Contacts of the strand formed by residues 312 - 317 (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 PHE 312 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310C LYS 4.4 7.9 - - - -
311C GLY* 1.3 78.8 - - - +
313C ILE* 1.3 68.4 + - - +
314C ASN* 3.6 22.4 - - - +
338C GLU* 4.0 36.1 - - + -
339C ALA* 3.4 0.8 - - - -
340C PHE* 2.9 57.1 + + + +
371C ILE* 4.3 18.2 - - + -
396C ASN* 4.4 0.9 - - - +
399C VAL* 4.2 7.9 - - - +
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Residues in contact with ILE 313 (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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312C PHE* 1.3 81.1 - - - +
314C ASN* 1.3 71.5 + - - +
315C ILE* 4.2 5.6 + - + -
337C TYR* 4.2 13.7 - - + -
338C GLU 3.3 8.7 - - - +
339C ALA* 3.9 8.3 - - + -
343C PRO* 5.4 0.2 - - + -
394C VAL* 3.8 49.4 - - + +
395C SER* 3.9 3.1 - - - -
396C ASN* 3.6 35.7 - - + +
399C VAL* 4.0 15.8 - - + +
401C ALA* 3.8 22.0 - - + +
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Residues in contact with ASN 314 (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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312C PHE* 3.6 22.7 - - - +
313C ILE* 1.3 81.6 + - - +
315C ILE* 1.3 61.4 + - - +
316C PHE* 3.2 19.6 - - + -
337C TYR* 3.2 4.6 - - - -
338C GLU* 2.8 59.7 + - + +
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Residues in contact with ILE 315 (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* 4.1 10.7 + - + -
314C ASN* 1.3 73.8 - - - +
316C PHE* 1.3 67.6 + - - +
317C PRO* 3.8 6.4 - - - +
335C VAL* 3.9 20.6 - - + -
337C TYR* 3.7 15.3 - - + -
392C PHE* 4.0 12.6 - - + -
394C VAL* 3.9 21.8 - - + -
401C ALA* 4.1 9.9 - - + -
402C ALA* 3.9 28.9 - - - +
403C ILE* 3.7 32.5 - - + +
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Residues in contact with PHE 316 (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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314C ASN* 3.2 33.4 - - + -
315C ILE* 1.3 78.1 - - - +
317C PRO* 1.3 67.9 - - + +
318C MET* 3.5 16.4 + - + +
335C VAL* 3.4 2.8 - - - -
336C GLU 2.7 50.8 + - - +
338C GLU* 3.8 17.3 - - + -
372C ARG* 3.9 31.2 - - - -
55H SER* 6.2 0.2 - - - -
57H TYR* 4.6 7.6 - - + +
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Residues in contact with PRO 317 (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 3.8 3.8 - - - +
316C PHE* 1.3 85.8 - - + +
318C MET* 1.3 61.8 + - - +
319C ILE 3.3 17.9 - - - +
321C THR* 3.9 20.0 - - + -
334C ILE 3.8 6.3 - - - +
335C VAL* 4.2 4.3 - - + -
403C ILE* 3.8 23.5 - - + -
405C PHE* 4.1 5.4 - - + -
54H TYR* 3.9 22.7 - - + +
55H SER* 3.7 14.4 - - - -
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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