Contacts of the strand formed by residues 394 - 400 (chain B) in PDB entry 2R8J
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 SER 394 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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392B VAL* 3.0 19.4 - - - +
393B LYS* 1.3 79.8 - - - +
395B MET* 1.3 66.8 + - - +
502B THR* 4.7 5.8 - - - +
503B ILE 3.6 5.6 - - - -
504B THR* 3.3 27.1 - - - -
506B PHE* 3.6 3.8 - - - -
10T T 3.7 14.7 + - - +
11T C 3.2 27.7 + - - -
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Residues in contact with MET 395 (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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392B VAL* 4.2 7.2 - - + -
394B SER* 1.3 84.0 - - - +
396B MET* 1.3 61.2 + - - +
423B LEU* 4.0 17.2 - - + +
426B ARG* 3.9 39.0 - - - +
427B ILE* 3.6 26.7 - - + -
430B LEU* 4.2 21.5 - - + -
501B MET 4.1 0.7 - - - +
502B THR* 3.2 5.6 - - - +
503B ILE* 3.0 39.8 + - + +
506B PHE* 3.3 31.4 - - + -
10T T 3.6 12.3 - - - +
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Residues in contact with MET 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B MET* 1.3 75.7 - - - +
397B SER* 1.3 74.0 + - - +
398B ASN* 4.3 15.9 - - + +
422B GLU* 4.2 2.6 - - - +
423B LEU* 4.0 3.6 - - - +
426B ARG* 3.8 8.8 + - - -
446B SER* 6.4 0.4 - - - -
500B SER* 4.7 10.1 - - - +
501B MET 3.7 4.0 - - - -
502B THR* 3.4 30.3 - - + +
9T A 3.7 24.0 + - + +
10T T 2.7 48.5 + - + +
11T C 5.6 4.5 - - - +
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Residues in contact with SER 397 (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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125B LYS* 3.9 1.9 - - - -
396B MET* 1.3 75.3 - - - +
398B ASN* 1.3 59.2 + - - +
419B PHE* 3.2 49.1 - - - -
422B GLU* 3.5 21.9 + - - -
423B LEU* 4.0 12.3 - - - -
500B SER* 3.4 1.7 - - - -
501B MET 3.0 29.9 + - - -
9T A 3.5 5.4 - - - -
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Residues in contact with ASN 398 (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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125B LYS* 2.8 27.2 + - - -
396B MET* 4.3 11.4 - - - -
397B SER* 1.3 75.2 + - - +
399B LYS* 1.3 78.9 + - - +
400B ASN* 3.7 13.5 + - - +
419B PHE* 3.6 4.3 - - - -
498B LYS* 3.5 33.2 - - - +
499B LEU 3.2 19.8 + - - -
500B SER* 3.6 16.4 - - - -
8T C 5.0 1.6 - - - +
9T A 3.2 24.4 + - - +
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Residues in contact with LYS 399 (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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56B TRP* 5.0 2.0 - - - -
121B VAL* 3.0 33.4 + - - +
122B GLU* 4.3 5.4 - - - +
124B HIS 3.0 14.8 + - - +
125B LYS* 4.9 9.1 - - + +
398B ASN* 1.3 85.8 + - - +
400B ASN* 1.3 73.2 + - - +
401B LEU* 3.1 30.5 + - + +
415B TRP* 3.6 32.3 - - + -
419B PHE* 3.4 22.7 - - + -
498B LYS* 3.8 1.2 - - - -
499B LEU* 3.0 25.7 + - + +
8T C 5.9 1.0 + - - -
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Residues in contact with ASN 400 (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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398B ASN* 4.0 9.5 + - - +
399B LYS* 1.3 86.0 + - - +
401B LEU* 1.3 61.5 + - - +
402B ARG* 3.7 18.7 + - + +
497B THR 3.9 4.9 - - - +
498B LYS* 3.4 29.0 + - - +
8T C 4.8 19.0 + - - +
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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