Contacts of the helix formed by residues 314 - 321 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270C MSE 4.8 15.7 - - + -
303C SER* 5.9 1.3 - - - +
304C SER 5.1 3.8 - - - +
305C ALA* 5.0 7.9 - - + -
307C PHE* 5.8 1.6 - - + -
310C ASP* 2.8 17.0 + - + +
313C SER* 1.3 85.8 + - - +
315C GLY* 1.3 60.6 + - - +
316C GLN 3.3 2.7 - - - -
317C TYR* 3.0 12.1 + - + +
318C VAL* 2.9 38.1 + - + +
286D LYS* 4.0 30.5 - - + +
290D GLY* 4.6 4.0 - - - -
301D PHE* 5.0 11.2 - - + -
302D PRO* 3.8 41.3 - - + +
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Residues in contact with GLY 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310C ASP 3.1 7.5 + - - -
311C LEU* 3.3 37.8 + - - -
313C SER 3.6 0.8 - - - -
314C LEU* 1.3 73.3 - - - +
316C GLN* 1.3 66.1 + - - +
318C VAL* 3.4 5.9 + - - +
319C GLN* 3.1 25.3 + - - +
374C HIS* 4.7 2.8 + - - -
421D GLY 4.8 1.6 - - - +
422D VAL* 4.5 5.3 - - - -
425D TYR* 5.7 2.0 - - - -
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Residues in contact with GLN 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311C LEU 4.4 0.2 + - - -
314C LEU 3.3 0.2 - - - -
315C GLY* 1.3 74.6 - - - +
317C TYR* 1.3 58.1 + - - +
319C GLN* 3.3 1.4 + - - +
320C GLU* 2.9 52.2 + - - +
291D GLU* 3.6 43.6 + - + +
294D GLY 2.9 29.9 + - - +
295D LYS* 3.5 12.7 - - - +
419D GLN* 3.0 23.7 - - + +
420D PRO* 4.1 2.3 - - - +
421D GLY* 2.8 26.6 + - - -
422D VAL* 3.9 16.0 + - + +
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Residues in contact with TYR 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268C ILE* 5.9 0.2 - - - +
314C LEU* 3.0 18.7 + - + +
316C GLN* 1.3 77.9 - - - +
318C VAL* 1.3 65.1 + - + +
321C GLY* 2.8 22.5 + - - +
322C ARG* 3.3 36.1 - - - +
323C ARG* 3.1 3.1 + - - -
325C LEU* 4.2 12.6 - - + -
267D THR 4.9 0.5 + - - -
290D GLY* 3.9 17.0 + - - +
293D GLU* 5.3 0.4 - - + -
294D GLY* 3.4 26.5 - - - -
298D LYS 4.0 6.1 - - - -
299D GLY 2.6 33.9 + - - -
300D ILE 3.5 15.9 - - - -
301D PHE* 3.6 36.2 + + - +
302D PRO* 4.3 9.9 - - + -
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Residues in contact with VAL 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C MSE 3.7 36.8 - - + -
307C PHE* 4.9 3.8 - - + -
314C LEU* 2.9 28.8 + - + +
315C GLY* 3.4 5.6 + - - +
317C TYR* 1.3 72.3 - - + +
319C GLN* 1.3 57.6 + - - +
323C ARG* 2.9 24.4 + - - -
325C LEU* 4.1 11.7 - - + -
327C GLU* 3.6 14.6 - - + +
374C HIS* 3.5 38.8 - - + +
379C VAL* 3.4 14.4 - - + +
301D PHE* 5.9 0.4 - - + -
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Residues in contact with GLN 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315C GLY 3.1 16.8 + - - +
316C GLN 3.7 2.9 - - - +
318C VAL* 1.3 79.4 - - - +
320C GLU* 1.3 73.5 + - + +
323C ARG* 3.3 12.6 + - - -
373C ALA* 3.0 33.3 + - - +
374C HIS* 3.3 24.2 - - + +
376C ASP* 4.7 1.4 - - - +
377C GLY* 3.6 25.9 - - - +
297D GLN* 4.9 2.3 + - - -
421D GLY* 3.4 22.6 - - - +
424D ALA* 3.8 19.5 - - + +
425D TYR* 4.7 2.3 + - - +
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Residues in contact with GLU 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316C GLN* 2.9 34.5 + - - +
319C GLN* 1.3 91.4 - - + +
321C GLY* 1.3 60.1 + - - +
323C ARG* 4.5 0.2 - - - -
294D GLY 3.7 3.6 - - - +
295D LYS* 3.2 12.0 - - - +
296D ASP 4.3 4.0 + - - +
297D GLN* 2.7 44.5 + - - +
420D PRO* 3.7 14.4 - - - +
421D GLY* 3.4 25.4 + - - -
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Residues in contact with GLY 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317C TYR* 2.8 26.8 + - - -
320C GLU* 1.3 74.5 - - - +
322C ARG* 1.3 62.4 + - - -
323C ARG* 2.8 19.8 + - - +
294D GLY* 3.7 11.9 + - - -
297D GLN* 3.3 13.2 - - - -
298D LYS 3.3 15.5 - - - -
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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