Contacts of the helix formed by residues 603 - 608 (chain B) in PDB entry 5YDJ
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 GLU 603 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359B GLU* 3.2 20.1 - - - +
385B GLN* 2.8 35.3 + - - +
386B SER* 4.1 4.0 + - - -
483B ASN* 2.9 33.6 + - - +
581B TYR* 4.1 14.3 + - + +
583B TYR* 3.5 41.3 - - + -
601B GLY* 3.8 5.5 + - - -
602B ASP* 1.3 78.5 + - - +
604B ILE* 1.3 70.7 + - - +
605B ASN 3.3 1.3 - - - -
606B TYR* 3.2 5.9 + - - +
607B VAL* 3.1 27.5 + - + +
629B ILE* 5.4 0.2 - - + -
633B TRP* 5.6 1.1 - - + -
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Residues in contact with ILE 604 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B TRP* 3.9 19.7 - - + -
275B TRP* 4.7 2.0 - - + -
290B VAL* 4.2 10.3 - - + +
291B TYR* 3.6 37.5 - - + +
359B GLU* 3.6 34.8 - - + +
360B SEB 6.3 0.2 - - + -
385B GLN* 4.1 4.3 - - - +
601B GLY* 3.6 17.7 - - - +
602B ASP 3.3 1.4 - - - -
603B GLU* 1.3 92.5 - - - +
605B ASN* 1.3 65.0 + - - +
607B VAL* 3.2 9.9 - - + +
608B PHE* 3.1 33.0 + - + +
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Residues in contact with ASN 605 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B MET* 4.9 11.7 - - - +
245B TRP* 4.8 4.5 - - - -
290B VAL* 4.2 17.5 - - - +
587B SER* 5.9 1.1 - - - -
601B GLY 4.5 4.5 - - - +
602B ASP* 3.9 10.1 - - - +
603B GLU 3.3 0.4 - - - -
604B ILE* 1.3 80.7 - - - +
606B TYR* 1.3 68.4 + - + +
608B PHE* 3.7 0.9 + - - +
609B GLY 3.3 5.7 + - - -
610B GLU* 2.9 69.9 + - + +
611B PRO* 3.3 1.5 - - - +
618B TYR* 3.4 18.5 + - + +
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Residues in contact with TYR 606 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583B TYR* 3.0 23.6 - - - +
585B HIS* 2.9 33.4 + + - -
587B SER* 3.1 26.5 + - - -
602B ASP 4.1 13.0 - - - -
603B GLU 3.2 4.3 + - - +
605B ASN* 1.3 81.2 - - + +
607B VAL* 1.3 62.3 + - - +
608B PHE 3.3 0.4 - - - -
609B GLY 3.5 1.9 + - - -
611B PRO* 3.7 15.0 - - + -
618B TYR* 3.7 11.4 - + - -
622B GLU* 3.4 39.2 + - + -
625B PHE* 3.7 16.2 - + + -
626B SER* 2.6 37.8 + - - +
629B ILE* 3.6 20.4 - - + -
630B MET* 3.6 0.9 - - - +
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Residues in contact with VAL 607 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275B TRP* 5.4 0.4 - - + -
296B LEU* 3.6 15.8 - - - +
357B PHE* 5.1 3.3 - - + -
385B GLN* 3.9 20.0 - - - +
603B GLU* 3.1 17.5 + - + +
604B ILE* 3.2 21.5 - - + +
606B TYR* 1.3 76.1 - - - +
608B PHE* 1.3 73.1 + - + +
609B GLY 3.4 0.2 - - - -
629B ILE* 3.5 22.4 - - + -
630B MET* 3.3 20.6 - - - +
633B TRP* 3.6 40.8 - - + +
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Residues in contact with PHE 608 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275B TRP* 3.5 57.2 - + - -
290B VAL 3.5 18.4 - - - +
291B TYR* 3.6 13.0 - + + -
292B ASP* 3.3 34.5 - - - +
293B HIS* 3.6 24.2 - - - -
295B ALA* 3.4 10.1 - - - +
296B LEU* 3.7 18.4 + - + -
304B VAL* 4.5 1.8 - - + -
357B PHE* 3.6 22.4 - + - -
604B ILE* 3.1 25.7 + - + +
605B ASN 4.4 1.1 - - - +
607B VAL* 1.3 85.4 - - + +
609B GLY* 1.3 61.8 + - - +
610B GLU* 3.5 2.4 + - + +
630B MET* 4.5 1.8 - - - -
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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