Contacts of the strand formed by residues 394 - 402 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285A GLU* 5.1 2.0 + - - -
289A PHE* 3.7 30.4 - + - -
307A TRP* 5.6 0.2 - - - -
333A TYR* 3.2 46.6 - + + -
337A TRP* 5.0 0.6 + + - -
379A SER* 4.6 2.6 + - - -
393A CYS* 1.3 73.3 - - - +
395A CYS* 1.3 59.2 + - - +
396A PHE 3.5 3.0 + - - -
397A PHE* 5.7 0.5 - - - -
410A MET* 3.3 31.4 - - + -
411A HIS 3.6 6.5 - - - -
412A GLN* 4.0 2.4 - - + +
424A ASN* 3.4 14.6 + - - -
427A SER* 5.8 0.2 - - - -
428A TYR* 2.6 35.7 + + - +
512A UMP 3.0 27.9 + + - -
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Residues in contact with CYS 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377A VAL 4.9 0.2 - - - -
378A CYS* 3.8 1.0 - - - -
379A SER* 2.8 27.6 + - - -
380A TRP* 3.4 27.3 + - + +
392A PRO* 3.6 23.6 - - + +
393A CYS 3.8 10.3 - - - -
394A HIS* 1.3 74.6 - - - +
396A PHE* 1.3 61.5 + - - +
397A PHE* 5.7 0.4 - - - -
411A HIS* 3.1 17.3 + - - -
413A ARG* 4.1 11.9 - - - -
376B ILE* 4.3 0.2 - - - -
396B PHE* 3.4 31.6 - - - -
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Residues in contact with PHE 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376A ILE* 3.6 35.7 - - + -
377A VAL 3.5 6.7 - - - -
378A CYS* 3.7 20.9 - - + -
394A HIS 3.5 2.2 + - - -
395A CYS* 1.3 79.4 - - - +
397A PHE* 1.3 69.3 + - - +
398A GLN* 4.5 2.9 - - + -
410A MET* 3.5 2.9 - - - +
411A HIS* 2.9 38.9 + - + -
380B TRP* 3.8 22.0 - + + -
395B CYS* 3.4 26.2 - - + -
396B PHE* 4.2 24.5 - + + -
411B HIS* 3.4 41.5 - + + -
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Residues in contact with PHE 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A TRP* 3.7 29.8 - + - -
359A LEU* 5.3 4.3 - - + -
376A ILE* 3.3 5.0 - - - +
377A VAL* 2.9 75.8 + - + +
379A SER* 5.2 2.0 - - - -
394A HIS 5.7 0.4 - - - -
396A PHE* 1.3 82.0 - - - +
398A GLN* 1.3 62.8 + - - +
399A PHE* 3.7 32.3 - + - -
408A CYS* 4.0 12.1 - - - -
409A MET 3.1 14.1 - - - +
410A MET* 3.9 11.7 - - + -
428A TYR* 3.5 20.0 - + + -
431A LEU* 3.6 26.5 - - + -
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Residues in contact with GLN 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373A ARG* 4.1 11.1 + - - +
375A LEU 3.2 9.0 - - - +
376A ILE* 3.7 19.4 - - + +
396A PHE* 4.7 1.3 - - + -
397A PHE* 1.3 77.4 - - - +
399A PHE* 1.3 76.6 + - - +
400A TYR* 6.0 0.2 - - - -
408A CYS* 3.5 2.6 - - - -
409A MET* 2.9 35.3 + - + +
257B PHE* 3.8 7.8 - - + -
411B HIS* 2.9 30.7 + - + +
413B ARG* 2.9 43.1 + - - +
451B ALA* 3.4 13.3 - - - +
452B ASP* 4.3 5.9 - - - +
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Residues in contact with PHE 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359A LEU* 5.9 3.1 - - + -
362A ILE* 3.7 26.0 - - + -
363A ILE* 6.2 0.9 - - + -
366A ILE* 3.9 14.8 - - + -
372A ASP 5.4 0.2 - - - +
375A LEU* 2.8 32.5 + - + +
377A VAL* 5.1 2.5 - - + -
397A PHE* 3.7 33.9 - + - -
398A GLN* 1.3 86.6 + - - +
400A TYR* 1.3 64.0 + - - +
406A LEU* 3.8 30.1 - - + -
407A SER 3.4 14.1 - - - -
408A CYS* 3.8 20.6 - - + -
431A LEU* 4.5 5.6 - - + -
432A THR* 4.1 12.1 - - - -
435A VAL* 3.9 23.6 - - + -
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Residues in contact with TYR 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375A LEU* 4.6 3.1 - - - -
398A GLN* 6.0 0.4 - - - -
399A PHE* 1.3 79.3 - - - +
401A VAL* 1.3 66.8 + - - +
402A SER* 3.5 27.3 + - - -
405A LYS 3.5 0.9 - - - +
406A LEU* 3.4 4.3 - - - +
407A SER* 2.7 44.3 + - - +
243B VAL* 5.4 0.2 - - - +
245B LYS* 3.6 18.8 - - - -
255B SER* 2.6 45.8 + - - -
256B LYS* 3.7 1.7 + - - -
257B PHE* 3.4 57.2 - + + -
452B ASP* 3.5 24.7 - - + -
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Residues in contact with VAL 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A ILE* 4.0 11.2 - - + -
370A PRO* 3.9 38.6 + - + +
371A ASN* 4.4 2.1 - - - +
375A LEU* 4.7 4.5 - - + -
400A TYR* 1.3 83.6 - - - +
402A SER* 1.3 66.4 + - - +
404A ASN* 4.6 5.6 - - - +
405A LYS 3.4 11.0 - - - +
406A LEU* 4.0 17.7 - - + -
441A LEU* 4.0 31.2 - - + -
245B LYS* 3.0 26.4 + - - +
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Residues in contact with SER 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A TYR* 3.5 28.9 + - - -
401A VAL* 1.3 78.4 - - - +
403A ASP* 1.3 73.8 + - - +
404A ASN 3.0 2.7 - - - +
405A LYS* 3.0 23.5 + - - +
243B VAL* 4.4 18.2 - - - +
245B LYS* 4.0 14.1 - - - -
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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