Contacts of the helix formed by residues 356 - 364 (chain C) in PDB entry 1XSK
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 VAL 356 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317C ASP* 4.1 22.2 - - + +
319C GLU* 5.7 4.3 - - - +
350C ILE* 4.1 3.6 - - + -
354C SER* 3.0 12.2 + - - +
355C PRO* 1.3 81.1 - - + +
357C PHE* 1.3 66.0 + - - +
359C GLU* 2.7 27.1 + - - +
360C LEU* 3.0 20.1 + - + -
397C TRP* 3.2 40.8 - - + -
401C LYS* 5.2 4.7 - - - -
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Residues in contact with PHE 357 (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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350C ILE* 3.7 22.9 - - + +
351C GLY 3.6 10.8 - - - +
352C GLN* 3.4 37.2 - - + +
354C SER 3.0 15.4 + - - +
356C VAL* 1.3 75.9 - - - +
358C LYS* 1.3 61.0 + - - +
360C LEU* 3.1 7.6 + - - +
361C GLN* 2.9 49.1 + - + -
366C LEU* 4.3 3.4 - - + +
374C LEU* 3.6 23.6 - - + -
376C GLN* 3.5 21.3 - - - -
383C GLY 3.5 19.5 - - - -
385C ALA* 3.6 16.8 - - + -
73D GLN* 4.6 9.2 - - + -
74D GLY 5.0 0.2 - - - -
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Residues in contact with LYS 358 (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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354C SER 4.4 0.6 + - - -
355C PRO 4.0 9.1 + - - +
356C VAL 3.2 0.8 - - - -
357C PHE* 1.3 81.1 - - + +
359C GLU* 1.3 60.0 + - - +
361C GLN* 3.8 16.7 - - - +
362C GLU* 3.2 47.5 + - + +
73D GLN* 5.8 3.8 - - - +
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Residues in contact with GLU 359 (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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355C PRO 4.2 2.4 + - - +
356C VAL* 2.7 29.6 + - - +
358C LYS* 1.3 72.5 - - - +
360C LEU* 1.3 62.9 + - - +
362C GLU* 3.9 5.5 - - - +
363C LYS* 3.0 54.9 + - + +
397C TRP* 2.9 37.1 + - - +
401C LYS* 5.5 1.0 + - - -
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Residues in contact with LEU 360 (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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350C ILE* 3.6 27.6 - - + -
356C VAL* 3.0 16.3 + - + +
357C PHE 3.5 5.6 - - - +
359C GLU* 1.3 76.6 - - + +
361C GLN* 1.3 60.5 + - - +
363C LYS* 3.3 3.1 + - - +
364C GLY 2.9 23.0 + - - -
365C TYR* 3.0 33.4 + - + -
366C LEU* 3.8 25.5 + - + -
387C TYR* 3.3 30.3 - - + +
397C TRP* 3.7 38.8 - - + +
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Residues in contact with GLN 361 (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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357C PHE* 2.9 34.1 + - + +
358C LYS* 3.8 13.8 - - - +
360C LEU* 1.3 76.2 - - - +
362C GLU* 1.3 61.9 + - + +
364C GLY* 2.8 23.0 + - - -
366C LEU* 4.1 6.9 - - - +
368C LYS* 5.8 0.5 - - - -
374C LEU* 3.7 30.2 - - + +
73D GLN* 3.1 28.8 + - - +
74D GLY* 3.8 10.2 - - - +
75D ALA 5.0 1.0 - - - +
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Residues in contact with GLU 362 (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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358C LYS* 3.2 49.5 + - + +
359C GLU* 3.9 5.6 - - - +
360C LEU 3.5 0.2 - - - -
361C GLN* 1.3 80.7 - - + +
363C LYS* 1.3 62.3 + - + +
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Residues in contact with LYS 363 (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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359C GLU* 3.0 52.4 + - + +
360C LEU 3.9 2.0 - - - +
361C GLN 3.0 1.2 - - - -
362C GLU* 1.3 79.5 - - + +
364C GLY* 1.3 61.7 + - - +
365C TYR* 3.5 50.6 + - + +
391C ASN* 5.2 0.9 + - - -
397C TRP* 4.6 7.5 - - - +
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Residues in contact with GLY 364 (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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360C LEU 2.9 0.4 + - - -
361C GLN* 2.8 15.0 + - - -
362C GLU 3.4 0.4 + - - -
363C LYS* 1.3 80.0 - - - +
365C TYR* 1.3 62.2 + - - +
366C LEU 3.3 9.3 + - - +
368C LYS* 4.1 27.7 - - - -
374C LEU* 6.4 1.1 - - - -
388C ASP* 5.2 1.7 - - - +
391C ASN* 3.2 18.6 + - - -
428C PHE* 5.2 1.2 - - - -
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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