Contacts of the strand formed by residues 353 - 358 (chain T) in PDB entry 5KZ5
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 CYS 353 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205T VAL* 5.0 1.1 - - + -
206T ASN 4.5 2.7 - - - +
207T ASN 3.4 16.4 - - - -
208T GLU 3.6 10.5 - - - -
210T GLY* 3.1 33.1 - - - +
235T GLN* 5.5 0.7 - - + -
258T LYS* 4.0 12.1 - - - +
349T HIS* 4.9 0.5 - - - +
350T TYR* 2.8 26.6 + - + +
351T PRO 3.2 0.2 - - - -
352T GLY* 1.3 79.3 - - - +
354T ILE* 1.4 64.6 + - - +
407T ARG* 3.4 33.9 - - - +
408T PHE 3.6 4.3 - - - -
409T GLY* 4.5 0.2 - - - -
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Residues in contact with ILE 354 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208T GLU 4.7 0.2 - - - -
209T ILE 3.6 7.0 - - - -
329T LEU* 4.6 5.6 - - + -
330T ILE* 3.8 39.7 - - + -
342T MET* 4.6 3.8 - - + -
349T HIS* 4.5 4.5 - - + +
350T TYR 4.4 2.7 - - - +
351T PRO* 3.8 18.2 - - + +
353T CYS* 1.4 80.3 - - - +
355T ASN* 1.4 63.7 + - - +
356T LEU* 3.9 25.8 - - + -
406T ILE* 4.6 0.4 - - - +
407T ARG* 3.5 8.1 - - - +
408T PHE* 2.9 44.9 + - + +
410T ILE* 3.9 26.7 - - + -
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Residues in contact with ASN 355 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208T GLU* 3.8 16.8 + - - +
209T ILE* 3.3 46.4 + - - +
342T MET* 3.6 14.3 - - - +
343T ASN* 3.0 42.4 + - - +
354T ILE* 1.4 74.0 - - - +
356T LEU* 1.3 75.7 + - - +
357T SER* 3.9 3.1 - - - -
395T ILE* 5.2 0.2 - - - +
405T SER* 5.8 1.8 - - - -
406T ILE* 2.9 31.0 + - - +
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Residues in contact with LEU 356 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330T ILE* 4.1 12.6 - - + -
333T ILE* 4.0 24.5 - - + -
334T MET* 3.7 24.7 - - + -
337T LEU* 5.0 0.7 - - + -
340T VAL* 4.0 14.4 - - + -
341T VAL 2.9 21.0 - - - +
342T MET* 4.1 1.3 - - - +
343T ASN* 3.2 14.0 + - - +
354T ILE* 3.9 20.9 - - + -
355T ASN* 1.3 81.4 + - - +
357T SER* 1.3 69.1 + - - +
358T PHE* 4.7 0.9 - - + -
373T VAL* 3.8 36.1 - - + -
406T ILE* 3.5 10.5 - - + +
408T PHE* 5.2 8.1 - - + -
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Residues in contact with SER 357 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341T VAL* 3.1 18.1 + - - +
343T ASN* 3.9 11.3 + - - -
355T ASN* 3.9 11.7 - - - -
356T LEU* 1.3 85.5 - - - +
358T PHE* 1.4 62.5 + - - +
359T ALA* 3.6 24.9 + - - +
360T TYR* 4.3 8.3 - - - -
401T LEU* 4.3 7.6 - - - +
404T SER 4.4 0.9 + - - -
405T SER* 5.1 1.5 - - - -
406T ILE* 4.1 18.6 + - - +
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Residues in contact with PHE 358 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337T LEU* 4.1 24.7 - - + -
338T PRO* 3.4 33.2 - - + -
339T ASP* 4.2 11.0 - - + -
340T VAL* 3.7 35.2 - - + +
356T LEU* 4.7 2.0 - - + -
357T SER* 1.4 74.3 + - - +
359T ALA* 1.3 64.0 - - - +
360T TYR* 3.8 7.9 - - - -
369T ALA* 3.2 47.9 - - + +
372T ASP* 3.7 23.6 - - + -
373T VAL* 4.1 14.6 - - + -
406T ILE* 3.6 8.3 - - - +
430T VAL* 6.0 1.1 - - + -
433T LEU* 5.4 8.5 - - + -
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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