Contacts of the strand formed by residues 372 - 378 (chain C) in PDB entry 5EWL
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 TYR 372 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124C ARG* 4.1 8.4 + - - -
142C PRO* 3.3 24.0 - - + +
143C PRO 4.8 0.3 + - - -
146C HIS* 3.9 19.1 - - - +
147C GLN* 3.9 21.6 + - + +
149C LEU* 5.8 3.0 - - + +
150C VAL* 3.6 27.6 - - + -
290C LEU* 4.4 21.5 - - + -
291C GLN 3.2 7.2 - - - +
292C LEU* 3.8 31.6 - - + -
293C ILE* 3.6 6.7 - - - -
370C ALA* 3.8 22.4 - - + +
371C GLN* 1.3 76.3 - - - +
373C SER* 1.3 62.4 + - - +
374C ILE* 5.6 0.2 - - + -
387C ILE* 3.2 8.1 - - - +
388C PHE* 2.9 46.6 + + + -
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Residues in contact with SER 373 (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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290C LEU* 3.4 8.8 - - - +
291C GLN* 2.8 38.5 + - - +
293C ILE* 3.6 17.2 - - - +
372C TYR* 1.3 70.7 - - - +
374C ILE* 1.3 60.9 + - - +
375C MET* 3.4 19.1 + - - +
384C GLN* 2.8 29.2 + - - -
386C GLY 3.7 6.1 - - - -
387C ILE* 4.2 1.3 - - - -
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Residues in contact with ILE 374 (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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150C VAL* 4.6 2.0 - - + -
154C MET* 3.9 25.8 - - + -
288C ILE* 3.8 27.1 - - + -
289C GLY 3.8 3.8 - - - +
290C LEU* 4.1 9.4 - - + -
372C TYR 4.6 0.2 - - - +
373C SER* 1.3 72.1 - - - +
375C MET* 1.3 54.8 + - - +
384C GLN* 3.5 1.9 - - - -
385C VAL* 2.8 45.9 + - + +
386C GLY* 2.8 17.5 + - - +
387C ILE 3.6 35.0 - - - +
388C PHE* 3.8 7.0 - - + +
393C ILE* 3.9 28.9 - - + -
400C ILE* 5.8 1.8 - - + -
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Residues in contact with MET 375 (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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275C ILE* 4.0 10.5 - - + -
288C ILE* 3.3 9.9 - - - +
289C GLY 2.9 34.1 + - - +
290C LEU 4.3 0.4 - - - -
291C GLN* 3.8 35.0 - - + +
373C SER* 3.7 32.1 - - - +
374C ILE* 1.3 72.1 - - - +
376C ASN* 1.3 61.6 + - - +
382C LEU* 3.8 50.7 - - + +
383C VAL 3.9 1.6 - - - -
384C GLN* 4.0 20.2 - - + +
385C VAL* 4.7 0.4 - - - -
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Residues in contact with ASN 376 (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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286C GLY 3.1 8.0 - - - +
287C ILE 3.0 19.3 - - - +
288C ILE* 3.4 16.3 - - + +
375C MET* 1.3 76.6 - - - +
377C LEU* 1.4 58.7 + - - +
378C GLN* 3.1 46.2 + - - +
382C LEU* 4.2 3.6 - - - -
383C VAL 2.9 30.5 + - - +
385C VAL* 3.7 19.1 - - + -
400C ILE* 3.9 4.4 - - - +
401C ILE* 3.0 32.0 + - - +
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Residues in contact with LEU 377 (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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280C LEU* 4.2 21.3 - - + +
283C ALA* 3.8 25.4 - - + +
284C PRO 3.7 16.2 - - - +
285C ASP* 3.6 26.7 - - - +
286C GLY* 2.9 38.2 + - - +
287C ILE* 3.2 26.8 + - + -
376C ASN* 1.4 69.3 + - - +
378C GLN* 1.3 58.1 + - - +
379C ASN 4.3 0.2 - - - -
380C ARG* 4.2 21.1 - - - -
381C LYS 3.8 7.4 - - - +
382C LEU* 4.2 7.5 - - + +
401C ILE* 4.6 4.2 - - - +
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Residues in contact with GLN 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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285C ASP* 4.8 0.2 - - - -
376C ASN* 3.1 30.0 + - - +
377C LEU* 1.3 72.0 - - - +
379C ASN* 1.3 89.1 + - - +
380C ARG 3.3 1.8 - - - -
381C LYS* 2.9 24.7 + - - +
383C VAL* 3.5 29.8 - - + +
385C VAL* 3.8 11.3 - - - +
398C ARG* 5.3 2.6 - - - +
399C LYS 2.7 28.0 + - - -
401C ILE* 3.2 30.4 - - + +
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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