Contacts of the helix formed by residues 312 - 324 (chain B) in PDB entry 3FIE
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 312 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B GLU 4.1 1.6 + - - -
311B TYR* 1.3 71.3 - - - +
313B ILE* 1.3 61.7 + - - +
314B ASN* 3.4 11.6 + - - +
315B GLU* 3.2 51.0 + - + +
316B TYR* 3.2 30.6 + - + -
33D GLN* 5.3 0.4 + - - -
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Residues in contact with ILE 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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128B PHE* 3.6 9.6 - - + -
304B VAL* 3.9 33.7 - - + +
305B ASN* 3.7 28.7 - - - +
306B SER* 3.7 9.9 - - - +
307B ALA* 4.0 21.1 - - + +
311B TYR 3.3 5.5 + - - +
312B ASP* 1.3 73.0 + - - +
314B ASN* 1.3 65.6 + - - +
316B TYR 3.4 0.2 + - - -
317B LYS* 2.8 37.0 + - + +
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Residues in contact with ASN 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B ASP* 3.4 8.9 + - - +
313B ILE* 1.3 85.6 - - - +
315B GLU* 1.3 57.6 + - - +
317B LYS* 3.2 16.1 + - - +
318B ASP* 2.8 42.3 + - - +
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Residues in contact with GLU 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B ASP* 3.2 41.0 + - + +
313B ILE 3.2 0.2 - - - -
314B ASN* 1.3 78.9 - - - +
316B TYR* 1.3 63.6 + - + +
318B ASP* 3.2 11.8 + - - +
319B TYR* 2.9 26.2 + - - +
27D THR* 5.2 1.6 + - - -
28D SER 4.7 6.8 - - - +
29D ASN* 3.3 41.0 - - - +
30D ARG* 3.5 15.9 + - - +
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Residues in contact with TYR 316 (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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115B LYS* 3.9 25.8 + - - -
118B LEU* 3.9 18.8 - - + -
128B PHE* 3.6 24.5 - - + -
150B ILE* 4.0 5.2 - - + +
311B TYR* 3.5 30.7 - + + -
312B ASP* 3.2 26.4 + - + +
315B GLU* 1.3 83.1 - - + +
317B LYS* 1.3 65.0 + - - +
319B TYR* 3.5 6.9 - - + +
320B PHE* 3.0 42.5 + + + -
29D ASN* 4.1 27.0 - - + +
30D ARG 5.4 0.7 + - - -
33D GLN* 3.2 36.7 + - - +
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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
----------------------------------------------------------
128B PHE* 4.0 15.5 - - + -
301B LEU* 3.3 36.5 + - + +
302B SER 3.9 10.7 + - - -
304B VAL* 2.8 35.3 + - - -
313B ILE* 2.8 27.2 + - + +
314B ASN* 3.2 16.4 + - - +
316B TYR* 1.3 78.9 - - - +
318B ASP* 1.3 58.8 + - - +
320B PHE 3.3 0.7 + - - -
321B GLN* 2.9 29.7 + - - +
332B GLY 5.2 3.6 + - - -
334B TYR* 3.7 27.1 + - - +
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Residues in contact with ASP 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B ASN* 2.8 30.6 + - - +
315B GLU* 3.5 10.3 - - - +
317B LYS* 1.3 75.2 - - - +
319B TYR* 1.3 63.9 - - - +
321B GLN* 3.1 20.2 + - - +
322B TRP* 3.0 21.5 + - - +
328B LYS* 4.8 10.9 + - - -
334B TYR* 4.9 3.8 + - - -
27D THR* 3.8 20.7 + - + +
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Residues in contact with TYR 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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112B SER 4.5 0.7 + - - -
113B TYR* 2.7 38.7 + - - -
115B LYS* 3.7 26.7 - - + +
315B GLU 2.9 14.0 + - - +
316B TYR* 3.5 17.7 - + + +
318B ASP* 1.3 76.5 - - - +
320B PHE* 1.3 71.1 + + + +
322B TRP* 3.1 13.5 + + - +
323B LYS* 2.9 25.7 + - + -
26D LEU* 3.2 30.0 - - + +
27D THR* 3.2 35.6 + - - -
29D ASN* 3.1 29.4 - - - +
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Residues in contact with PHE 320 (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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115B LYS* 3.7 21.3 - - + -
116B PRO 3.5 19.7 - - - -
117B TYR* 3.6 34.5 - + + -
118B LEU* 3.7 30.1 - - + -
128B PHE* 4.0 15.7 - + - -
297B ILE* 5.9 0.2 - - + -
301B LEU* 4.2 15.7 - - + -
316B TYR* 3.0 35.9 + + - +
317B LYS 4.2 2.0 - - - +
319B TYR* 1.3 77.6 - + - +
321B GLN* 1.3 65.4 + - - +
323B LYS* 3.8 10.8 - - + -
324B TYR* 3.1 48.5 + + + +
326B LEU* 4.1 2.1 - - - +
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Residues in contact with GLN 321 (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 LEU* 4.2 1.1 - - - -
317B LYS 2.9 13.9 + - - +
318B ASP* 3.3 24.1 - - - +
320B PHE* 1.3 77.0 - - - +
322B TRP* 1.3 62.8 + - - +
325B GLY* 3.3 1.7 + - - -
326B LEU* 2.9 61.4 + - - +
327B ASP* 4.2 1.4 - - - +
328B LYS* 3.6 24.8 - - - +
334B TYR* 3.5 32.0 + - + -
340B LYS* 4.9 5.3 - - - +
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Residues in contact with TRP 322 (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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110B GLU* 4.7 4.9 - - - -
113B TYR* 3.5 40.4 - + + -
237B TYR* 3.5 24.2 - - - -
318B ASP 3.0 11.2 + - - +
319B TYR* 3.2 13.9 - + - +
321B GLN* 1.3 75.7 - - - +
323B LYS* 1.3 91.5 + - + +
325B GLY* 2.9 16.2 + - - -
344B ILE* 4.7 1.7 - - - +
347B LYS* 4.8 7.6 - - - -
25D ASN* 3.7 35.3 + - - +
26D LEU* 3.3 34.8 - - + -
27D THR* 4.0 14.8 - - + +
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Residues in contact with LYS 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B TYR 5.2 0.7 - - - +
114B ALA 4.7 2.5 - - - -
115B LYS 2.7 35.0 + - - +
116B PRO* 3.7 0.4 - - - +
117B TYR 3.9 0.2 - - - +
187B PHE 3.6 6.9 + - - -
236B LEU 2.8 28.9 + - - -
237B TYR* 3.3 48.0 + - + +
294B TYR* 4.8 0.2 - - - -
319B TYR* 2.9 15.4 + - + +
320B PHE* 4.0 9.2 - - + +
322B TRP* 1.3 97.2 - - + +
324B TYR* 1.3 100.0 + - + +
344B ILE* 3.4 11.8 - - - +
347B LYS* 5.4 0.3 + - - -
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Residues in contact with TYR 324 (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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117B TYR* 3.7 10.1 - + - +
186B GLY 2.8 29.7 + - - -
187B PHE* 3.2 8.1 + - - -
294B TYR* 3.5 45.6 - + + +
297B ILE* 3.5 31.9 - - + -
320B PHE* 3.1 43.2 + + + +
323B LYS* 1.3 116.0 + - + +
325B GLY* 1.3 65.5 + - - +
326B LEU* 3.3 25.1 - - + +
336B VAL* 4.9 2.1 - - - +
341B PHE* 5.1 2.9 - - - +
344B ILE* 3.6 11.1 - - - +
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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