Contacts of the strand formed by residues 417 - 423 (chain C) in PDB entry 3IXK
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 417 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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345C ARG 3.8 0.3 - - - +
346C ILE* 3.5 3.1 - - - -
347C THR* 3.1 41.3 + - + +
389C PHE* 3.6 2.5 - - - -
404C VAL* 3.5 5.2 - - - -
415C THR* 3.6 4.5 + - - +
416C ALA* 1.3 76.0 - - - +
418C VAL* 1.3 67.7 + - - +
419C GLU* 3.7 31.0 - - + +
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Residues in contact with VAL 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C SER 4.7 3.5 - - - +
237C TRP* 3.5 39.0 + - + -
344C PHE* 4.1 9.9 - - + -
345C ARG 3.3 10.3 - - - +
346C ILE* 4.3 6.3 - - + -
389C PHE* 3.6 27.4 - - + -
402C PHE 3.7 11.9 - - - +
403C ALA* 3.7 9.2 - - - +
404C VAL* 3.2 25.5 - - + +
417C ALA* 1.3 80.1 - - - +
419C GLU* 1.3 66.0 + - - +
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Residues in contact with GLU 419 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237C TRP* 4.4 2.9 - - - +
344C PHE* 3.3 5.9 - - - +
345C ARG* 2.4 90.6 + - + +
347C THR* 4.6 1.7 + - - -
417C ALA* 3.7 23.7 - - + +
418C VAL* 1.3 80.9 - - - +
420C GLY* 1.3 59.3 + - - +
422C PHE* 3.4 9.2 - - + -
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Residues in contact with GLY 420 (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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341A ASN* 4.7 6.6 - - - +
423A VAL* 5.4 0.5 - - - +
237C TRP* 3.2 25.6 - - - -
344C PHE* 4.2 3.1 - - - -
419C GLU* 1.3 76.6 - - - +
421C PRO* 1.3 76.3 - - - +
422C PHE* 3.7 7.9 - - - -
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Residues in contact with PRO 421 (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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339A VAL* 4.7 3.8 - - + -
340A THR 3.9 6.7 - - - +
341A ASN* 4.0 13.9 - - + +
342A GLN* 4.3 10.3 - - + -
421A PRO* 5.5 4.3 - - + -
422A PHE 4.5 6.7 - - - +
423A VAL* 3.9 29.6 - - + +
237C TRP* 3.3 15.2 - - + -
342C GLN* 3.8 22.9 - - + -
343C SER 3.6 4.9 - - - +
420C GLY* 1.3 87.3 - - - +
422C PHE* 1.3 66.8 + - - +
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Residues in contact with PHE 422 (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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421A PRO* 4.8 0.4 - - - +
334C TYR* 3.8 28.5 - + + -
342C GLN* 3.3 9.0 - - - +
343C SER* 2.7 46.0 + - - +
344C PHE* 4.0 7.0 - - - -
345C ARG* 3.8 35.9 - - + -
419C GLU* 3.4 26.5 - - + -
420C GLY* 3.7 12.1 - - - -
421C PRO* 1.3 78.0 - - - +
423C VAL* 1.3 65.4 + - - +
424C THR* 4.9 0.2 - - - +
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Residues in contact with VAL 423 (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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421A PRO* 3.6 37.9 - - + +
253C ARG* 5.7 2.9 + - - -
341C ASN* 3.3 13.0 - - + +
422C PHE* 1.3 73.9 - - - +
424C THR* 1.3 74.3 + - - +
425C LEU* 4.9 11.2 - - + +
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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