Contacts of the strand formed by residues 392 - 403 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95H ASN 4.9 8.3 - - - +
361H TRP* 4.4 15.7 - - + -
376H MET 4.4 0.2 - - - -
377H ILE* 3.3 8.4 - - - +
378H TRP* 2.8 48.7 + - + -
390H PHE* 3.7 2.9 - - - -
391H SER* 1.3 87.4 - - - +
394H LYS* 1.3 72.0 + - - +
395H GLN* 4.8 3.4 - - + +
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Residues in contact with LYS 394 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364H ARG* 4.6 3.8 - - - +
366H LYS* 4.3 1.8 - - - +
375H GLU* 2.8 41.6 + - + +
376H MET 3.2 5.4 - - - +
377H ILE* 4.0 18.1 - - + +
390H PHE* 3.7 24.8 - - + -
392H VAL* 1.3 84.2 - - - +
395H GLN* 1.3 61.2 + - - +
396H ASP* 3.9 18.6 + - - +
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Residues in contact with GLN 395 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96H GLY* 3.8 5.7 - - - -
97H TRP* 2.9 66.4 - - - +
361H TRP* 5.0 4.1 - - + -
375H GLU* 3.5 2.4 - - - -
376H MET* 2.6 42.1 + - + +
392H VAL* 4.8 4.9 - - + +
394H LYS* 1.3 73.0 - - - +
396H ASP* 1.3 62.8 + - - +
397H ILE* 3.2 17.5 - - + +
446H PHE* 5.8 0.9 - - - -
453H THR* 3.3 14.5 + - - +
454H VAL 3.4 13.0 - - - +
455H GLY* 3.9 17.5 - - - +
458H TRP* 6.0 0.3 - - - -
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Residues in contact with ASP 396 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366H LYS* 2.7 34.6 + - - +
374H PHE 4.3 0.7 - - - -
375H GLU* 4.3 0.2 - - - +
394H LYS* 3.9 19.0 + - - +
395H GLN* 1.3 72.8 - - - +
397H ILE* 1.3 66.1 + - - +
398H VAL 5.1 1.8 - - - +
399H ALA* 6.4 0.2 - - - -
455H GLY* 3.3 10.4 - - - -
456H TRP 2.9 37.6 + - - +
458H TRP* 4.1 2.3 - - - -
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Residues in contact with ILE 397 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97H TRP* 5.5 1.1 - - + -
374H PHE* 3.2 28.5 + - + +
376H MET* 4.0 15.7 - - + +
395H GLN* 3.2 35.7 - - + +
396H ASP* 1.3 78.4 - - - +
398H VAL* 1.3 78.8 + - + +
422H PHE* 4.1 19.3 - - + -
424H VAL* 4.6 1.8 - - + -
444H ILE* 3.7 18.4 - - + -
446H PHE* 3.8 22.4 - - + -
456H TRP 3.3 8.4 - - - +
458H TRP* 3.3 27.3 + - + +
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Residues in contact with VAL 398 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366H LYS* 2.9 9.0 - - - +
373H GLY* 2.9 3.7 - - - -
374H PHE* 2.8 42.3 + - + +
396H ASP* 5.8 0.9 - - - -
397H ILE* 1.3 100.4 - - + +
399H ALA* 1.3 73.8 + - - +
402H ASP* 3.9 24.2 - - + +
403H TRP 4.4 8.7 - - - +
404H SER* 4.8 2.0 - - - -
424H VAL* 5.1 0.9 - - + -
426H LEU* 4.5 9.0 - - + -
444H ILE* 3.9 15.0 - - + -
456H TRP 3.8 1.1 + - - -
457H SER* 3.9 4.5 - - - +
458H TRP 4.2 6.5 - - - +
459H PRO* 4.5 11.0 - - + -
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Residues in contact with ALA 399 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366H LYS* 4.1 5.8 - - - +
373H GLY* 3.2 7.3 - - - -
396H ASP* 6.4 0.4 - - - -
398H VAL* 1.3 76.6 - - - +
400H ILE* 1.3 59.8 + - + +
401H THR* 3.6 17.7 - - + +
402H ASP* 2.9 24.8 + - - +
456H TRP 4.8 0.2 + - - -
457H SER* 2.9 29.8 + - - +
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Residues in contact with ILE 400 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366H LYS* 3.5 43.9 - - + +
367H SER* 4.2 19.1 - - - +
372H SER* 3.4 19.3 - - - -
373H GLY* 4.0 8.3 - - - -
399H ALA* 1.3 72.1 - - - +
401H THR* 1.3 60.5 + - + +
402H ASP 3.1 4.0 + - - -
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Residues in contact with THR 401 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399H ALA* 3.6 11.6 - - + +
400H ILE* 1.3 79.5 - - + +
402H ASP* 1.3 75.9 + - - +
403H TRP* 5.7 3.1 + - - -
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Residues in contact with ASP 402 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372H SER* 3.7 2.6 - - - -
373H GLY* 2.8 31.9 + - - -
398H VAL* 3.9 6.9 - - + +
399H ALA* 2.9 19.0 + - - +
400H ILE 3.1 1.7 - - - -
401H THR* 1.3 102.4 + - - +
403H TRP* 1.3 63.3 + - - +
457H SER* 4.4 2.1 + - - -
459H PRO* 3.5 37.7 - - + +
461H GLY 5.7 0.7 + - - -
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Residues in contact with TRP 403 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370H SER* 4.5 11.4 - - - -
371H ARG* 3.8 14.8 - - + +
372H SER* 3.8 17.9 - - - -
398H VAL* 4.4 3.9 - - - +
401H THR 5.7 2.6 + - - -
402H ASP* 1.3 77.7 - - - +
404H SER* 1.3 59.9 + - - +
426H LEU* 3.8 20.4 - - - +
427H ILE 3.4 22.2 - - - +
428H ARG* 3.5 31.8 - - - +
432H LYS* 3.5 51.6 - - + -
433H GLU* 3.5 22.6 + - + +
460H ASP* 5.0 4.7 + - - +
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Residues in contact with SER 404 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365H THR* 3.8 5.7 - - - +
371H ARG* 2.9 26.0 + - - +
373H GLY* 2.7 33.9 + - - -
374H PHE* 4.5 9.0 - - - -
398H VAL* 4.8 2.5 - - - -
402H ASP 3.6 0.2 + - - -
403H TRP* 1.3 76.6 - - - +
405H GLY* 1.3 66.1 + - - -
424H VAL* 4.5 8.5 - - - -
425H GLU 3.1 10.8 - - - -
426H LEU* 4.0 6.3 - - - -
427H ILE* 3.0 28.2 + - - +
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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