Contacts of the strand formed by residues 392 - 403 (chain E) in PDB entry 2HU4
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 VAL 392 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95E ASN 5.0 7.6 - - - +
96E GLY* 6.4 0.2 - - - -
361E TRP* 4.3 15.5 - - + -
376E MET 4.3 0.4 - - - -
377E ILE* 3.2 10.6 - - - +
378E TRP* 2.8 46.1 + - + -
390E PHE* 3.9 2.8 - - - -
391E SER* 1.3 90.9 - - - +
394E LYS* 1.3 71.8 + - - +
395E GLN* 4.7 4.0 - - + +
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Residues in contact with LYS 394 (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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364E ARG* 4.8 4.2 - - - +
366E LYS* 4.3 3.8 - - - +
375E GLU* 2.9 43.2 + - + +
376E MET 3.3 4.5 - - - +
377E ILE* 4.3 15.2 - - + +
390E PHE* 4.1 25.0 - - + -
392E VAL* 1.3 80.8 - - - +
395E GLN* 1.3 62.4 + - - +
396E ASP* 4.1 17.2 + - - +
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Residues in contact with GLN 395 (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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96E GLY* 3.5 5.5 - - - -
97E TRP* 2.8 65.8 - - + +
361E TRP* 4.9 2.5 - - + -
375E GLU* 3.6 1.5 - - - -
376E MET* 2.8 30.8 + - + +
392E VAL* 5.2 6.4 - - + +
394E LYS* 1.3 74.2 - - - +
396E ASP* 1.3 63.8 + - - +
397E ILE* 3.0 25.8 - - + +
446E PHE* 5.4 1.9 - - - -
453E THR* 3.4 11.7 + - - -
454E VAL* 3.2 15.5 - - - +
455E GLY* 3.8 18.8 - - - +
458E TRP* 5.7 0.3 - - - -
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Residues in contact with ASP 396 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366E LYS* 2.8 29.6 + - - +
374E PHE 4.2 3.1 - - - -
375E GLU* 4.3 1.4 - - - +
394E LYS* 4.1 16.6 + - - +
395E GLN* 1.3 72.8 - - - +
397E ILE* 1.3 66.1 - - - +
398E VAL 5.0 1.8 - - - +
399E ALA* 6.5 0.2 - - - -
455E GLY* 3.1 13.4 - - - -
456E TRP* 3.0 36.8 + - - +
458E TRP* 4.2 2.8 - - - -
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Residues in contact with ILE 397 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97E TRP* 5.5 0.4 - - + -
374E PHE* 2.9 30.1 + - + +
376E MET* 4.0 14.8 - - + -
395E GLN* 3.0 43.3 - - + +
396E ASP* 1.3 80.8 - - - +
398E VAL* 1.3 75.5 + - + +
422E PHE* 4.0 15.5 - - + -
424E VAL* 4.7 2.0 - - + -
444E ILE* 3.7 16.4 - - + -
446E PHE* 3.8 25.8 - - + -
456E TRP 3.3 7.4 - - - +
458E TRP* 3.0 30.4 + - + +
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Residues in contact with VAL 398 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366E LYS* 2.9 14.2 + - - +
373E GLY* 3.1 9.5 - - - +
374E PHE* 2.8 35.6 + - + +
396E ASP* 5.7 1.6 - - - -
397E ILE* 1.3 97.7 - - + +
399E ALA* 1.3 70.8 + - - +
402E ASP* 3.9 19.7 - - + +
403E TRP 4.2 9.4 - - - +
404E SER* 4.9 1.3 - - - -
424E VAL* 5.1 0.7 - - + -
426E LEU* 4.7 8.3 - - + -
444E ILE* 3.7 17.3 - - + -
456E TRP 3.7 1.1 + - - -
457E SER* 3.9 9.0 - - - +
458E TRP 4.2 8.1 - - - +
459E PRO* 4.7 6.3 - - + -
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Residues in contact with ALA 399 (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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366E LYS* 4.1 5.2 - - - +
373E GLY* 3.1 12.3 - - - -
396E ASP* 6.5 0.2 - - - -
398E VAL* 1.3 74.6 - - - +
400E ILE* 1.3 57.9 + - + +
401E THR* 3.0 19.7 - - + +
402E ASP* 3.0 24.0 + - - +
457E SER* 3.1 27.2 + - - +
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Residues in contact with ILE 400 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366E LYS* 3.6 43.7 - - + +
367E SER* 3.9 21.1 - - - +
372E SER* 3.3 22.5 + - - +
373E GLY* 4.0 7.6 - - - +
399E ALA* 1.3 72.6 - - + +
401E THR* 1.3 60.7 + - + +
402E ASP 3.2 0.7 - - - -
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Residues in contact with THR 401 (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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399E ALA* 3.8 10.2 - - + +
400E ILE* 1.3 80.0 - - + +
402E ASP* 1.3 73.1 + - - +
403E TRP* 5.8 2.9 + - - -
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Residues in contact with ASP 402 (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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372E SER* 3.3 5.3 - - - -
373E GLY* 2.7 32.7 + - - -
398E VAL* 3.9 7.1 - - + +
399E ALA* 3.0 11.3 + - - +
400E ILE 3.2 0.9 - - - -
401E THR* 1.3 94.0 + - - +
403E TRP* 1.3 61.4 + - - +
457E SER* 4.1 8.5 + - - -
459E PRO* 3.5 38.6 - - + +
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Residues in contact with TRP 403 (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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370E SER* 4.1 12.3 - - - -
371E ARG* 3.6 12.8 - - + +
372E SER* 3.5 25.6 - - - -
398E VAL* 4.2 8.3 - - - +
401E THR 5.8 2.0 + - - -
402E ASP* 1.3 79.2 - - - +
404E SER* 1.3 61.8 + - - +
426E LEU* 4.2 15.8 - - - +
427E ILE 3.5 21.3 - - - +
428E ARG* 3.6 31.5 - - - -
432E LYS* 3.6 53.4 - - + -
433E GLU* 3.3 20.6 + - + +
459E PRO* 5.4 0.2 - - - +
460E ASP* 5.3 3.3 + - - +
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Residues in contact with SER 404 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365E THR* 3.9 6.2 - - - +
371E ARG* 2.7 28.9 + - - +
373E GLY* 2.9 32.7 + - - -
374E PHE* 4.6 9.2 - - - -
398E VAL* 4.9 2.2 - - - -
402E ASP 3.8 0.2 + - - -
403E TRP* 1.3 74.4 - - - +
405E GLY* 1.3 65.7 + - - -
424E VAL* 4.6 7.2 - - - -
425E GLU 3.0 13.0 - - - -
426E LEU* 4.2 4.9 - - - +
427E ILE* 2.8 30.8 + - - +
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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