Contacts of the strand formed by residues 395 - 400 (chain C) in PDB entry 1U7F
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 TRP 395 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277A VAL* 3.5 30.7 - - + -
237C TYR* 3.1 8.2 - - - -
238C TYR* 2.8 73.1 + + + +
240C LEU 2.7 26.5 + - - -
373C ARG* 3.8 35.7 - - + -
374C MET 3.0 16.4 - - - +
375C SER* 3.8 5.6 - - - -
376C PHE* 4.7 2.7 - - - -
389C VAL* 3.3 32.5 + - + -
390C THR* 4.5 4.3 - - + -
392C THR* 3.2 29.8 - - - +
394C CYS* 1.3 75.0 - - - +
396C ILE* 1.3 79.7 + - - +
397C GLU* 4.1 8.1 - - + -
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Residues in contact with ILE 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C ILE* 3.0 37.0 - - + -
236C SER 3.2 14.1 - - - +
237C TYR* 4.0 7.9 - - + -
257C VAL* 3.6 25.6 - - + -
269C PHE* 3.5 22.4 - - + -
271C LEU* 4.4 2.2 - - + -
372C ILE 3.8 1.0 - - - +
373C ARG* 3.4 2.8 - - - -
374C MET* 2.7 56.1 + - + +
376C PHE* 4.2 15.3 - - + -
395C TRP* 1.3 82.7 - - - +
397C GLU* 1.3 58.0 + - - +
398C LEU* 4.5 8.5 - - + -
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Residues in contact with GLU 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A SER* 2.7 29.7 + - - -
234C SER 3.9 0.3 - - - +
235C ILE* 3.3 5.9 - - - +
236C SER* 2.7 44.7 + - - +
238C TYR* 3.5 17.3 + - + -
371C THR* 3.1 29.9 + - + +
372C ILE 3.5 4.5 - - - +
373C ARG* 3.2 27.7 + - - +
395C TRP* 4.1 13.2 - - + -
396C ILE* 1.3 73.7 - - - +
398C LEU* 1.3 63.5 + - - +
399C HIS* 3.4 17.9 + - + -
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Residues in contact with LEU 398 (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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232C TRP* 5.0 1.8 - - + -
233C CYS* 4.4 14.6 - - - -
234C SER 3.6 2.7 - - - -
235C ILE* 3.6 32.5 - - + -
296C LEU* 3.9 29.4 - - + -
303C VAL* 5.0 5.6 - - + -
342C ILE* 4.7 12.8 - - + -
370C CYS 3.6 0.7 - - - +
371C THR* 3.2 8.8 - - - +
372C ILE* 2.8 58.0 + - + +
374C MET* 4.9 6.5 - - + -
396C ILE* 4.5 11.9 - - + -
397C GLU* 1.3 73.6 - - - +
399C HIS* 1.3 64.4 + - - +
400C LEU* 4.1 9.6 - - + -
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Residues in contact with HIS 399 (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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273A LEU* 3.1 33.9 + - + +
274A LEU* 4.8 2.2 - - + -
275A SER* 3.4 16.4 + - - -
233C CYS* 3.0 25.8 - - - -
234C SER* 3.1 27.1 + - - +
236C SER* 5.6 6.5 - - - -
370C CYS 3.5 3.1 - - - -
371C THR* 3.6 16.0 + - - -
397C GLU* 3.4 29.4 + - + -
398C LEU* 1.3 80.4 - - - +
400C LEU* 1.3 63.4 + - - +
401C ASN* 3.4 4.4 + - - +
404C LEU* 4.2 17.8 - - + +
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Residues in contact with LEU 400 (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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232C TRP* 3.7 29.6 - - + +
233C CYS* 3.8 11.7 - - + -
303C VAL* 4.5 7.4 - - + -
343C PHE* 3.3 55.0 - - + -
370C CYS* 2.9 19.9 + - - +
372C ILE* 3.9 13.7 - - + -
398C LEU* 4.6 11.0 - - + +
399C HIS* 1.3 71.7 - - - +
401C ASN* 1.3 58.1 - - - +
402C GLY 3.4 0.9 - - - -
403C PRO* 3.4 18.6 - - + +
404C LEU* 3.0 31.3 + - - +
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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