Contacts of the helix formed by residues 315 - 324 (chain D) in PDB entry 3K75
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 SER 315 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266D TYR* 3.5 20.5 - - - -
313D VAL* 3.3 17.4 - - - +
314D ASP* 1.3 82.3 - - - +
316D GLU* 1.3 63.0 + - - +
317D GLN* 3.2 19.7 + - - +
318D ASP* 3.2 24.7 + - - +
319D ILE 3.7 0.7 + - - -
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Residues in contact with GLU 316 (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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182D ARG* 2.8 44.8 + - - +
266D TYR* 3.9 22.9 - - + +
269D VAL* 3.4 13.0 - - + +
270D LEU* 3.7 11.2 - - + +
315D SER* 1.3 70.2 - - - +
317D GLN* 1.3 65.9 + - - +
319D ILE* 3.0 23.6 + - + +
320D PHE* 3.1 22.7 + - + -
327D TYR* 3.5 16.9 + - + -
333D ARG* 3.0 30.9 + - - -
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Residues in contact with GLN 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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315D SER* 3.1 11.5 + - - +
316D GLU* 1.3 79.1 - - - +
318D ASP* 1.3 65.5 + - - +
320D PHE* 2.9 7.1 + - - +
321D ASP* 2.6 69.6 + - - +
325D TRP 5.3 0.3 - - - +
327D TYR* 3.2 44.2 + - + +
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Residues in contact with ASP 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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96B PRO* 5.2 0.5 - - - +
312D PRO 4.2 8.0 - - - +
313D VAL* 3.6 13.5 - - - -
314D ASP* 2.6 33.1 + - - +
315D SER* 3.2 21.1 + - - +
317D GLN* 1.3 77.0 - - - +
319D ILE* 1.3 63.5 + - - +
321D ASP* 3.2 12.7 + - - +
322D TYR* 3.0 31.9 + - + -
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Residues in contact with ILE 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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266D TYR 3.4 30.7 - - - +
267D CYS* 4.1 9.6 - - - -
270D LEU* 3.8 31.9 - - + -
282D MET* 4.2 4.0 - - + -
293D ILE* 4.1 13.7 - - + -
298D ILE* 3.8 24.2 - - + +
313D VAL* 3.7 25.4 - - + -
315D SER 3.9 0.4 - - - +
316D GLU* 3.0 18.1 + - - +
318D ASP* 1.3 73.7 - - - +
320D PHE* 1.3 70.4 + - - +
322D TYR* 3.3 16.7 + - - +
323D ILE* 3.4 11.1 + - - +
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Residues in contact with PHE 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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270D LEU* 4.7 4.0 - - + -
278D PHE* 3.8 19.3 - + - -
282D MET* 3.5 28.7 - - + -
316D GLU* 3.1 27.4 + - + -
317D GLN* 2.9 15.3 + - - +
319D ILE* 1.3 77.7 - - - +
321D ASP* 1.3 59.5 + - - +
323D ILE* 3.0 13.0 + - - +
324D GLN 2.8 22.7 + - - -
325D TRP* 3.2 35.2 + + + +
326D ARG 3.5 25.4 - - - -
327D TYR* 3.3 31.4 - + - -
328D ARG* 3.7 17.9 - - + -
333D ARG* 4.1 9.9 - - - -
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Residues in contact with ASP 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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96B PRO* 4.1 20.6 - - + +
97B SER* 4.6 7.1 + - - -
100B ARG* 4.4 16.7 + - - +
136B TYR* 3.5 10.9 - - - -
317D GLN* 2.6 51.7 + - - +
318D ASP* 3.4 13.3 - - - +
320D PHE* 1.3 71.4 - - - +
322D TYR* 1.3 64.4 + - - +
324D GLN* 2.7 19.7 + - - +
325D TRP 5.2 1.8 - - - +
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Residues in contact with TYR 322 (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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67B PHE* 4.4 5.2 - + - -
92B SER* 5.1 3.2 + - - -
94B MET 6.0 0.2 - - - -
95B SER* 5.4 5.1 - - - -
96B PRO* 3.9 23.8 - - + +
136B TYR* 2.9 35.8 + - - +
289D LYS* 5.5 0.2 - - - +
291D PHE* 3.3 16.5 - - + -
298D ILE* 3.9 26.5 - - + -
311D LEU* 3.4 39.4 - - + +
312D PRO* 2.6 47.4 + - - +
313D VAL* 4.0 8.3 - - + -
318D ASP* 3.0 29.6 + - + -
319D ILE* 3.3 8.0 + - - +
321D ASP* 1.3 77.0 - - - +
323D ILE* 1.3 59.7 + - - +
324D GLN* 4.5 0.9 - - - +
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Residues in contact with ILE 323 (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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282D MET* 3.6 43.1 - - + +
285D HIS* 3.5 25.3 + - + -
286D ALA* 4.0 22.2 - - + -
289D LYS* 3.5 18.5 - - + +
291D PHE* 4.1 11.9 - - + -
293D ILE* 4.4 3.4 - - + -
298D ILE* 4.0 22.7 - - + -
319D ILE 3.5 4.9 - - - +
320D PHE 3.0 15.9 - - - +
322D TYR* 1.3 76.3 - - - +
324D GLN* 1.3 72.2 + - - +
325D TRP* 3.3 21.3 + - + -
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Residues in contact with GLN 324 (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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100B ARG* 6.1 2.4 - - - +
135B PRO* 3.3 33.9 + - - +
136B TYR* 3.8 27.4 - - + +
285D HIS* 4.5 1.9 + - - -
289D LYS* 3.7 29.6 + - - +
320D PHE 2.8 3.5 + - - -
321D ASP* 2.7 21.9 + - - +
322D TYR 4.5 1.0 - - - +
323D ILE* 1.3 79.8 - - - +
325D TRP* 1.3 61.0 + - - +
326D ARG 4.4 0.2 + - - -
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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