Contacts of the strand formed by residues 394 - 402 (chain B) in PDB entry 3K2H
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 HIS 394 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285B GLU* 5.1 1.8 + - - -
289B PHE* 3.7 30.1 - + - -
307B TRP* 5.7 0.2 - - - -
333B TYR* 3.2 46.0 - + - -
337B TRP* 4.9 0.8 + + - -
379B SER* 4.6 2.3 + - - -
392B PRO* 3.8 0.2 - - - +
393B CYS* 1.3 73.5 - - - +
395B CYS* 1.3 60.2 + - - +
396B PHE 3.5 2.4 + - - -
397B PHE* 5.7 0.9 - - - -
410B MET* 3.3 31.6 - - + -
411B HIS 3.6 6.5 - - - -
412B GLN* 4.1 2.4 - - + +
424B ASN* 3.2 14.6 + - - -
427B SER* 5.8 0.4 - - - -
428B TYR* 2.5 40.5 + + - +
512B UMP 3.0 28.4 + + - -
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Residues in contact with CYS 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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396A PHE* 3.4 31.2 - - - -
377B VAL 4.9 0.2 - - - -
378B CYS* 3.8 2.1 - - - -
379B SER* 2.8 28.5 + - - -
380B TRP* 3.4 26.4 + - + +
392B PRO* 3.6 20.9 - - + +
393B CYS 3.8 11.0 - - - -
394B HIS* 1.3 73.7 - - - +
396B PHE* 1.3 61.6 + - - +
397B PHE* 5.7 0.7 - - - -
411B HIS* 3.1 18.1 + - - -
413B ARG* 4.1 13.7 - - - -
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Residues in contact with PHE 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A TRP* 4.0 21.3 - - + -
395A CYS* 3.4 26.2 - - - -
396A PHE* 4.2 24.2 - + + -
411A HIS* 3.3 41.3 - + - -
376B ILE* 3.6 37.2 - - + -
377B VAL 3.6 6.3 - - - -
378B CYS* 3.7 20.0 - - + -
394B HIS 3.5 2.2 + - - -
395B CYS* 1.3 80.4 - - + +
397B PHE* 1.3 68.2 + - - +
398B GLN* 4.3 2.7 - - + -
410B MET* 3.4 4.4 - - - +
411B HIS* 2.8 39.4 + - + -
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Residues in contact with PHE 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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337B TRP* 3.7 30.7 - + - -
359B LEU* 5.2 4.7 - - + -
375B LEU 3.9 0.2 - - - +
376B ILE* 3.3 4.5 - - - +
377B VAL* 2.9 76.9 + - + -
379B SER* 5.3 0.9 - - - -
394B HIS 5.7 0.2 - - - -
395B CYS 5.7 0.2 - - - -
396B PHE* 1.3 82.4 - - - +
398B GLN* 1.3 61.6 + - - +
399B PHE* 3.7 34.3 - + - -
408B CYS* 4.0 12.3 - - - -
409B MET 3.1 12.8 - - - +
410B MET* 4.0 11.9 - - + -
428B TYR* 3.6 18.4 - + + -
431B LEU* 3.7 22.0 - - + -
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Residues in contact with GLN 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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257A PHE* 3.7 6.0 - - + -
411A HIS* 2.9 30.1 + - - +
413A ARG* 2.9 44.0 + - - +
451A ALA* 3.4 12.5 - - - +
452A ASP* 4.4 5.3 - - - +
373B ARG* 3.8 11.7 + - - +
375B LEU 3.2 8.3 - - - +
376B ILE* 3.8 17.6 - - + +
396B PHE* 4.6 0.7 - - + -
397B PHE* 1.3 76.6 - - - +
399B PHE* 1.3 75.9 + - - +
400B TYR* 6.2 0.2 - - - -
408B CYS* 3.3 3.6 - - - -
409B MET* 2.8 37.8 + - + +
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Residues in contact with PHE 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B LEU* 5.8 3.6 - - + -
362B ILE* 3.8 25.8 - - + -
363B ILE* 6.1 1.1 - - + -
366B ILE* 3.9 13.9 - - + -
372B ASP 5.2 0.9 - - - +
373B ARG 6.2 0.2 - - - -
375B LEU* 2.8 33.4 + - + +
377B VAL* 5.0 2.9 - - + -
397B PHE* 3.7 34.1 - + - -
398B GLN* 1.3 90.1 + - - +
400B TYR* 1.3 64.1 + - - +
406B LEU* 3.9 29.4 - - + -
407B SER 3.3 14.1 - - - -
408B CYS* 3.8 20.9 - - + -
431B LEU* 4.5 7.2 - - + -
432B THR* 4.1 12.3 - - - -
435B VAL* 3.8 22.9 - - + -
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Residues in contact with TYR 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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245A LYS* 3.6 18.8 - - - -
255A SER* 2.7 48.0 + - - -
256A LYS* 3.7 1.1 + - - -
257A PHE* 3.3 57.9 - + + -
452A ASP* 3.7 25.8 - - + -
372B ASP 6.0 0.2 - - - -
375B LEU* 4.3 4.2 - - - +
399B PHE* 1.3 79.2 - - - +
401B VAL* 1.3 66.1 + - - +
402B SER* 3.4 27.5 + - - -
405B LYS 3.5 1.6 - - - +
406B LEU* 3.4 4.9 - - - +
407B SER* 2.8 43.8 + - - +
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Residues in contact with VAL 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A LYS* 2.8 30.7 + - - +
366B ILE* 4.0 11.2 - - + -
370B PRO* 3.8 39.2 + - + +
371B ASN* 4.4 2.1 - - - +
375B LEU* 4.7 3.1 - - + -
400B TYR* 1.3 84.2 - - - +
402B SER* 1.3 66.6 + - - +
404B ASN* 4.5 4.7 - - - +
405B LYS 3.4 11.2 - - - +
406B LEU* 3.9 17.9 - - + -
441B LEU* 4.0 31.2 - - + -
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Residues in contact with SER 402 (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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243A VAL* 4.2 19.3 - - - +
245A LYS* 4.0 13.9 - - - -
400B TYR* 3.4 30.0 + - - -
401B VAL* 1.3 78.7 - - - +
403B ASP* 1.3 70.8 - - - +
404B ASN 3.1 2.2 - - - -
405B LYS* 3.1 24.8 + - - +
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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