Contacts of the strand formed by residues 375 - 379 (chain H) in PDB entry 1UW9
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 MET 375 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155H ILE* 3.6 36.3 - - + +
158H GLU* 3.8 16.8 - - - +
159H ARG* 4.7 12.6 - - + +
169H LEU* 4.1 19.5 - - + -
324H ASP 2.9 19.6 + - - +
325H HIS* 3.3 18.3 - - + +
326H LEU 2.9 26.9 + - - -
349H MET* 4.2 0.4 - - - -
374H VAL* 1.3 68.1 - - - +
376H PRO* 1.3 73.5 - - - +
377H VAL* 3.6 1.0 + - - +
396H ASP 5.2 0.2 - - - +
397H ASP* 3.5 10.8 - - - +
398H ALA* 3.4 30.7 - - - +
399H CYS* 4.1 10.8 - - + +
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Residues in contact with PRO 376 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326H LEU 3.3 7.4 - - - +
328H SER* 3.7 21.5 - - - +
346H VAL* 4.4 12.6 - - + -
349H MET* 3.6 10.1 - - + -
350H ARG* 3.6 24.9 - - + +
374H VAL 3.3 10.0 - - - +
375H MET* 1.3 85.3 - - + +
377H VAL* 1.3 60.9 + - - +
378H ALA 4.1 0.2 - - - -
394H PHE* 4.5 4.9 - - + -
397H ASP 3.2 27.6 - - - +
398H ALA* 3.3 8.0 - - + +
399H CYS 2.9 23.2 + - - -
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Residues in contact with VAL 377 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292H HIS* 3.7 12.8 - - + -
325H HIS* 3.7 37.0 - - + +
326H LEU 2.9 13.3 + - - +
327H HIS* 3.2 18.8 - - + +
328H SER* 2.9 26.4 + - - -
329H GLY 3.9 1.0 + - - -
375H MET* 3.9 1.8 - - + +
376H PRO* 1.3 76.3 - - - +
378H ALA* 1.3 61.7 + - - +
379H SER* 3.6 3.7 + - - -
399H CYS* 3.2 13.5 - - + +
401H GLN* 3.4 42.0 - - + +
1478O CAP 4.7 0.2 + - - -
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Residues in contact with ALA 378 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328H SER* 3.9 0.2 + - - -
329H GLY 3.4 20.0 - - - +
330H THR* 3.8 9.6 - - + -
376H PRO 4.1 1.2 - - - -
377H VAL* 1.3 70.0 - - - +
379H SER* 1.3 59.9 + - - +
382H ILE* 3.6 3.7 - - + +
390H LEU* 4.2 5.4 - - + -
394H PHE* 3.7 25.8 - - + -
398H ALA* 5.5 0.4 - - + +
399H CYS 2.8 8.3 + - - +
400H LEU* 3.5 19.7 - - + -
401H GLN 2.8 26.5 + - - -
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Residues in contact with SER 379 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173H THR* 4.5 1.2 + - - -
327H HIS* 3.8 15.3 - - - -
329H GLY 4.4 0.8 + - - -
330H THR* 3.3 18.9 + - - +
335H LEU* 4.2 5.2 - - - +
377H VAL* 3.6 3.3 + - - -
378H ALA* 1.3 75.3 - - - +
380H GLY* 1.3 59.6 + - - +
401H GLN* 3.4 38.2 + - - +
1478O CAP 2.8 49.6 + - - -
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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