Contacts of the helix formed by residues 307 - 314 (chain C) in PDB entry 4XQ2
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 PRO 307 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303C TYR* 3.7 2.8 - - - -
306C GLY* 1.3 85.3 - - - +
308C ALA* 1.3 65.9 + - - +
309C GLU* 4.4 11.9 - - + +
310C ARG* 3.2 36.8 + - + +
311C LEU 3.4 8.0 + - - -
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Residues in contact with ALA 308 (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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303C TYR* 4.5 8.7 - - + -
306C GLY 3.5 4.0 + - - -
307C PRO* 1.3 71.1 - - - +
309C GLU* 1.3 64.0 + - - +
311C LEU* 3.2 5.7 + - - +
312C LEU* 3.0 25.8 + - - +
333C CYS* 3.6 31.6 - - - -
336C LEU* 4.2 3.8 - - + -
354C GLU 4.0 11.9 - - - +
355C SER* 4.9 5.7 + - - +
357C ILE* 3.8 13.6 - - + +
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Residues in contact with GLU 309 (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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307C PRO* 3.2 9.5 - - + +
308C ALA* 1.3 77.0 + - - +
310C ARG* 1.3 80.8 + - + +
312C LEU* 3.1 21.7 + - + +
313C ASP* 3.3 16.5 + - - +
336C LEU* 3.6 29.5 - - + +
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Residues in contact with ARG 310 (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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307C PRO* 3.2 34.1 + - + +
309C GLU* 1.3 90.4 + - + +
311C LEU* 1.3 63.9 + - - +
313C ASP* 2.8 37.5 + - - +
314C ARG* 3.1 40.7 + - - +
381C THR* 5.3 14.4 - - - -
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Residues in contact with LEU 311 (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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301C PHE* 4.3 13.0 - - + -
303C TYR* 3.8 42.6 - - + -
307C PRO 3.4 3.2 + - - -
308C ALA 3.2 8.2 + - - +
310C ARG* 1.3 78.9 - - - +
312C LEU* 1.3 63.5 + - + +
314C ARG* 3.1 24.4 + - - +
315C PHE* 3.4 19.6 - - + -
357C ILE* 3.6 36.6 - - + -
376C ALA* 3.5 41.3 - - + +
377C LEU* 3.8 7.9 - - + +
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Residues in contact with LEU 312 (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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308C ALA 3.0 20.7 + - - +
309C GLU* 3.1 10.5 + - + +
311C LEU* 1.3 75.1 - - - +
313C ASP* 1.3 62.6 + - - +
314C ARG 3.2 0.7 + - - -
315C PHE* 3.4 17.1 + - + +
320C CYS* 4.5 21.2 - - + +
331C VAL* 3.7 36.3 - - + +
332C GLU* 4.3 12.8 - - - -
333C CYS* 4.0 22.7 - - + +
336C LEU* 4.2 14.8 - - + -
337C MSE 5.3 2.7 - - + -
357C ILE* 4.4 9.4 - - + -
37D ARG* 3.0 21.8 + - + -
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Residues in contact with ASP 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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309C GLU 3.3 8.4 + - - +
310C ARG* 2.8 38.2 + - - +
311C LEU 3.3 0.2 - - - -
312C LEU* 1.3 78.6 - - - +
314C ARG* 1.3 63.4 + - + +
315C PHE 3.3 3.3 + - - +
316C THR* 5.8 0.3 - - - +
37D ARG* 3.4 34.0 + - - +
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Residues in contact with ARG 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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303C TYR* 2.3 40.6 + - - -
305C GLY 5.5 0.6 + - - -
310C ARG* 3.1 33.9 + - - +
311C LEU* 3.1 17.7 + - - +
313C ASP* 1.3 78.4 - - + +
315C PHE* 1.3 62.1 + - - +
316C THR* 3.6 12.0 + - - +
372C ASP* 4.1 3.1 - - - +
375C ARG* 4.5 9.4 - - - +
376C ALA* 3.0 41.5 + - - +
377C LEU 5.0 0.2 + - - -
379C GLY* 3.2 39.0 + - - +
380C GLY* 3.6 5.7 - - - +
381C THR* 4.7 8.5 + - - +
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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