Contacts of the helix formed by residues 306 - 319 (chain B) in PDB entry 4XZC
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 306 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B TYR* 3.1 15.5 + - + +
127B GLN* 5.7 0.9 - - - +
130B ALA* 3.6 19.3 - - + +
133B TRP* 6.1 0.2 - - - -
134B ARG* 2.4 41.9 + - - -
304B GLN 3.4 2.9 + - - +
305B ILE* 1.3 70.1 - - - +
307B SER* 1.3 57.0 + - - +
308B ILE* 3.8 7.3 + - - +
309B PHE* 2.7 42.0 + - + +
310B SER 2.9 11.3 + - - -
466B HIS 5.3 1.4 - - - +
468B GLN 5.0 3.2 - - - +
469B ASN* 3.2 26.0 + - - +
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Residues in contact with SER 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B ILE* 3.5 8.8 + - - -
306B ASP* 1.3 70.6 + - - +
308B ILE* 1.3 64.8 + - - +
310B SER* 4.0 1.2 - - - -
311B SER* 3.0 27.9 + - - -
388B GLU* 2.5 31.7 + - - +
392B CYS* 3.6 8.9 - - - -
412B LYS* 4.1 9.0 - - - +
466B HIS* 3.4 44.6 + - - -
467B PHE* 5.3 0.2 - - - -
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Residues in contact with ILE 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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83B ALA* 3.8 17.5 - - + -
133B TRP* 3.9 19.6 - - + -
134B ARG* 3.8 6.5 - - - +
139B PHE* 3.6 43.5 - - + -
306B ASP* 3.8 12.3 + - - +
307B SER* 1.3 80.6 - - - +
309B PHE* 1.3 66.1 + - - +
312B TYR* 3.3 39.1 + - + -
392B CYS* 3.6 11.6 - - - -
393B PHE* 3.8 15.5 - - + -
466B HIS 5.0 0.2 + - - -
467B PHE* 3.9 14.8 - - + +
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Residues in contact with PHE 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B TRP* 4.3 3.4 - + - -
96B PHE* 3.7 23.5 - + - -
106B TRP* 4.0 13.2 - + - -
126B TYR* 3.4 47.3 - + - -
129B ALA* 3.9 12.6 - - + -
130B ALA* 3.5 29.4 - - + -
133B TRP* 3.6 40.4 - + + -
306B ASP* 2.7 33.3 + - - +
308B ILE* 1.3 74.5 - - + +
310B SER* 1.3 66.2 + - - +
311B SER 3.0 1.2 + - - -
312B TYR* 3.2 3.8 + - - +
313B TYR* 2.9 27.0 + - + +
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Residues in contact with SER 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B TYR* 2.5 30.6 + - - -
305B ILE* 3.4 11.8 - - - +
306B ASP 2.9 8.2 + - - -
307B SER 4.3 0.9 - - - -
309B PHE* 1.3 76.1 - - - +
311B SER* 1.3 57.8 + - - +
313B TYR* 3.6 8.9 - - - +
314B TRP* 2.8 66.6 + - - -
378B PRO 3.1 11.9 + - - -
379B GLY* 4.9 1.1 - - - -
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Residues in contact with SER 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B SER 3.0 21.8 + - - -
308B ILE 3.7 4.9 - - - -
309B PHE 3.0 0.6 - - - -
310B SER* 1.3 78.8 - - - +
312B TYR* 1.3 53.0 + - - +
314B TRP* 3.1 10.6 + - - +
315B ALA* 2.7 34.5 + - - +
388B GLU* 3.5 8.0 + - - +
389B MET* 3.3 30.2 + - - +
392B CYS* 3.5 7.0 - - - -
393B PHE* 3.7 26.1 - - - -
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Residues in contact with TYR 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ALA 2.4 25.3 + - - -
88B MET* 3.1 32.3 + - + -
89B VAL* 3.4 22.9 + - + +
92B GLY 3.9 21.5 - - - +
93B LEU* 4.1 16.4 - - + +
96B PHE* 4.0 3.1 - - + -
133B TRP* 3.3 34.8 - + - +
308B ILE* 3.3 39.8 + - + +
309B PHE 3.2 3.2 + - - +
311B SER* 1.3 75.7 - - - +
313B TYR* 1.3 57.5 + - - +
315B ALA* 3.5 3.9 - - + +
316B TRP* 2.6 36.7 + - - +
325B PHE* 4.6 5.8 - + - -
393B PHE* 3.9 14.4 - + - -
