Contacts of the helix formed by residues 314 - 321 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283C GLU* 5.7 0.9 - - - +
286C LYS* 3.9 38.6 - - + +
290C GLY* 5.7 0.4 - - - -
301C PHE* 4.7 18.4 - - + -
302C PRO* 4.4 23.1 - - + +
270D MSE 4.7 14.8 - - + -
303D SER* 5.7 1.6 - - - +
304D SER 5.3 3.8 - - - +
305D ALA* 5.2 6.1 - - + -
307D PHE* 5.6 2.0 - - + -
310D ASP* 2.7 20.5 + - + +
313D SER* 1.3 91.7 - - - +
315D GLY* 1.3 56.8 + - - -
316D GLN 3.3 2.9 - - - -
317D TYR* 3.0 13.3 + - + +
318D VAL* 2.8 37.5 + - + +
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Residues in contact with GLY 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421C GLY 4.6 1.6 - - - +
422C VAL* 4.5 4.7 - - - -
425C TYR* 5.8 2.5 - - - -
307D PHE* 5.6 0.2 - - - -
310D ASP 3.1 7.3 + - - -
311D LEU* 3.4 38.6 + - - -
313D SER 3.6 0.4 - - - -
314D LEU* 1.3 77.4 - - - +
316D GLN* 1.3 62.2 + - - +
318D VAL* 3.4 5.6 + - - +
319D GLN* 3.1 25.3 + - - +
374D HIS* 4.6 3.3 + - - -
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Residues in contact with GLN 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C GLU* 3.7 44.3 - - + +
294C GLY 2.9 30.0 + - - +
295C LYS* 3.6 11.7 - - - +
419C GLN* 3.0 24.0 - - + +
420C PRO* 4.2 1.5 - - - +
421C GLY* 2.8 28.1 + - - -
422C VAL* 3.9 16.2 - - + +
311D LEU 4.4 0.2 + - - -
313D SER 4.9 0.8 + - - -
314D LEU 3.3 0.6 - - - -
315D GLY* 1.3 74.6 - - - +
317D TYR* 1.3 63.5 + - - +
319D GLN* 3.3 1.4 + - - +
320D GLU* 2.8 46.7 + - - +
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Residues in contact with TYR 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267C THR 4.9 0.5 + - - -
290C GLY* 3.8 16.3 + - - +
294C GLY* 3.5 28.0 - - - -
298C LYS 4.1 1.1 - - - -
299C GLY 2.5 28.3 + - - -
300C ILE 3.4 22.2 - - - -
301C PHE* 3.6 36.1 + + + +
302C PRO* 4.3 10.8 - - + -
314D LEU* 3.0 17.7 + - + +
316D GLN* 1.3 81.4 - - - +
318D VAL* 1.3 62.7 + - + +
321D GLY* 2.8 23.3 + - - -
322D ARG* 3.4 38.2 - - + +
323D ARG* 3.0 2.9 + - - -
325D LEU* 4.1 11.2 - - + -
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Residues in contact with VAL 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301C PHE* 5.8 0.7 - - + -
270D MSE 3.8 36.8 - - + -
307D PHE* 4.9 3.4 - - + -
314D LEU* 2.8 29.4 + - + +
315D GLY* 3.9 4.5 - - - +
317D TYR* 1.3 73.0 - - + +
319D GLN* 1.3 57.5 + - - +
323D ARG* 2.7 27.3 + - - +
325D LEU* 4.1 8.5 - - + -
327D GLU* 3.7 13.9 - - - +
374D HIS* 3.4 40.8 - - + +
379D VAL* 3.2 13.3 - - + +
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Residues in contact with GLN 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297C GLN* 5.2 1.6 + - - -
421C GLY* 3.4 26.0 - - - +
424C ALA* 3.7 19.7 - - + +
425C TYR* 4.7 1.6 + - - +
315D GLY 3.1 15.2 + - - +
316D GLN 3.8 2.7 - - - +
318D VAL* 1.3 80.5 - - - +
320D GLU* 1.3 72.1 + - + +
323D ARG* 3.2 12.4 + - - +
373D ALA* 2.9 34.2 + - - +
374D HIS* 3.3 24.5 + - + +
376D ASP* 4.6 1.2 - - - +
377D GLY* 3.6 28.1 - - - +
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Residues in contact with GLU 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294C GLY 3.6 3.4 - - - +
295C LYS* 3.2 13.5 - - - +
296C ASP 4.3 4.3 + - - +
297C GLN* 2.7 40.7 + - - +
420C PRO* 3.6 16.6 - - - +
421C GLY* 3.4 25.3 + - - -
316D GLN* 2.8 36.9 + - - +
319D GLN* 1.3 91.7 - - + +
321D GLY* 1.3 64.9 + - - +
323D ARG* 4.5 1.1 - - - -
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Residues in contact with GLY 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294C GLY* 3.7 12.1 + - - -
297C GLN* 3.2 15.1 - - - -
298C LYS 3.3 14.6 - - - -
317D TYR* 2.8 26.5 + - - -
320D GLU* 1.3 74.7 - - - +
322D ARG* 1.3 64.1 + - - -
323D ARG* 2.9 18.7 + - - +
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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