Contacts of the helix formed by residues 494 - 500 (chain L) in PDB entry 6PSS
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 ILE 494 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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459L THR* 5.6 2.2 - - + -
463L LEU* 4.1 18.2 - - + -
480L PRO* 4.1 20.4 - - + +
483L LEU* 4.3 19.3 - - + +
484L ALA 4.6 3.4 - - - +
487L MET* 3.8 26.9 - - + -
489L MET* 3.7 36.6 - - + +
491L GLU* 3.7 24.5 - - + +
492L ASP 3.1 2.0 - - - +
493L LYS* 1.3 80.5 - - - +
495L ARG* 1.3 67.3 + - + +
496L LYS 3.6 0.7 - - - -
497L VAL* 3.7 17.2 - - + +
498L LEU* 3.7 14.6 + - + +
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Residues in contact with ARG 495 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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936I ARG* 3.6 38.8 - - - +
937I ASP* 4.3 5.4 + - - -
480L PRO* 3.4 42.5 + - + +
481L GLU* 3.5 16.8 - - - +
491L GLU* 2.6 47.6 + - - +
492L ASP* 3.2 9.2 + - - +
494L ILE* 1.3 80.8 - - - +
496L LYS* 1.3 60.7 + - - +
497L VAL 3.1 1.3 - - - -
498L LEU* 3.2 9.8 + - + +
499L LYS* 3.1 44.7 + - - +
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Residues in contact with LYS 496 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47J ARG* 4.5 18.8 - - - +
456L MET* 5.2 13.0 - - + -
492L ASP 3.2 18.6 + - - +
493L LYS* 3.6 33.9 - - - +
495L ARG* 1.3 74.9 - - - +
497L VAL* 1.3 69.2 + - + +
499L LYS* 3.5 18.7 + - + +
500L ILE* 3.2 25.1 + - + +
43O A 5.8 4.4 - - - -
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Residues in contact with VAL 497 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456L MET* 4.7 9.2 - - + -
459L THR* 3.8 26.0 - - + -
460L ILE* 3.7 37.6 - - + +
463L LEU* 3.9 20.2 - - + -
493L LYS* 3.2 28.5 - - + +
494L ILE* 3.7 11.9 - - + +
495L ARG 3.1 0.2 - - - -
496L LYS* 1.3 83.4 - - + +
498L LEU* 1.3 60.5 + - - +
499L LYS 3.5 0.7 + - - -
500L ILE* 3.6 21.9 + - - +
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Residues in contact with LEU 498 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1044I PRO* 4.1 24.1 - - + +
460L ILE* 5.6 6.3 - - + -
463L LEU* 3.8 29.8 - - + -
464L ASN* 5.7 2.9 - - - +
480L PRO* 5.2 13.7 - - + -
483L LEU* 4.7 15.7 - - + -
494L ILE* 3.7 10.9 + - + +
495L ARG* 3.2 10.5 + - + +
497L VAL* 1.3 75.9 - - + +
499L LYS* 1.3 61.7 + - - +
500L ILE 3.3 5.8 + - - +
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Residues in contact with LYS 499 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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842I ASP* 4.0 26.5 + - + +
844I LYS* 5.3 11.2 - - - +
936I ARG* 5.9 3.2 - - - +
1044I PRO* 4.8 9.5 - - - +
1045I GLY* 4.2 32.3 - - - +
257J GLY 5.1 6.2 - - - +
258J GLY* 4.8 16.3 - - - +
495L ARG* 3.1 37.5 + - - +
496L LYS* 3.8 14.8 - - + +
497L VAL 3.2 1.2 - - - -
498L LEU* 1.3 75.8 - - - +
500L ILE* 1.3 64.8 + - + +
501L ALA* 3.6 2.3 + - - +
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Residues in contact with ILE 500 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46J TYR* 3.7 34.5 - - + +
448L ARG* 4.5 3.9 + - - +
450L ILE* 6.0 3.6 - - + -
452L ILE* 3.7 27.4 - - + -
456L MET* 4.6 15.3 - - + -
460L ILE* 5.0 5.8 - - + -
496L LYS* 3.2 21.3 - - + +
497L VAL* 3.9 15.4 - - - +
498L LEU* 3.3 6.6 - - - +
499L LYS* 1.3 79.2 - - + +
501L ALA* 1.3 73.3 + - - +
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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