Contacts of the strand formed by residues 467 - 474 (chain C) in PDB entry 5E9W
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 467 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176C ASN* 5.5 5.8 - - - -
285C PHE* 3.8 33.4 - + - -
288C HIS* 5.2 2.7 - + - -
318C THR* 3.6 6.1 - - - +
319C PRO* 3.5 38.9 - - + +
320C ASN* 4.3 2.3 - - - +
360C PHE* 3.6 32.6 - + - -
370C GLU* 4.6 4.3 + - - -
394C THR* 3.7 2.8 - - - -
395C PHE* 2.9 50.3 + + + +
463C ALA 4.1 14.4 - - - -
464C THR* 3.1 17.2 + - - +
465C SER 3.1 5.7 - - - +
466C ILE* 1.3 87.6 - - + +
468C LEU* 1.3 61.3 + - - +
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Residues in contact with LEU 468 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C THR* 3.3 4.9 - - - -
318C THR* 2.8 56.4 + - + +
319C PRO 4.4 1.8 - - - +
320C ASN* 3.7 35.2 - - + +
321C SER 5.1 0.4 - - - +
373C VAL 6.1 0.4 - - - +
375C PHE* 4.2 24.2 - - + -
392C LYS* 4.1 22.4 - - + -
393C LYS 3.3 17.3 - - - +
394C THR* 4.2 3.4 - - - +
395C PHE* 3.6 5.4 - - - -
467C TYR* 1.3 74.4 - - - +
469C VAL* 1.3 77.0 + - - +
470C PHE* 4.0 10.5 - - + -
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Residues in contact with VAL 469 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C MET* 4.1 14.1 - - + +
183C LEU* 4.6 11.0 - - + -
316C GLY 3.4 9.4 - - - +
317C THR* 4.0 6.1 - - + -
391C TYR* 3.7 17.3 - - + -
392C LYS* 3.5 2.8 - - - -
393C LYS* 2.7 43.0 + - + +
395C PHE* 3.4 30.1 - - + -
398C PHE* 3.5 34.1 - - + -
468C LEU* 1.3 76.7 - - - +
470C PHE* 1.3 62.4 + - - +
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Residues in contact with PHE 470 (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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183C LEU* 4.7 3.7 - - - +
283C CYS 4.6 0.2 - - - -
287C CYS* 3.6 31.0 - - - -
314C PHE* 3.7 29.8 - + - -
315C ILE* 3.4 6.7 - - - +
316C GLY* 2.9 63.5 + - - +
317C THR 3.8 4.0 - - - -
318C THR* 4.4 12.8 - - + -
375C PHE* 3.6 33.0 - + + -
378C LEU* 4.4 5.6 - - + -
391C TYR* 3.5 9.6 - - - +
468C LEU* 4.0 16.2 - - + -
469C VAL* 1.3 76.8 - - - +
471C ALA* 1.3 63.9 + - - +
472C PHE* 3.7 17.0 - + + -
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Residues in contact with ALA 471 (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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187C PHE* 3.3 42.4 - - + -
314C PHE 3.3 7.0 - - - -
315C ILE* 3.9 7.6 - - + -
389C LEU* 3.4 5.9 - - - +
390C VAL* 2.7 36.0 + - + +
391C TYR* 3.1 14.2 + - + +
470C PHE* 1.3 77.0 - - - +
472C PHE* 1.3 59.4 + - - +
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Residues in contact with PHE 472 (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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313C TYR* 3.3 8.3 - - - -
314C PHE* 2.7 52.2 + + + +
375C PHE* 3.7 28.0 - + - -
378C LEU* 4.3 12.1 - - + -
379C ASN* 3.6 41.5 - - - -
382C ALA* 3.9 16.2 - - + -
387C MET* 3.7 22.2 - - + +
388C LYS 3.3 6.5 - - - +
389C LEU* 3.7 22.4 - - + -
390C VAL* 3.8 3.4 - - - +
470C PHE* 3.7 30.3 - + - -
471C ALA* 1.3 73.7 - - - +
473C GLU* 1.3 59.8 + - - +
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Residues in contact with GLU 473 (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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311C GLY* 3.8 15.4 - - - +
312C GLY 3.4 6.3 - - - +
313C TYR* 3.8 28.9 + - + -
387C MET* 3.3 6.6 - - - -
388C LYS* 2.7 37.3 + - + +
390C VAL* 3.6 18.3 - - + +
472C PHE* 1.3 73.2 - - - +
474C LYS* 1.3 74.8 + - - +
475C GLN* 3.2 13.3 - - - +
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Residues in contact with LYS 474 (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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305C CYS 2.9 30.8 + - - -
306C GLU* 4.3 7.5 + - - +
308C LEU* 3.3 22.9 - - + +
309C SER 3.4 23.8 - - - +
310C PRO* 3.5 11.0 - - + -
311C GLY* 2.6 29.1 + - - -
312C GLY 2.8 14.4 + - - +
385C TYR* 2.7 32.5 + - - +
386C ASN* 3.7 14.1 - - + +
387C MET* 3.4 11.6 - - - +
473C GLU* 1.3 73.0 - - - +
475C GLN* 1.3 65.6 + - - +
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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
------------------------------------------------------------
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