3.9 28.3 - - + +
256A ILE* 4.1 29.8 - - + -
564A LEU* 4.0 21.3 - - + +
567A ALA* 5.2 1.1 - - + -
568A LYS* 4.8 11.4 - - + -
602A ARG 3.0 16.2 + - - +
603A LEU* 3.3 10.9 + - + +
605A TYR* 1.4 75.0 - - - +
607A GLY* 1.3 65.3 + - - +
609A THR* 3.7 6.3 - - - -
610A ARG* 2.7 45.1 + - - +
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Residues in contact with GLY 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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357A LEU* 4.2 7.6 - - - -
564A LEU* 3.9 19.7 - - - -
575A VAL* 4.2 5.4 - - - +
577A LEU* 4.0 18.0 - - - +
603A LEU 3.0 14.5 + - - -
604A ALA 3.1 5.1 + - - -
606A VAL* 1.3 76.7 - - - +
608A ILE* 1.3 61.0 + - - +
610A ARG* 3.3 17.2 - - - +
611A ALA 4.3 0.2 + - - -
615A LEU* 5.0 0.5 - - - +
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Residues in contact with ILE 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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292A ILE* 3.5 40.3 - - + +
295A ALA* 4.4 4.5 - - + +
296A ALA* 3.9 18.4 - - + +
299A VAL* 4.1 30.5 - - + -
577A LEU* 5.3 6.7 - - + -
604A ALA* 2.8 28.6 + - + +
605A TYR* 4.2 4.9 - - - +
607A GLY* 1.3 71.8 - - - +
609A THR* 1.3 58.7 + - - +
610A ARG 2.9 6.8 + - - -
611A ALA* 3.3 14.2 + - - +
615A LEU* 3.9 27.0 - - + +
617A LEU* 5.6 2.0 - - + -
637A PHE* 6.5 0.4 - - + -
641A ILE* 4.8 13.0 - - + -
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Residues in contact with THR 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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33A ALA* 3.7 17.5 - - + +
254A GLN* 5.3 0.2 + - - -
285A ASN* 5.6 1.5 + - - -
287A ARG* 3.0 30.0 + - - -
288A SER* 4.2 7.6 + - - -
292A ILE* 4.9 1.3 - - - -
293A LEU* 4.5 7.2 - - + -
296A ALA* 3.6 28.5 - - + -
311A ILE* 4.0 20.9 - - + -
605A TYR* 2.7 28.5 + - + +
606A VAL* 3.7 2.6 - - - -
607A GLY 3.5 0.2 - - - -
608A ILE* 1.3 70.9 - - + +
610A ARG* 1.3 73.5 + - - +
611A ALA 3.4 2.9 - - - -
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Residues in contact with ARG 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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33A ALA* 4.2 3.6 - - - +
254A GLN* 3.7 20.8 + - - -
287A ARG* 3.6 20.5 - - - +
357A LEU* 4.7 4.7 - - + -
567A ALA* 3.2 31.0 - - + +
569A GLY* 3.3 27.7 + - - +
570A LEU 2.6 41.5 + - - +
571A GLU* 3.4 6.8 - - - +
572A PHE* 2.9 38.4 + - + -
575A VAL* 4.0 10.5 - - + -
606A VAL* 2.7 28.2 + - - +
607A GLY* 3.3 15.9 - - - +
608A ILE 2.9 0.6 + - - -
609A THR* 1.3 104.1 + - - +
611A ALA* 1.3 61.2 + - - +
612A GLU 3.8 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