Contacts of the helix formed by residues 309 - 322 (chain B) in PDB entry 4FGU
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 309 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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305B THR* 4.2 8.3 - - - +
306B PRO* 3.1 38.9 + - + +
308B PRO* 1.3 77.9 - - - +
310B VAL* 1.3 59.3 + - - +
311B PRO* 3.4 2.7 - - - -
312B LEU* 3.1 7.1 + - + +
313B THR* 2.9 34.3 + - + +
342B ARG* 3.0 30.0 + - - +
403B ARG* 3.5 18.2 + - - -
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Residues in contact with VAL 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B TYR* 4.3 6.1 - - + +
44B ARG* 3.5 24.5 - - - +
218B ALA* 3.8 14.8 - - + -
228B TYR* 3.6 20.0 - - + -
305B THR* 3.7 16.4 - - + -
306B PRO 3.3 15.6 + - - +
307B SER* 3.5 18.4 - - - +
309B ASP* 1.3 76.6 - - - +
311B PRO* 1.3 72.0 - - + +
312B LEU 3.1 0.7 + - - -
313B THR* 3.2 17.2 + - - -
314B ILE* 3.2 24.6 + - + +
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Residues in contact with PRO 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B TYR* 4.5 26.7 - - + -
44B ARG* 5.6 1.3 - - - +
307B SER 4.1 3.4 - - - +
308B PRO 3.9 16.2 - - - +
309B ASP 3.5 1.6 - - - -
310B VAL* 1.3 98.1 - - + +
312B LEU* 1.3 66.1 + - + +
314B ILE* 3.9 2.8 + - - +
315B MET* 3.4 35.5 + - + +
338B HIS* 5.1 13.7 - - + +
396B PRO 5.8 1.6 - - - +
399B GLU* 4.5 23.6 - - + +
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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
----------------------------------------------------------
309B ASP* 3.1 9.4 + - + +
311B PRO* 1.3 82.6 - - + +
313B THR* 1.3 59.9 + - + +
314B ILE 3.2 1.8 - - - -
315B MET* 3.1 6.8 + - - +
316B LYS* 2.8 49.9 + - + +
335B ILE* 4.0 18.6 - - + +
338B HIS* 3.8 27.8 - - + -
339B LEU* 3.7 34.5 - - + -
342B ARG* 3.6 40.6 - - - +
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Residues in contact with THR 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B TYR* 5.4 0.6 - - - -
228B TYR* 3.6 20.3 - - - -
305B THR* 3.4 23.0 + - - +
309B ASP* 2.9 20.6 + - + +
310B VAL* 3.2 17.3 + - - -
312B LEU* 1.3 75.3 - - + +
314B ILE* 1.3 57.2 + - - +
316B LYS* 3.9 15.6 - - + +
317B ARG* 3.1 29.8 + - - +
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Residues in contact with ILE 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B TYR* 3.5 36.1 - - + +
221B TYR* 3.9 15.0 - - + +
226B SER 3.4 18.8 - - - +
227B THR* 4.0 20.6 - - + -
228B TYR* 3.8 21.5 - - + -
310B VAL* 3.2 30.8 + - + +
311B PRO 4.0 4.5 - - - +
312B LEU 3.2 0.6 - - - -
313B THR* 1.3 76.1 - - - +
315B MET* 1.3 58.3 + - + +
317B ARG* 3.4 2.4 + - - +
318B LYS* 2.9 44.7 + - + +
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Residues in contact with MET 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B TYR* 3.2 38.6 - - + +
311B PRO* 3.4 18.3 + - + +
312B LEU* 3.1 9.2 + - - +
314B ILE* 1.3 75.0 - - + +
316B LYS* 1.3 60.5 + - - +
318B LYS* 4.0 6.4 - - + +
319B LEU* 3.1 31.5 + - - +
331B LEU* 4.4 10.6 - - + +
334B GLU* 3.5 28.0 - - - +
335B ILE* 3.2 38.3 - - + +
338B HIS* 3.7 32.1 - - + +
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Residues in contact with LYS 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B LEU* 2.8 45.6 + - + +
313B THR* 3.9 15.3 - - + +
315B MET* 1.3 72.4 - - + +
317B ARG* 1.3 61.4 + - - +
319B LEU* 3.4 11.3 + - + +
320B MET* 3.4 19.8 + - - +
335B ILE* 5.4 11.4 - - + -
339B LEU* 5.3 7.6 - - - +
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Residues in contact with ARG 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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221B TYR* 3.4 42.6 - - + +
223B GLU* 2.7 44.1 + - - +
303B ASP* 5.4 3.8 + - - -
313B THR 3.1 18.7 + - - +
314B ILE 3.7 2.9 - - - +
316B LYS* 1.3 75.1 - - - +
318B LYS* 1.3 67.6 + - + +
320B MET* 3.1 23.7 + - - +
321B ASN* 2.8 43.9 + - - +
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Residues in contact with LYS 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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41B TYR* 5.7 4.3 + - + +
221B TYR* 4.1 11.0 - - - +
226B SER* 3.7 30.6 + - - +
314B ILE* 2.9 38.1 + - + +
315B MET* 4.1 3.6 - - + +
317B ARG* 1.3 77.5 - - + +
319B LEU* 1.3 60.1 + - - +
321B ASN* 3.3 8.3 + - - +
322B THR* 2.9 31.7 + - - +
327B GLU* 5.3 8.2 + - - +
331B LEU* 3.9 26.6 - - + +
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Residues in contact with LEU 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 MET 3.1 18.9 + - - +
316B LYS* 3.5 9.2 - - + +
317B ARG 3.2 0.2 - - - -
318B LYS* 1.3 76.6 - - - +
320B MET* 1.3 58.3 + - - +
322B THR* 3.2 22.7 - - - +
328B SER* 4.5 17.1 + - - +
331B LEU* 3.8 15.9 - - + +
332B THR* 3.7 29.6 - - + +
335B ILE* 4.1 26.7 - - + -
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Residues in contact with MET 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B LYS 3.4 8.2 + - - +
317B ARG* 3.1 17.8 + - - +
319B LEU* 1.3 79.8 - - - +
321B ASN* 1.3 72.2 + - - +
322B THR 3.6 2.4 + - - +
323B ASN* 4.6 5.9 - - - +
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Residues in contact with ASN 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B ARG* 2.8 52.7 + - - +
318B LYS* 3.9 7.8 + - - +
319B LEU 3.3 0.6 - - - -
320B MET* 1.3 89.9 + - - +
322B THR* 1.3 58.8 + - - +
323B ASN* 4.2 2.5 + - - +
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Residues in contact with THR 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B LYS* 2.9 19.2 + - - +
319B LEU* 3.2 14.9 - - - +
320B MET 3.4 1.1 - - - +
321B ASN* 1.3 79.5 - - - +
323B ASN* 1.3 69.9 + - - +
324B ASP* 3.7 12.6 - - + +
327B GLU* 3.5 48.6 + - + +
328B SER* 3.5 14.3 + - - -
331B LEU* 4.8 2.6 - - - +
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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