Contacts of the strand formed by residues 387 - 391 (chain A) in PDB entry 1HMU
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 ALA 387 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A PHE* 4.2 5.6 - - + -
284A ASN* 3.5 17.1 + - - +
359A ASN 3.4 2.1 - - - +
360A VAL* 3.2 5.2 - - - -
361A ARG 3.0 27.3 + - - +
383A LEU 3.3 24.0 - - - +
385A ASP 3.5 1.0 - - - -
386A GLY* 1.3 75.4 - - - +
388A THR* 1.3 59.8 + - - +
389A ASN 3.9 0.2 - - - -
409A ILE* 3.7 21.5 - - + -
410A PRO 3.2 6.5 - - - -
412A ILE* 3.9 4.9 - - + -
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Residues in contact with THR 388 (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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283A PHE* 4.4 2.0 - - - -
358A PHE* 3.7 29.1 - - + -
359A ASN 3.5 4.5 - - - -
360A VAL* 3.9 4.0 - - + -
386A GLY 3.6 9.4 - - - +
387A ALA* 1.3 70.3 - - - +
389A ASN* 1.3 61.8 + - - +
390A ILE* 3.4 14.2 + - - +
397A TYR* 3.7 2.3 + - - -
410A PRO* 2.7 37.7 + - - +
411A GLY* 3.3 15.6 + - - -
462A TRP* 3.3 30.1 - - - +
488A LEU 4.1 3.1 + - - -
580A TYR* 4.8 3.8 + - - +
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Residues in contact with ASN 389 (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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281A MET 4.8 0.3 - - - +
282A ASP* 3.0 37.5 + - - +
283A PHE* 3.2 37.8 + - + -
284A ASN* 3.4 9.8 - - - +
357A SER* 3.5 1.9 + - - +
358A PHE* 3.4 4.9 - - - -
359A ASN* 2.8 38.5 + - + +
387A ALA 3.7 1.6 + - - -
388A THR* 1.3 68.5 - - - +
390A ILE* 1.3 59.1 + - - +
391A GLN* 2.6 33.0 + - - +
397A TYR* 3.8 8.0 - - - -
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Residues in contact with ILE 390 (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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356A TYR* 5.6 0.4 - - + -
357A SER 3.6 5.6 - - - +
358A PHE* 3.4 41.7 - - + -
388A THR* 3.7 20.2 - - - +
389A ASN* 1.3 75.5 - - - +
391A GLN* 1.3 62.4 + - - +
392A LEU* 4.1 7.8 - - + +
396A GLU* 4.1 9.9 - - - +
397A TYR* 3.2 26.6 + - - +
488A LEU 4.4 9.6 - - - +
489A ASN* 4.1 17.7 + - - +
525A ILE* 3.7 24.5 - - + +
527A TYR* 5.2 2.7 - - + +
582A VAL* 4.3 17.7 - - + -
584A PRO* 4.9 5.2 - - + -
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Residues in contact with GLN 391 (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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275A ALA 4.4 2.3 - - - +
277A ARG* 3.7 27.5 - - + +
280A TYR* 3.0 29.7 + - - +
281A MET 3.9 5.9 + - - -
282A ASP* 3.9 8.1 + - - +
356A TYR* 3.4 3.3 - - - +
357A SER* 3.0 36.0 + - - +
359A ASN* 4.8 1.6 + - - -
389A ASN* 2.6 34.9 + - - +
390A ILE* 1.3 78.0 - - - +
392A LEU* 1.3 64.5 + - - +
394A GLY 2.8 26.3 + - - +
396A GLU* 3.8 8.5 - - - +
397A TYR* 4.4 8.5 - - + -
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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