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Residues in contact with TYR 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B PHE* 3.4 39.3 - + + -
103B ILE* 4.4 4.0 - - + -
106B TRP* 3.8 23.6 - + - -
107B ASP* 2.7 35.5 + - - -
110B TYR* 3.0 31.2 - + - -
309B PHE* 2.9 20.7 + + + +
310B SER* 3.6 6.5 - - - +
312B TYR* 1.3 75.1 - - - +
314B TRP* 1.3 62.7 + + - +
316B TRP* 3.5 13.8 - + - +
317B LYS* 2.7 45.4 + - + +
379B GLY* 3.3 31.9 - - - -
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Residues in contact with TRP 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B TYR* 3.9 6.1 - - - -
305B ILE* 4.6 5.8 - - + -
310B SER* 2.8 47.1 + - - +
311B SER 3.5 2.7 - - - +
313B TYR* 1.3 80.9 - + - +
315B ALA* 1.3 65.1 + - - +
317B LYS* 4.3 2.9 - - - -
318B ALA* 3.0 27.8 + - - +
360B ILE* 4.0 2.1 - - + +
363B LEU* 3.8 9.1 - - + +
378B PRO 3.7 15.9 - - - -
379B GLY 3.0 19.4 + - - -
380B VAL 3.6 21.3 - - - -
381B LEU* 3.3 52.1 - - + +
385B ARG* 4.0 15.7 - - + -
388B GLU* 4.0 23.6 - - + -
389B MET* 3.6 23.8 - - + -
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Residues in contact with ALA 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LEU* 3.8 15.7 - - + -
311B SER 2.7 20.9 + - - +
312B TYR* 3.5 10.5 - - + +
314B TRP* 1.3 74.5 - - - +
316B TRP* 1.3 66.2 + - - +
318B ALA* 3.2 7.6 + - - +
319B GLY 3.2 8.3 + - - -
320B ILE* 3.2 21.4 + - + +
325B PHE* 5.3 0.9 - - + -
328B LEU* 4.3 13.5 - - + -
360B ILE* 5.4 0.4 - - - -
389B MET* 4.7 5.6 - - + +
393B PHE* 4.3 13.7 - - + -
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Residues in contact with TRP 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LEU* 3.0 39.7 - - + +
96B PHE* 3.3 24.5 - - + +
97B ASP* 3.3 37.1 + - - -
100B LYS* 4.1 18.6 - - - -
103B ILE* 4.0 15.0 - - + -
107B ASP* 3.6 28.5 - - - -
312B TYR 2.6 21.3 + - - +
313B TYR* 3.5 21.3 - + - +
315B ALA* 1.3 71.5 - - - +
317B LYS* 1.3 85.3 + - + +
319B GLY* 3.0 16.6 + - - -
320B ILE 4.2 3.5 + - - +
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Residues in contact with LYS 317 (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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107B ASP* 3.8 23.3 + - - +
110B TYR* 3.7 32.1 - - + +
313B TYR* 2.7 44.1 + - + +
314B TRP* 3.9 4.5 - - - +
316B TRP* 1.3 86.2 - - + +
318B ALA* 1.3 58.4 + - - +
319B GLY* 3.6 0.7 + - - -
359B LYS* 5.0 6.8 + - - +
363B LEU* 3.4 35.2 - - + +
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Residues in contact with ALA 318 (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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314B TRP 3.0 18.3 + - - +
315B ALA 3.7 3.6 - - - +
316B TRP 3.1 0.4 - - - -
317B LYS* 1.3 77.1 - - - +
319B GLY* 1.3 57.7 + - - +
320B ILE* 3.7 7.9 - - + -
356B TRP* 3.6 11.3 - - - +
359B LYS* 3.1 32.4 - - - +
360B ILE* 3.5 36.8 - - + +
363B LEU* 4.1 7.6 - - + -
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Residues in contact with GLY 319 (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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315B ALA 3.2 0.4 + - - -
316B TRP 3.0 10.8 + - - -
317B LYS 3.4 1.0 - - - -
318B ALA* 1.3 80.1 - - - +
320B ILE* 1.3 67.4 + - - +
321B THR* 3.7 8.3 + - - +
324B THR* 4.1 6.1 - - - +
356B TRP* 4.8 4.0 - - - +
359B LYS* 4.6 11.0 - - - -
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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