Contacts of the strand formed by residues 346 - 349 (chain C) in PDB entry 1RR8
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 HIS 346 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203C TRP* 3.4 79.3 + + + +
208C GLU* 5.4 0.8 + - - -
341C CYS 3.7 0.2 - - - +
342C ILE* 3.4 9.5 - - - +
343C MET 3.1 29.3 + - - +
344C ASP 2.9 14.8 + - - +
345C ASN* 1.3 97.1 + - + +
347C LYS* 1.3 62.3 + - - +
348C GLU* 3.8 6.3 + - + +
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Residues in contact with LYS 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C TRP* 6.0 0.2 - - - -
336C LYS 5.9 1.4 + - - -
340C PHE* 4.1 39.0 - - + -
341C CYS 3.4 5.4 - - - +
342C ILE* 3.9 23.1 - - + -
346C HIS* 1.3 73.8 + - - +
348C GLU* 1.3 64.0 + - - +
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Residues in contact with GLU 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C TRP* 3.2 26.7 - - + -
205C TRP* 5.1 0.7 - - - -
340C PHE* 3.6 4.8 - - - -
341C CYS* 2.8 37.7 + - - +
343C MET* 4.2 17.5 - - + +
346C HIS* 4.2 14.8 - - + +
347C LYS* 1.3 78.9 - - - +
349C ARG* 1.3 62.5 + - - +
429C LEU* 3.5 29.2 - - + +
433C SER* 3.4 17.8 - - - -
434C ARG* 3.1 27.8 + - - +
435C ILE 4.9 0.7 + - - -
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Residues in contact with ARG 349 (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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335C LEU* 4.8 19.0 - - + +
339C GLY 3.6 11.4 - - - +
340C PHE* 3.6 35.8 - - + -
348C GLU* 1.3 77.8 - - - +
350C ILE* 1.3 61.0 + - - +
429C LEU* 3.6 11.4 - - - +
430C ASN* 3.0 52.8 + - + +
432C SER* 4.8 5.2 + - - +
750C GLU* 3.4 31.1 + - - -
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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
------------------------------------------------------------
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