Contacts of the strand formed by residues 388 - 395 (chain C) in PDB entry 4K94
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 GLY 388 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350C TYR* 4.3 2.0 - - - -
351C MET* 5.2 0.2 - - - -
387C GLY* 1.3 75.0 - - - -
389C THR* 1.3 63.6 + - - -
390C TYR* 3.5 9.9 - - - -
405C PHE 3.5 0.3 - - - +
406C ASN* 3.6 2.9 - - - -
407C VAL 2.7 34.1 + - - -
469C PHE* 4.2 7.4 - - - -
470C GLY* 3.5 18.3 - - - -
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Residues in contact with THR 389 (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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349C ILE 3.9 5.0 - - - +
350C TYR* 3.5 18.2 - - - -
351C MET* 4.7 8.6 + - - +
388C GLY* 1.3 70.1 - - - -
390C TYR* 1.3 62.1 + - - +
391C THR* 3.7 12.0 + - - +
404C ALA* 3.6 30.5 - - + -
405C PHE 3.3 6.7 - - - +
406C ASN* 3.3 17.1 + - - +
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Residues in contact with TYR 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333C LEU* 3.6 19.7 - - + -
348C TRP* 4.5 3.3 - - + -
349C ILE 3.5 5.8 - - - +
350C TYR* 3.5 46.1 - + + -
355C PHE* 4.0 8.7 - + - -
377C LEU* 3.8 21.3 - - + -
379C LEU* 3.8 27.7 - - + +
382C LEU* 4.3 2.8 - - - +
386C GLU* 2.6 34.7 + - - +
388C GLY 3.5 15.5 - - - -
389C THR* 1.3 74.1 - - - +
391C THR* 1.3 60.9 + - - +
403C ILE 3.9 0.9 - - - +
405C PHE* 2.8 40.8 + - - +
407C VAL* 3.7 22.9 - - + -
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Residues in contact with THR 391 (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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347C GLN 3.8 0.3 - - - +
348C TRP* 3.4 8.2 - - - -
349C ILE* 2.8 48.7 + - - +
389C THR* 3.7 18.4 + - - +
390C TYR* 1.3 74.7 - - - +
392C PHE* 1.3 72.2 + - - +
393C LEU* 4.0 10.5 + - + -
402C ALA* 4.0 16.4 - - + -
403C ILE 3.4 13.9 - - - +
404C ALA* 4.1 5.1 - - + +
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Residues in contact with PHE 392 (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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315C ILE* 4.0 14.6 - - + -
335C VAL* 4.0 13.2 - - + -
337C TYR* 3.8 22.4 - + - -
346C GLN* 4.2 16.8 - - + -
347C GLN 3.7 4.3 - - - -
348C TRP* 3.3 45.5 - + + -
359C TRP* 5.0 0.4 - + - -
375C SER* 3.3 29.8 - - - -
390C TYR 4.1 0.2 + - - -
391C THR* 1.3 74.1 - - - +
393C LEU* 1.3 67.3 + - - +
394C VAL* 3.8 30.5 - - + -
402C ALA* 3.1 6.8 - - - +
403C ILE* 2.9 43.1 + - + -
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Residues in contact with LEU 393 (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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345C HIS 3.8 1.9 - - - +
346C GLN* 3.5 3.1 - - - -
347C GLN* 2.9 52.8 + - + +
349C ILE* 3.5 30.3 - - + -
391C THR* 4.3 10.1 - - + -
392C PHE* 1.3 77.3 - - - +
394C VAL* 1.3 63.6 + - - +
401C ALA 3.6 3.4 - - - +
402C ALA* 3.3 27.1 - - + -
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Residues in contact with VAL 394 (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 ILE* 3.8 28.9 - - + +
315C ILE* 3.9 8.3 - - + -
337C TYR* 4.0 13.2 - - + -
343C PRO* 3.6 29.4 - - + -
344C GLU 4.3 4.7 - - - +
345C HIS 4.8 0.9 - - - -
346C GLN* 4.0 11.7 - - + -
392C PHE* 3.8 23.1 - - + -
393C LEU* 1.3 75.8 - - - +
395C SER* 1.3 66.2 + - - +
400C ASN* 3.7 0.3 - - - +
401C ALA 2.8 41.8 + - - +
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Residues in contact with SER 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C ILE* 3.9 4.9 - - - -
343C PRO* 4.3 0.9 - - - -
344C GLU* 2.5 49.0 + - - +
345C HIS* 4.2 16.5 + - - +
394C VAL* 1.3 79.0 - - - +
396C ASN* 1.3 60.8 + - - +
399C VAL 3.1 13.7 - - - -
400C ASN* 3.5 19.5 - - - -
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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