Contacts of the helix formed by residues 314 - 321 (chain B) in PDB entry 3IFS
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 LEU 314 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A LYS* 4.2 23.6 - - + +
290A GLY* 4.5 4.0 - - - -
301A PHE* 4.8 13.5 - - + -
302A PRO* 3.9 41.1 - - + +
270B MSE 4.5 18.8 - - + -
303B SER* 5.7 0.7 - - - +
304B SER 5.0 5.4 - - - +
305B ALA* 4.9 8.3 - - + -
307B PHE* 5.6 1.6 - - + -
310B ASP* 2.8 17.4 + - + +
313B SER* 1.3 84.2 + - - +
315B GLY* 1.3 60.2 + - - +
316B GLN 3.3 3.4 - - - -
317B TYR* 3.1 13.1 + - + +
318B VAL* 2.9 36.3 + - + +
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Residues in contact with GLY 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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421A GLY 4.7 1.9 - - - +
422A VAL* 4.5 5.2 - - - -
425A TYR* 5.8 2.6 - - - -
307B PHE* 5.8 0.2 - - - -
310B ASP 3.1 6.9 + - - -
311B LEU* 3.3 37.5 + - - -
313B SER 3.6 0.8 - - - -
314B LEU* 1.3 77.4 - - - +
316B GLN* 1.3 61.9 + - - +
318B VAL* 3.5 5.4 + - - +
319B GLN* 3.1 24.6 + - - +
374B HIS* 4.7 3.0 + - - -
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Residues in contact with GLN 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A GLY 4.3 0.2 - - - +
291A GLU* 3.6 44.3 + - + +
294A GLY 2.9 26.4 + - - +
295A LYS* 3.7 11.7 - - - +
419A GLN* 3.0 22.7 - - + +
420A PRO* 4.3 2.3 - - - +
421A GLY* 2.8 27.6 + - - -
422A VAL* 3.9 14.7 + - + +
313B SER 5.0 0.2 + - - -
314B LEU 3.3 0.4 - - - -
315B GLY* 1.3 74.5 - - - +
317B TYR* 1.3 59.8 + - - +
319B GLN* 3.2 2.6 + - - +
320B GLU* 2.8 52.1 + - - +
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Residues in contact with TYR 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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267A THR 4.9 0.5 + - - -
290A GLY* 3.9 16.2 + - - +
294A GLY* 3.4 31.9 - - - -
298A LYS 4.0 2.2 - - - -
299A GLY* 2.5 34.4 + - - -
300A ILE 3.4 15.7 - - - -
301A PHE* 3.6 37.8 + + - +
302A PRO* 4.4 9.0 - - + -
268B ILE* 6.0 0.2 - - - +
314B LEU* 3.1 19.6 + - + +
316B GLN* 1.3 77.9 - - - +
318B VAL* 1.3 63.8 + - + +
321B GLY* 2.8 22.9 + - - -
322B ARG* 3.4 37.6 - - + +
323B ARG* 3.1 3.5 + - - -
325B LEU* 4.2 11.4 - - + -
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Residues in contact with VAL 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A PHE* 5.8 0.4 - - + -
270B MSE 3.7 37.0 - - + -
307B PHE* 4.8 5.4 - - + -
314B LEU* 2.9 28.1 + - + +
315B GLY* 4.0 4.3 - - - +
317B TYR* 1.3 73.9 - - + +
319B GLN* 1.3 57.5 + - - +
323B ARG* 2.9 23.2 + - - -
325B LEU* 4.0 10.8 - - + -
327B GLU* 3.6 14.6 - - - +
374B HIS* 3.5 37.6 - - + +
379B VAL* 3.3 13.6 - - + +
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Residues in contact with GLN 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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297A GLN* 4.9 2.3 + - - -
421A GLY* 3.4 22.9 - - - +
424A ALA* 3.9 18.4 - - + +
425A TYR* 4.7 2.3 + - - +
315B GLY 3.1 18.8 + - - +
316B GLN 3.7 2.9 - - - +
318B VAL* 1.3 80.4 - - - +
320B GLU* 1.3 73.0 + - + +
323B ARG* 3.3 12.6 + - - +
373B ALA* 3.0 33.6 + - - +
374B HIS* 3.4 22.9 - - - +
376B ASP* 4.7 1.2 - - - +
377B GLY* 3.6 25.2 - - - +
379B VAL* 5.5 0.2 - - - -
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Residues in contact with GLU 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A GLY 3.7 4.3 - - - +
295A LYS* 3.3 12.7 - - - +
296A ASP 4.4 3.8 + - - +
297A GLN* 2.7 42.2 + - - +
420A PRO* 3.6 16.2 - - - +
421A GLY* 3.3 23.9 + - - -
316B GLN* 2.8 35.8 + - - +
319B GLN* 1.3 90.6 - - + +
321B GLY* 1.3 57.0 + - - +
323B ARG* 4.4 0.9 - - - +
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Residues in contact with GLY 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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294A GLY* 3.7 11.4 + - - -
297A GLN* 3.2 16.1 - - - -
298A LYS 3.3 15.3 - - - -
317B TYR* 2.8 27.1 + - - -
320B GLU* 1.3 74.9 - - - +
322B ARG* 1.3 68.0 + - - -
323B ARG* 3.0 12.8 + - - +
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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