Contacts of the strand formed by residues 350 - 354 (chain C) in PDB entry 1EQR
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 ALA 350 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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304C PHE* 6.1 0.2 - - + -
306C VAL* 6.4 1.6 - - + -
307C PHE* 4.0 13.2 - - + -
348C GLY 4.3 0.2 - - - -
349C LEU* 1.3 75.6 - - - +
351C TYR* 1.3 61.4 + - - +
368C VAL* 3.7 28.0 - - + -
393C PHE* 3.5 2.9 - - - -
394C PHE* 2.8 48.9 + - + +
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Residues in contact with TYR 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B THR* 5.4 9.7 - - - +
331C ARG* 5.0 9.5 + - - -
334C ILE* 3.7 40.5 - - + +
349C LEU 4.1 9.2 - - - -
350C ALA* 1.3 77.0 - - - +
352C ILE* 1.3 69.1 + - - +
353C LYS* 4.2 11.7 + - - -
365C ASN 4.4 7.6 - - - -
366C SER* 2.8 22.0 + - - -
367C PRO* 3.6 37.6 - - + +
368C VAL* 4.2 2.7 - - - +
391C MET* 4.0 17.7 - - + -
392C ILE 3.2 11.7 - - - +
393C PHE* 3.7 18.2 - - + -
394C PHE* 4.2 0.9 - - - -
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Residues in contact with ILE 352 (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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351C TYR* 1.3 80.6 - - - +
353C LYS* 1.3 61.8 + - - +
354C VAL* 3.5 10.2 + - + -
364C ILE* 4.2 30.3 - - + -
366C SER* 3.5 20.9 - - - +
368C VAL* 4.4 1.3 - - + -
369C ALA 6.1 0.2 - - - +
372C LEU* 4.6 12.3 - - + -
377C ILE* 4.8 13.0 - - + -
380C ILE* 4.5 16.4 - - + -
381C LEU* 4.5 7.0 - - + -
391C MET* 3.6 3.3 - - - +
392C ILE* 2.9 35.0 + - + +
394C PHE* 3.3 33.7 - - + -
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Residues in contact with LYS 353 (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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327C ALA* 3.2 44.5 + - + +
329C LEU 3.4 15.6 + - - -
330C THR* 5.4 1.0 - - - +
331C ARG 5.6 0.8 - - - +
334C ILE* 4.1 12.6 - - - +
351C TYR* 4.2 10.1 + - + -
352C ILE* 1.3 72.1 - - - +
354C VAL* 1.3 59.4 + - - +
355C ASN* 3.5 13.1 + - - +
364C ILE* 3.3 5.4 - - - +
365C ASN* 2.9 52.0 + - + +
390C ASP 4.2 0.4 - - - -
391C MET* 3.7 23.5 - - + -
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Residues in contact with VAL 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327C ALA* 4.1 1.1 - - - +
352C ILE* 3.9 4.9 - - + +
353C LYS* 1.3 71.5 - - - +
355C ASN* 1.3 53.1 + - - +
357C ARG* 3.3 38.1 - - + -
364C ILE* 4.4 5.4 - - + -
381C LEU* 3.5 36.1 - - + -
386C ALA* 4.2 6.1 - - + -
387C GLN 3.7 13.0 - - - +
388C ASP* 4.4 0.9 - - - -
389C GLY* 2.5 37.9 + - - -
390C ASP 3.1 19.2 + - - +
392C ILE* 3.9 17.0 - - + -
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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