Contacts of the strand formed by residues 392 - 403 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95D ASN 5.2 6.7 - - - +
361D TRP* 4.5 15.4 - - + -
376D MET 4.5 0.2 - - - -
377D ILE* 3.4 4.0 - - - -
378D TRP* 3.0 44.3 + - + -
390D PHE* 3.8 7.5 - - - -
391D SER* 1.3 89.9 - - - +
394D LYS* 1.3 75.0 + - - +
395D GLN* 4.6 4.5 - - + +
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Residues in contact with LYS 394 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364D ARG* 4.7 4.2 - - - +
366D LYS* 4.3 8.3 - - - +
375D GLU* 2.6 45.3 + - + +
376D MET 3.4 8.5 - - - +
377D ILE* 4.1 11.9 - - + +
390D PHE* 4.0 25.7 - - + -
392D VAL* 1.3 83.8 - - - +
395D GLN* 1.3 62.8 + - - +
396D ASP* 4.2 10.8 + - - +
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Residues in contact with GLN 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D GLY* 3.7 7.5 - - - -
97D TRP* 2.8 68.2 + - - +
361D TRP* 4.8 3.7 - - + -
375D GLU* 3.5 1.7 - - - -
376D MET* 2.9 42.1 + - + +
392D VAL* 4.6 6.7 - - + +
394D LYS* 1.3 76.1 - - - +
396D ASP* 1.3 61.9 + - - +
397D ILE* 2.9 14.1 - - + +
446D PHE* 5.4 1.7 - - - -
453D THR* 3.7 9.0 + - - -
454D VAL* 3.5 12.5 - - - +
455D GLY* 3.7 17.9 - - - +
458D TRP* 5.9 0.5 - - - -
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Residues in contact with ASP 396 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366D LYS* 2.9 26.7 + - - +
374D PHE 4.2 3.8 - - - -
375D GLU* 4.4 1.1 - - - -
394D LYS* 4.2 15.5 - - - +
395D GLN* 1.3 73.3 - - - +
397D ILE* 1.3 66.3 + - - +
398D VAL 4.9 2.5 - - - +
399D ALA* 6.0 0.4 - - - +
455D GLY* 3.1 11.5 - - - -
456D TRP* 3.0 37.0 + - - +
458D TRP* 4.2 2.1 - - - -
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Residues in contact with ILE 397 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D TRP* 5.5 0.2 - - + -
374D PHE* 3.1 27.1 + - + +
376D MET* 3.8 19.7 - - + +
395D GLN* 2.9 42.8 - - + +
396D ASP* 1.3 78.6 - - - +
398D VAL* 1.3 79.7 + - + +
422D PHE* 4.1 12.8 - - + -
424D VAL* 4.6 2.5 - - + -
444D ILE* 3.8 6.7 - - + -
446D PHE* 3.6 41.1 - - + -
456D TRP 3.3 7.5 - - - +
458D TRP* 3.1 26.1 + - - +
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Residues in contact with VAL 398 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366D LYS* 3.0 10.4 - - - +
373D GLY* 4.1 6.7 - - - +
374D PHE* 2.8 42.1 + - + +
396D ASP* 5.7 1.1 - - - -
397D ILE* 1.3 98.8 - - + +
399D ALA* 1.3 75.2 + - - +
402D ASP* 3.9 20.6 - - + +
403D TRP 4.6 6.7 - - - +
404D SER* 5.1 1.8 - - - -
424D VAL* 5.3 1.1 - - + -
426D LEU* 4.4 8.5 - - + -
444D ILE* 3.9 15.9 - - + -
456D TRP 3.7 1.3 + - - -
457D SER* 3.9 4.9 - - - +
458D TRP 4.0 6.1 - - - +
459D PRO* 4.3 11.9 - - + -
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Residues in contact with ALA 399 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366D LYS* 4.1 5.6 - - - +
373D GLY* 3.3 7.3 - - - -
396D ASP* 6.0 0.9 - - - +
398D VAL* 1.3 78.7 - - - +
400D ILE* 1.3 65.1 + - + +
401D THR* 3.8 16.8 - - - +
402D ASP* 3.0 18.2 + - - +
457D SER* 3.0 27.4 + - - +
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Residues in contact with ILE 400 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366D LYS* 3.5 43.2 - - + +
367D SER* 4.4 17.3 - - - +
372D SER* 3.5 19.4 - - - +
373D GLY* 4.1 8.3 - - - -
399D ALA* 1.3 71.9 - - - +
401D THR* 1.3 60.6 + - + +
402D ASP 3.1 4.9 + - - -
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Residues in contact with THR 401 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399D ALA* 3.8 11.3 - - - +
400D ILE* 1.3 79.2 - - + +
402D ASP* 1.3 72.7 + - - +
403D TRP* 5.7 2.9 + - - -
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Residues in contact with ASP 402 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372D SER* 3.5 4.9 - - - -
373D GLY* 2.9 27.2 + - - -
398D VAL* 3.9 6.5 - - + +
399D ALA* 3.0 16.1 + - - +
400D ILE 3.1 0.8 - - - -
401D THR* 1.3 94.8 + - - +
403D TRP* 1.3 65.4 + - - +
457D SER* 4.4 1.6 + - - -
459D PRO* 3.3 40.6 - - + +
460D ASP 5.1 1.0 + - - +
461D GLY* 5.2 3.5 + - - -
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Residues in contact with TRP 403 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370D SER* 4.0 10.8 - - - -
371D ARG* 3.6 15.7 - - + +
372D SER* 3.4 19.7 - - - -
398D VAL* 4.6 2.3 - - - +
401D THR 5.7 2.3 + - - -
402D ASP* 1.3 79.5 + - - +
404D SER* 1.3 59.2 + - - +
426D LEU* 3.8 20.1 - - - +
427D ILE 3.4 22.9 - - - +
428D ARG* 3.6 31.0 - - - -
432D LYS* 3.6 46.9 - - + -
433D GLU* 3.5 22.5 + - + +
460D ASP* 5.1 4.7 + - + +
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Residues in contact with SER 404 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365D THR* 3.6 9.1 - - - +
371D ARG* 2.9 28.8 + - - +
372D SER 3.5 0.2 + - - -
373D GLY 2.9 34.9 + - - -
374D PHE* 4.6 8.3 - - - -
398D VAL* 5.1 2.9 - - - -
402D ASP 3.6 0.8 + - - -
403D TRP* 1.3 73.5 - - - +
405D GLY* 1.3 67.1 + - - -
424D VAL* 4.8 5.8 - - - -
425D GLU 3.2 10.5 - - - -
426D LEU* 4.2 6.5 - - - -
427D ILE* 3.1 25.8 + - - +
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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