Contacts of the strand formed by residues 391 - 394 (chain B) in PDB entry 5IYB
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 LYS 391 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B GLU* 2.9 40.0 + - + +
199B LYS 3.4 15.9 - - - +
200B MET* 4.5 4.9 - - + +
201B ALA* 4.0 1.1 - - - +
385B ARG 4.5 13.0 - - - +
386B ASP* 3.0 30.5 + - - +
387B HIS 4.4 4.7 - - - +
388B TYR* 3.0 30.2 + - + +
389B GLY 3.5 1.0 + - - -
390B ASN* 1.3 85.4 - - + +
392B ARG* 1.3 91.0 + - - +
487B SER* 4.9 3.6 + - - -
498B PRO* 5.8 4.2 - - - +
524B LYS* 4.0 7.5 - - - +
619B GLY 4.2 1.9 - - - +
620B ARG* 5.0 1.2 - - - -
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Residues in contact with ARG 392 (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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197B GLN 3.8 0.7 - - - +
198B GLU* 3.6 2.9 - - - +
199B LYS* 2.9 53.9 + - + +
201B ALA* 4.1 23.3 - - + +
202B THR* 4.7 6.5 - - + +
204B THR* 5.8 0.4 + - - -
388B TYR 4.5 2.4 + - - -
389B GLY* 3.8 20.4 + - - -
391B LYS* 1.3 104.9 + - - +
393B LEU* 1.3 64.9 - - - +
394B ASP* 4.1 2.0 - - - +
615B TYR* 3.9 26.9 - - - -
617B ASP* 2.8 33.0 + - - +
618B ALA 3.9 11.4 - - - +
619B GLY* 3.3 21.5 - - - +
620B ARG* 3.4 22.7 - - - +
666B ASP* 5.6 1.0 + - - -
668B LEU* 5.6 1.2 - - - +
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Residues in contact with LEU 393 (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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196B ALA* 4.7 6.3 - - + -
197B GLN 3.4 4.0 - - - +
198B GLU* 3.5 39.3 - - + +
388B TYR* 5.9 0.2 - - + -
392B ARG* 1.3 71.5 - - - +
394B ASP* 1.3 67.8 + - - +
395B LEU* 3.3 11.7 + - + +
398B PRO* 4.7 2.6 - - - +
485B LEU* 3.7 38.1 - - + -
526B LEU* 4.6 1.6 - - + -
532B ILE* 3.6 31.6 - - + +
618B ALA 5.0 0.2 - - - -
619B GLY* 2.8 32.6 + - - +
621B ILE* 4.1 22.0 - - + -
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Residues in contact with ASP 394 (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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195B ILE 4.4 0.2 - - - +
196B ALA* 3.7 5.4 - - - -
197B GLN* 2.7 45.1 + - + +
199B LYS* 3.1 45.6 + - - +
392B ARG* 4.6 1.6 - - - +
393B LEU* 1.3 74.9 + - - +
395B LEU* 1.3 61.7 + - - +
398B PRO* 3.7 20.4 - - + +
399B LEU* 4.2 18.8 - - + +
463B ARG* 3.7 17.2 + - - +
618B ALA 5.7 1.0 - - - +
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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