Contacts of the helix formed by residues 315 - 324 (chain K) in PDB entry 4EC4
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 315 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283K GLN* 4.6 3.5 - - - +
313K SER 3.9 2.4 + - - -
314K GLU* 1.3 71.0 - - - +
316K PRO* 1.4 72.2 - - - +
317K TRP* 3.9 15.6 + - - +
318K GLU* 2.9 54.6 + - + +
319K GLN* 3.1 15.7 + - - +
338K TYR* 4.0 7.4 + - - -
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Residues in contact with PRO 316 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279K VAL* 3.7 21.3 - - + -
283K GLN* 3.5 47.6 - - + +
284K LEU* 3.9 17.7 - - + +
287K ALA* 4.4 3.4 - - + -
289K PHE* 3.6 10.4 - - + -
310K TRP* 4.1 13.0 - - + -
314K GLU 3.3 7.1 - - - +
315K ASP* 1.4 92.3 - - - +
317K TRP* 1.3 56.8 + - + +
319K GLN* 3.5 1.6 + - - +
320K HIS* 3.1 26.7 + - - +
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Residues in contact with TRP 317 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283K GLN* 3.1 35.3 + - - +
286K ARG* 3.1 60.2 - - - +
287K ALA* 3.5 20.4 - - + -
315K ASP* 3.2 13.6 - - - +
316K PRO* 1.3 74.9 - - + +
318K GLU* 1.3 64.4 + - - +
320K HIS* 3.5 5.4 + - - +
321K ALA* 3.3 22.9 + - - +
329K TYR* 4.8 1.8 - + - -
330K LEU* 4.3 12.8 - - + +
333K GLN* 3.6 37.0 - - + -
334K LYS* 3.4 35.8 - - + +
338K TYR* 3.5 22.5 + - + +
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Residues in contact with GLU 318 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315K ASP* 2.9 33.3 + - + +
317K TRP* 1.3 79.5 - - - +
319K GLN* 1.3 72.3 + - - +
321K ALA* 5.0 0.2 - - - -
322K LYS* 3.1 25.3 + - - +
338K TYR* 3.5 6.2 + - - +
342K ILE* 3.4 37.3 - - + +
345K THR* 6.0 1.4 - - - +
346K HIS* 3.8 21.5 + - - -
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Residues in contact with GLN 319 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402D 0O6 3.5 30.5 - - + +
307K LEU* 3.7 22.9 - - + +
310K TRP* 3.6 27.6 - - + -
314K GLU* 3.8 15.2 - - + +
315K ASP 3.1 9.6 + - - +
316K PRO 4.0 0.4 - - - +
317K TRP 3.3 0.2 - - - -
318K GLU* 1.3 99.7 + - - +
320K HIS* 1.3 64.3 + - - +
322K LYS* 3.2 31.6 + - - +
323K TRP* 3.1 30.0 + - + +
346K HIS* 5.1 0.4 + - - -
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Residues in contact with HIS 320 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287K ALA* 2.7 29.3 + - + +
288K GLY* 4.4 0.2 - - - -
289K PHE* 3.4 18.5 - + + -
300K CYS* 3.5 17.3 - - + -
303K CYS* 3.8 3.3 - - - -
307K LEU* 4.3 2.1 - - - +
316K PRO 3.1 16.2 + - - +
317K TRP* 3.7 8.3 - - - +
319K GLN* 1.3 75.0 - - - +
321K ALA* 1.3 56.9 + - - +
324K TYR* 3.0 41.3 + + + +
327K CYS* 3.1 12.7 - - + -
329K TYR* 4.6 6.1 - + - -
330K LEU* 3.8 23.9 - - + +
401K ZN 2.1 36.4 - - - -
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Residues in contact with ALA 321 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317K TRP 3.3 13.6 + - - +
320K HIS* 1.3 76.2 - - - +
322K LYS* 1.3 56.2 + - - +
324K TYR 4.4 0.2 - - - -
325K PRO* 3.7 8.8 - - - +
330K LEU* 3.3 23.7 - - + +
338K TYR* 4.3 9.0 - - + -
339K ILE* 4.1 16.6 - - + -
342K ILE* 3.7 18.6 - - + -
343K HIS* 2.7 32.1 + - - -
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Residues in contact with LYS 322 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250D PHE* 4.2 24.6 - - + +
402D 0O6 4.3 3.2 + - - -
403D P33 4.6 1.2 - - - +
314K GLU* 5.4 2.0 + - - -
318K GLU 3.1 15.0 + - - +
319K GLN* 3.2 44.6 + - - +
321K ALA* 1.3 82.1 - - - +
323K TRP* 1.3 94.2 + - + +
324K TYR 3.6 0.2 + - - -
325K PRO* 4.0 1.2 - - - +
342K ILE* 3.9 6.5 - - + +
343K HIS* 2.9 25.8 + - - -
346K HIS* 3.3 37.9 - - + +
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Residues in contact with TRP 323 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249D ASN* 4.1 12.1 - - + -
250D PHE* 3.5 49.8 - + + -
251D PRO* 4.5 4.5 - - + -
402D 0O6 3.1 84.9 + + + -
403D P33 3.4 25.5 - - - +
307K LEU* 3.4 23.1 - - + -
319K GLN* 3.1 16.4 + - + +
322K LYS* 1.3 107.0 - - + +
324K TYR* 1.3 85.4 + - + +
325K PRO* 3.3 8.3 - - - +
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Residues in contact with TYR 324 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402D 0O6 3.6 54.6 - + + +
403D P33 5.5 2.9 - - - -
251K PRO* 3.8 23.6 - - + -
289K PHE* 5.7 2.0 - + - -
303K CYS* 4.0 17.9 - - - -
305K GLY* 3.5 35.8 - - - -
306K GLY 2.8 28.5 + - - -
307K LEU* 3.7 19.1 - - + -
319K GLN 5.2 0.7 - - - -
320K HIS* 3.0 26.3 + + + +
322K LYS 3.5 0.2 - - - -
323K TRP* 1.3 89.7 - - + +
325K PRO* 1.3 64.4 - - - +
326K GLY 3.4 2.0 - - - -
327K CYS* 3.2 19.3 - - + +
330K LEU* 4.0 2.1 - - - +
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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