Contacts of the strand formed by residues 492 - 497 (chain E) in PDB entry 6M17
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 LEU 492 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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351E TYR* 3.8 37.5 - - + +
452E LEU* 4.4 19.1 - - + +
453E TYR 3.5 4.7 - - - +
454E ARG* 3.6 40.6 - - + +
469E SER 5.2 1.8 - - - +
470E THR* 4.8 17.7 - - + +
490E PHE* 3.6 22.9 - - + +
491E PRO* 1.3 97.8 - - + +
493E GLN* 1.3 76.7 + - - +
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Residues in contact with GLN 493 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B LYS* 2.4 35.3 + - - +
34B HIS* 2.3 47.3 + - + +
35B GLU* 3.4 11.2 - - - +
452E LEU* 3.0 11.9 - - - +
453E TYR* 2.9 42.8 + - + +
455E LEU* 3.2 30.0 - - + +
490E PHE* 4.7 3.2 + - - +
492E LEU* 1.3 110.7 + - - +
494E SER* 1.3 58.3 + - - +
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Residues in contact with SER 494 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B HIS* 3.6 18.6 + - - -
38B ASP* 5.3 0.7 - - - +
449E TYR* 3.6 37.1 - - - +
451E TYR 3.5 9.2 - - - -
452E LEU* 4.0 15.9 - - - -
453E TYR* 4.5 0.2 - - - -
493E GLN* 1.3 78.4 - - - +
495E TYR* 1.3 66.5 + - - +
496E GLY* 3.2 3.6 + - - -
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Residues in contact with TYR 495 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B HIS* 5.1 2.0 - - - -
350E VAL* 4.6 1.6 - - + -
401E VAL 4.4 15.9 - - - -
402E ILE* 4.3 4.9 - - - +
403E ARG* 3.1 44.4 + - + -
406E GLU* 2.7 27.8 + - - -
418E ILE* 3.7 11.6 - - - +
448E ASN 2.8 19.9 - - - +
449E TYR* 4.0 3.1 - - - -
451E TYR* 3.0 31.4 + - + +
452E LEU 4.5 3.8 - - - -
453E TYR* 3.8 38.6 - + + -
494E SER* 1.3 71.9 - - - +
496E GLY* 1.3 59.8 + - - +
497E PHE* 3.4 35.2 + + + -
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Residues in contact with GLY 496 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ASP* 3.7 19.4 + - - +
353B LYS* 3.1 26.4 + - - +
447E GLY* 4.5 1.1 - - - -
448E ASN 4.0 5.4 - - - -
449E TYR* 4.0 18.6 - - - -
494E SER 3.2 6.1 + - - -
495E TYR* 1.3 70.7 - - - +
497E PHE* 1.3 65.1 + - - -
498E GLN* 3.6 7.0 + - - +
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Residues in contact with PHE 497 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353B LYS* 6.0 1.1 - - - -
401E VAL* 4.5 3.8 - - + -
402E ILE 4.2 9.6 - - - -
403E ARG* 4.2 10.5 - - + -
442E ASP 4.7 2.5 - - - -
443E SER* 3.8 21.1 + - - -
444E LYS 3.5 4.2 + - - +
447E GLY* 3.1 6.6 - - - -
448E ASN* 2.9 30.7 + - + -
451E TYR* 4.1 26.7 - + + -
495E TYR* 3.4 49.2 + + + -
496E GLY* 1.3 73.2 - - - +
498E GLN* 1.3 59.0 + - - +
501E ASN* 4.7 1.6 - - - -
505E TYR 3.5 25.8 - - - -
506E GLN 4.3 0.2 - - - -
507E PRO* 3.8 38.8 - - + -
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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