Contacts of the strand formed by residues 375 - 379 (chain L) in PDB entry 1RBO
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 LEU 375 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155L ILE* 3.6 31.1 - - + +
158L GLU* 3.5 35.9 - - + +
159L ARG* 5.4 7.2 - - + +
169L LEU* 4.1 18.6 - - + -
324L ASP 3.0 15.9 + - - +
325L HIS* 3.1 13.6 - - + +
326L ILE 3.0 23.9 + - - -
374L VAL* 1.3 71.3 - - - +
376L PRO* 1.4 66.1 - - - +
377L VAL* 4.7 0.2 - - - -
397L ASP* 3.7 32.8 - - + +
398L SER 3.9 4.0 - - - +
399L VAL* 4.1 12.3 - - + -
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Residues in contact with PRO 376 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326L ILE* 3.5 9.0 - - + +
328L SER* 3.4 22.0 - - - +
346L VAL* 4.2 16.8 - - + -
349L LEU* 4.9 6.7 - - + -
350L ARG* 3.6 22.0 - - + +
374L VAL 3.4 9.6 - - - +
375L LEU* 1.4 82.6 - - - +
377L VAL* 1.3 60.5 + - - +
378L ALA 4.2 0.4 - - - -
394L PHE* 4.5 5.8 - - + -
397L ASP 3.3 24.9 - - - +
398L SER* 3.3 8.7 - - - -
399L VAL 2.9 23.2 + - - -
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Residues in contact with VAL 377 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292L HIS* 3.9 8.7 - - + -
325L HIS* 3.5 32.5 - - + +
326L ILE 2.9 14.9 + - - +
327L HIS* 3.4 20.3 - - + +
328L SER* 2.9 25.2 + - - -
329L GLY 3.8 1.6 + - - -
375L LEU 4.0 0.4 - - - +
376L PRO* 1.3 76.7 - - - +
378L ALA* 1.3 64.5 + - - +
379L SER 3.8 1.9 + - - -
399L VAL* 3.3 22.7 - - + +
401L GLN* 3.4 38.8 - - + +
476L CAP 4.8 0.2 + - - -
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Residues in contact with ALA 378 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329L GLY 3.5 19.1 - - - +
330L THR* 3.8 10.1 - - + -
376L PRO 4.2 1.0 + - - -
377L VAL* 1.3 70.7 - - - +
379L SER* 1.3 61.3 + - - +
382L ILE* 3.7 4.5 - - + +
390L LEU* 4.3 5.8 - - + -
394L PHE* 3.8 23.3 - - + -
398L SER* 5.8 0.4 - - - -
399L VAL 2.8 6.5 + - - +
400L LEU* 3.6 19.2 - - + -
401L GLN* 2.8 27.7 + - - +
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Residues in contact with SER 379 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173L THR* 4.5 1.7 + - - -
327L HIS* 3.6 26.0 - - - -
329L GLY* 4.6 1.3 + - - -
330L THR* 3.2 18.5 + - - +
335L LEU* 4.7 2.6 - - - +
377L VAL* 3.8 2.7 + - - -
378L ALA* 1.3 75.3 - - - +
380L GLY* 1.3 59.8 + - - +
382L ILE* 4.4 0.9 - - - -
401L GLN* 3.5 27.9 + - - +
476L CAP 2.9 48.7 + - - -
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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