Contacts of the helix formed by residues 307 - 315 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B TYR* 4.0 3.5 - - - -
306B GLY* 1.3 83.8 - - - +
308B ALA* 1.3 65.4 + - - +
309B GLU* 4.0 25.8 - - + +
310B ARG* 3.2 44.7 + - + +
311B LEU 3.4 7.1 + - - -
314B ARG* 5.0 1.0 + - - +
355B SER* 5.3 0.7 - - - +
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Residues in contact with ALA 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B TYR* 4.4 3.8 - - - -
306B GLY 3.4 4.5 + - - -
307B PRO* 1.3 71.6 - - - +
309B GLU* 1.3 63.7 + - - +
311B LEU* 3.0 10.4 + - - +
312B LEU* 3.0 26.7 + - - +
333B CYS* 3.6 32.5 - - + -
336B LEU* 4.4 3.4 - - + -
354B GLU 3.8 11.0 - - - +
355B SER* 4.4 8.4 + - - +
357B ILE* 4.1 14.4 - - + -
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Residues in contact with GLU 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B PRO* 4.0 15.3 - - + +
308B ALA* 1.3 80.3 - - - +
310B ARG* 1.3 91.5 + - - +
312B LEU* 3.5 16.0 + - - +
313B ASP* 3.5 17.8 - - - +
336B LEU* 4.0 24.2 - - + +
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Residues in contact with ARG 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B PRO* 3.2 33.7 + - + +
309B GLU* 1.3 95.6 + - - +
311B LEU* 1.3 66.2 + - - +
313B ASP* 3.3 17.2 + - - +
314B ARG* 3.3 35.5 + - - +
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Residues in contact with LEU 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B PHE* 4.7 1.3 - - + -
303B TYR* 3.5 55.0 - - + +
307B PRO 3.4 2.2 + - - -
308B ALA 3.0 8.8 + - - +
310B ARG* 1.3 78.4 - - - +
312B LEU* 1.3 65.1 + - + +
314B ARG* 3.0 25.3 + - - +
315B PHE* 3.3 22.3 - - + -
357B ILE* 3.7 26.7 - - + -
376B ALA* 3.3 38.4 - - + +
377B LEU* 3.9 12.1 - - + +
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Residues in contact with LEU 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ARG* 3.3 15.3 + - + -
308B ALA 3.0 15.5 + - - +
309B GLU* 3.6 10.5 - - - +
310B ARG 3.3 0.4 - - - -
311B LEU* 1.3 77.3 - - - +
313B ASP* 1.3 60.6 + - - +
315B PHE* 3.2 20.7 - - + -
320B CYS* 4.1 18.3 - - - +
331B VAL* 3.9 27.6 - - + -
332B GLU 4.3 0.7 - - - -
333B CYS* 4.0 21.8 - - + +
336B LEU* 4.0 23.6 - - + -
337B MSE 3.9 28.9 - - + -
357B ILE* 4.6 8.7 - - + -
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Residues in contact with ASP 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ARG* 3.2 39.0 + - - +
309B GLU* 3.5 18.1 - - - +
310B ARG* 3.3 9.5 + - - +
311B LEU 3.2 1.0 - - - -
312B LEU* 1.3 74.9 - - - +
314B ARG* 1.3 64.8 + - + +
315B PHE 3.2 6.3 + - - +
316B THR* 5.3 1.6 - - - +
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Residues in contact with ARG 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B TYR* 3.4 22.4 + - - -
305B GLY 5.5 2.6 + - - -
306B GLY* 6.1 1.0 - - - -
307B PRO* 5.0 1.8 + - - +
310B ARG* 3.3 45.2 + - - +
311B LEU* 3.0 15.7 + - - +
313B ASP* 1.3 76.1 - - + +
315B PHE* 1.3 64.1 + - - +
316B THR* 3.3 12.1 + - - +
372B ASP* 4.2 2.4 - - - +
375B ARG* 5.2 3.4 + - - +
376B ALA* 3.3 40.8 + - - +
377B LEU 4.0 3.4 + - - -
378B ALA 4.7 0.2 - - - -
379B GLY* 3.7 25.8 - - - -
380B GLY 5.2 0.7 - - - +
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Residues in contact with PHE 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ARG* 2.9 25.6 + - - +
311B LEU* 3.3 32.1 - - + -
312B LEU* 3.2 29.4 - - + +
313B ASP 3.2 3.5 - - - +
314B ARG* 1.3 77.5 - - - +
316B THR* 1.3 62.0 + - - +
317B LEU 3.5 0.4 - - - -
318B PHE* 3.7 46.9 - + + +
331B VAL* 3.8 31.0 - - + -
357B ILE* 5.2 1.8 - - + -
359B LEU* 4.9 2.7 - - + -
372B ASP* 3.6 11.4 - - - +
373B LEU* 4.0 25.1 - - + -
376B ALA* 3.9 20.4 - - + -
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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