Contacts of the helix formed by residues 351 - 361 (chain C) in PDB entry 4X4R
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 ASP 351 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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347C PRO* 4.2 5.3 - - - +
348C GLN* 3.6 20.3 + - - +
349C PHE 3.8 0.4 - - - -
350C GLU* 1.3 74.0 - - + +
352C GLU* 1.3 63.8 + - - +
353C ARG* 3.2 6.4 + - + +
354C ASN* 2.9 39.0 + - - +
355C VAL* 3.4 12.0 - - - +
2H G 4.5 17.5 + - - +
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Residues in contact with GLU 352 (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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193A ARG* 5.4 2.9 - - - +
194A ARG* 4.0 20.6 + - - +
243A ARG* 3.4 31.6 + - - +
350C GLU 2.9 5.2 + - - +
351C ASP* 1.3 68.6 - - - +
353C ARG* 1.3 63.5 + - + +
354C ASN 3.2 0.2 - - - -
355C VAL* 3.7 3.3 - - - +
356C LYS* 2.8 33.7 + - - +
504C TAR 3.1 45.2 - - - +
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Residues in contact with ARG 353 (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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351C ASP* 3.2 3.7 + - + -
352C GLU* 1.3 85.8 - - + +
354C ASN* 1.3 66.1 + - - +
356C LYS* 3.7 6.5 + - - +
357C LYS* 3.4 48.2 + - - +
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Residues in contact with ASN 354 (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 PRO* 3.8 7.2 - - + -
351C ASP* 2.9 27.4 + - - +
352C GLU 3.2 0.4 - - - -
353C ARG* 1.3 81.5 - - - +
355C VAL* 1.3 59.4 + - - +
356C LYS 3.2 0.4 - - - -
357C LYS* 3.3 8.7 + - - -
358C PHE* 2.9 28.8 + - - +
15D C 3.1 43.2 + - - +
16D G 4.4 5.9 + - - +
2H G 2.9 22.2 + - - +
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Residues in contact with VAL 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A HIS* 4.9 0.2 - - - +
347C PRO* 3.8 14.6 - - + -
348C GLN 3.5 21.1 - - - +
349C PHE 4.1 9.2 - - - +
351C ASP 3.4 17.3 - - - +
352C GLU* 3.3 2.6 + - - +
354C ASN* 1.3 76.9 - - - +
356C LYS* 1.3 58.2 + - - +
358C PHE* 3.2 2.3 + - + +
359C LEU* 2.9 48.5 + - + +
374C TRP* 3.5 31.4 - - + +
504C TAR 3.6 20.4 - - - +
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Residues in contact with LYS 356 (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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247A GLU* 3.3 33.4 + - - -
352C GLU* 2.8 19.4 + - - +
353C ARG* 3.8 7.0 - - - +
355C VAL* 1.3 77.8 - - - +
357C LYS* 1.3 61.3 + - + +
359C LEU* 4.1 2.1 - - - +
360C SER* 3.2 23.4 + - - -
504C TAR 3.3 43.3 + - - +
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Residues in contact with LYS 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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353C ARG* 3.4 46.2 + - - +
354C ASN* 3.3 16.8 + - - +
356C LYS* 1.3 77.1 - - + +
358C PHE* 1.3 62.1 + - - +
360C SER* 2.5 24.6 + - - -
361C ARG* 3.7 4.5 + - - +
15D C 3.4 40.0 + - - +
16D G 5.2 6.1 - - - +
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Residues in contact with PHE 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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344C ARG* 4.0 9.2 - - + -
345C MET 3.8 7.2 - - - -
346C GLY* 3.7 27.6 - - - -
347C PRO* 3.8 15.3 - - + -
354C ASN 2.9 17.3 + - - +
355C VAL 3.5 4.7 - - - +
357C LYS* 1.3 78.3 - - - +
359C LEU* 1.3 68.1 + - + +
360C SER 3.1 1.3 + - - -
361C ARG* 3.4 7.4 + - - +
363C ARG* 2.3 41.8 + - - -
367C PRO* 4.6 3.6 - - + -
374C TRP* 4.1 11.2 - + + -
375C TRP 4.1 9.6 - - - -
376C ALA* 3.5 31.2 - - + -
15D C 3.5 48.2 + + - +
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Residues in contact with LEU 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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240A HIS* 3.5 33.7 - - + +
355C VAL* 2.9 33.4 + - + +
356C LYS* 4.4 2.7 - - - +
358C PHE* 1.3 82.8 - - + +
360C SER* 1.3 60.9 + - - +
361C ARG 3.3 6.2 - - - +
363C ARG* 4.2 2.2 - - - +
367C PRO* 3.3 36.9 - - + +
374C TRP* 3.7 22.2 - - + -
504C TAR 4.1 6.3 - - - +
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Residues in contact with SER 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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356C LYS* 3.2 14.8 + - - -
357C LYS* 2.5 26.5 + - - -
359C LEU* 1.3 78.8 - - - +
361C ARG* 1.3 66.1 + - - +
362C ASN* 3.3 12.5 + - - +
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Residues in contact with ARG 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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344C ARG* 4.5 1.6 - - - +
357C LYS 4.2 8.3 - - - +
358C PHE 3.4 6.5 + - - +
359C LEU 3.3 6.5 - - - +
360C SER* 1.3 82.9 + - - +
362C ASN* 1.3 66.3 + - - +
363C ARG* 3.1 34.8 + - + +
378C GLU* 3.4 24.7 + - - -
14D U 3.3 30.1 + - - -
15D C 3.4 38.6 + - - +
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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