Contacts of the strand formed by residues 428 - 433 (chain A) in PDB entry 3HIG
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 ARG 428 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426A PRO* 3.3 4.0 - - - +
427A LEU* 1.3 83.8 - - + +
429A ARG* 1.3 63.5 + - - +
444A GLY* 3.4 0.6 - - - -
445A LEU* 3.0 48.0 + - + +
705A ASP* 2.9 22.1 + - - -
707A SER* 3.0 38.6 + - - -
708A LEU* 3.6 16.0 - - - +
713A THR* 3.5 23.6 + - - +
285B HIS* 3.6 42.6 + - + +
482B THR* 3.3 16.4 - - - +
683B PRO* 5.2 3.6 - - - -
684B ASN* 4.3 14.1 - - + +
685B THR 4.1 7.0 - - - +
686B ALA* 4.6 1.3 - - - -
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Residues in contact with ARG 429 (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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426A PRO* 3.8 16.4 - - + -
428A ARG* 1.3 77.2 - - - +
430A HIS* 1.3 61.5 - - - +
431A PHE* 3.9 12.5 - - - +
442A TYR* 3.7 18.2 - - - +
443A ALA 3.2 13.2 - - - +
444A GLY* 4.2 0.4 - - - -
285B HIS* 4.9 1.1 - - - -
383B HIS* 4.4 4.2 + - - +
384B GLU 3.4 20.8 + - - -
385B LEU* 4.2 7.3 - - - +
390B ASP* 2.8 46.8 + - - +
455B THR* 4.2 18.8 + - - +
457B THR* 3.6 9.5 + - - -
462B ASP* 3.0 38.3 + - - +
464B ILE* 4.3 7.8 - - + +
482B THR* 3.3 13.1 + - + +
483B GLY 3.5 13.3 + - - -
684B ASN* 4.0 3.8 + - - -
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Residues in contact with HIS 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A ARG* 1.3 76.6 - - - +
431A PHE* 1.3 70.8 + - - +
432A ASN* 2.9 42.8 + - + -
441A PHE* 4.0 6.6 - + + +
442A TYR* 3.5 8.4 - - - -
443A ALA* 2.9 34.9 + - - +
211B PHE* 3.6 7.3 - + - -
285B HIS* 4.2 9.1 + - + -
457B THR* 4.1 1.1 - - + -
459B TYR 3.6 22.4 - - - -
460B ASN 3.6 13.9 + - - -
462B ASP* 2.7 23.4 + - - +
483B GLY* 4.4 0.2 - - - -
484B TYR* 3.4 19.7 - + - -
684B ASN* 3.7 14.1 - - - +
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Residues in contact with PHE 431 (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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429A ARG* 3.9 16.1 - - - +
430A HIS* 1.3 84.3 - - - +
432A ASN* 1.3 58.0 + - - +
433A SER* 3.3 33.3 + - - -
439A PHE* 3.6 26.5 - + + -
441A PHE 4.0 1.8 - - - -
442A TYR* 4.4 8.3 - - + -
383B HIS* 3.5 50.7 - + + -
384B GLU* 4.4 4.7 - - + -
457B THR* 3.5 14.8 - - - +
459B TYR 4.7 0.9 - - - +
462B ASP* 3.2 8.9 + - - +
744B TYR* 3.2 26.9 - + - -
746B GLY* 3.8 20.6 - - - -
748B TYR* 4.0 5.8 - + - -
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Residues in contact with ASN 432 (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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430A HIS* 2.9 29.6 + - + +
431A PHE* 1.3 70.3 - - - +
433A SER* 1.3 60.1 + - - +
439A PHE* 3.3 5.8 - - - +
440A ASN* 2.7 62.2 + - - +
441A PHE* 2.9 42.7 + - + +
209B GLY* 5.3 1.8 + - - -
210B TYR* 3.9 15.7 + - - -
211B PHE* 3.3 25.1 - - - -
484B TYR* 4.9 0.2 - - - -
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Residues in contact with SER 433 (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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431A PHE* 3.3 24.4 + - - -
432A ASN* 1.3 78.8 - - - +
434A ASN* 1.3 56.9 + - - +
435A PHE* 2.9 50.4 + - - -
438A GLY 3.6 6.3 - - - -
440A ASN* 3.4 9.3 + - - -
210B TYR* 4.7 1.9 + - - -
383B HIS* 4.3 8.3 + - - -
457B THR* 6.0 2.9 - - - -
748B TYR* 2.8 26.7 + - - -
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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