Contacts of the strand formed by residues 376 - 379 (chain C) in PDB entry 5UHC
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 376 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179C LEU* 4.1 31.2 + - + +
180C VAL 3.8 7.7 + - - +
181C ARG* 5.1 0.9 - - - +
370C ILE 4.2 9.2 - - - +
371C ASP* 4.2 15.5 + - - +
372C HIS 2.7 15.8 + - - +
373C PHE* 3.3 51.5 - - + +
375C ASN* 1.3 79.2 - - - +
377C ARG* 1.3 62.1 + - - +
378C LEU* 4.2 0.5 + - - +
457C ALA* 3.9 23.8 - - - +
463C LEU* 5.0 1.2 - - - +
472C VAL* 3.6 36.5 + - - +
479C HIS* 4.9 7.3 + - - -
495C GLY 5.6 3.4 + - - -
496C LEU* 5.9 0.6 - - - +
511C PHE* 4.2 5.5 - - - -
512C ILE* 5.8 3.3 + - - +
14H G 2.8 27.7 + - - -
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Residues in contact with ARG 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C LEU* 3.3 6.8 - - - +
180C VAL* 2.6 60.2 + - + +
182C SER* 3.9 20.0 - - - +
183C PRO* 4.5 4.3 - - - +
311C VAL* 3.8 38.4 - - - +
375C ASN 3.9 0.4 + - - -
376C ARG* 1.3 74.8 - - - +
378C LEU* 1.3 63.4 + - - +
379C ARG* 4.1 10.7 - - - +
383C GLU* 2.4 45.3 + - - -
509C PHE 3.1 23.7 + - - +
510C GLY* 3.3 18.6 - - - +
511C PHE* 4.3 7.2 - - + -
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Residues in contact with LEU 378 (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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56C VAL* 5.6 1.3 - - + -
177C SER* 3.8 18.4 - - - +
178C GLN 3.6 14.4 - - - +
179C LEU* 3.8 19.7 - - + -
376C ARG 4.2 0.2 + - - -
377C ARG* 1.3 73.6 - - - +
379C ARG* 1.3 58.8 + - - +
380C THR* 3.7 27.0 + - + -
455C LEU* 3.7 27.1 - - + -
500C LEU* 5.6 1.3 - - + -
506C VAL* 4.2 15.1 - - + +
510C GLY* 2.7 39.5 + - - +
512C ILE* 4.0 28.9 - - + -
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Residues in contact with ARG 379 (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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177C SER* 3.8 0.5 - - - -
178C GLN* 2.9 69.7 + - + +
180C VAL* 3.5 24.3 - - + +
377C ARG* 4.1 6.5 - - - +
378C LEU* 1.3 71.0 - - - +
380C THR* 1.3 66.6 + - - +
383C GLU* 3.2 39.4 + - + +
384C LEU* 3.5 26.2 - - - +
387C ASN* 3.6 24.7 - - - +
460C PRO 4.3 5.1 + - - -
461C GLY* 4.5 10.9 + - - -
13H T 6.2 0.4 - - - +
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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