Contacts of the strand formed by residues 381 - 385 (chain C) in PDB entry 1XPM
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 381 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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376C ASN 4.0 0.2 - - - +
377C ILE* 3.4 3.5 - - - +
378C GLU* 3.0 31.2 + - - +
379C ASN* 3.6 14.4 - - + +
380C ASN* 1.3 77.7 - - - +
382C ARG* 1.3 72.4 + - - +
383C GLU* 3.6 9.7 + - + +
183D TYR* 3.5 44.2 - - + -
186D TRP* 3.8 18.4 - - + +
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Residues in contact with ARG 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C ASP* 2.9 33.4 + - - +
82C VAL* 3.8 40.1 + - - +
91C GLN* 6.2 0.4 - - - +
356C VAL* 4.3 19.8 - - - +
374C LEU* 3.6 18.3 - - + +
376C ASN 3.7 5.2 - - - -
377C ILE* 4.0 26.1 - - + +
380C ASN 4.2 2.0 + - - +
381C VAL* 1.3 82.9 - - - +
383C GLU* 1.3 60.3 + - - +
384C TYR* 3.5 36.0 - - + +
183D TYR* 4.6 11.4 + - - +
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Residues in contact with GLU 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374C LEU* 3.5 8.7 - - - +
375C SER* 2.9 33.8 + - - +
376C ASN* 2.9 20.5 + - + +
378C GLU* 5.4 9.2 - - + +
381C VAL* 4.2 12.8 - - + +
382C ARG* 1.3 76.4 - - - +
384C TYR* 1.3 61.9 + - - +
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Residues in contact with TYR 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C ASP* 2.6 40.7 + - - -
52C VAL* 3.3 32.1 - - + +
53C SER* 4.1 8.3 - - - -
91C GLN* 5.0 13.6 + - + -
95C LEU* 4.2 31.2 - - + -
372C PHE* 5.2 0.7 - - + -
373C TYR 3.3 16.2 - - - +
374C LEU* 3.8 13.7 - - + -
375C SER* 3.9 4.9 - - - -
382C ARG* 3.5 39.0 - - + +
383C GLU* 1.3 75.0 - - - +
385C HIS* 1.3 65.4 + - - +
386C ARG* 3.2 24.2 + - - +
183D TYR* 5.9 0.2 - - - -
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Residues in contact with HIS 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368C ASP 3.4 9.6 + - - -
369C ARG* 3.3 26.0 + - - +
371C ILE 2.9 27.1 + - - -
372C PHE* 3.2 27.4 - - - -
373C TYR* 2.7 53.1 + + + +
375C SER* 3.9 7.1 + - - -
384C TYR* 1.3 73.2 - - - +
386C ARG* 1.3 79.7 + - - +
388C GLU* 4.8 2.4 + - - +
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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