Contacts of the helix formed by residues 315 - 324 (chain B) in PDB entry 4HY4
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313B GLY 3.5 4.6 + - - +
314B ASP* 1.3 72.9 - - - +
316B PRO* 1.3 69.3 - - - +
317B TRP* 3.0 23.6 + - - +
318B VAL* 3.0 37.5 + - + +
319B GLU* 3.0 18.3 + - - +
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Residues in contact with PRO 316 (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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279B VAL* 3.9 12.1 - - + -
283B GLN* 3.8 28.7 - - + +
284B LEU* 3.7 30.5 - - + -
287B ALA* 3.7 19.7 - - + -
289B PHE* 3.7 7.1 - - + -
310B TRP* 4.0 14.8 - - + -
314B ASP 3.7 9.2 - - - +
315B ASP* 1.3 86.0 - - - +
317B TRP* 1.3 56.1 + - - +
319B GLU* 3.8 1.1 - - + +
320B HIS* 2.9 28.8 + - - +
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Residues in contact with TRP 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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283B GLN 5.8 0.9 - - - -
286B SER* 3.2 26.8 + - - -
287B ALA* 3.6 27.4 - - + +
315B ASP* 3.0 12.8 + - - +
316B PRO* 1.3 74.8 - - - +
318B VAL* 1.3 65.0 + - - +
320B HIS* 3.3 11.5 + - - +
321B ALA* 3.1 18.0 + - - +
329B PHE* 3.6 25.1 - + - -
330B LEU* 3.6 37.7 - - + -
333B MET* 3.6 27.6 - - + -
334B LYS* 3.5 39.0 - - + +
338B PHE* 3.7 14.1 - - + -
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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
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315B ASP* 3.0 33.0 + - + +
317B TRP* 1.3 75.3 - - - +
319B GLU* 1.3 68.9 + - - +
321B ALA 3.2 1.7 + - - -
322B LYS* 2.8 27.9 + - + +
338B PHE* 4.2 20.9 - - + -
342B ILE* 3.7 23.6 - - + +
345B ARG* 4.3 10.1 - - - +
346B TYR* 4.2 19.1 - - - +
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Residues in contact with GLU 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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307B LEU* 3.8 21.2 - - + +
310B TRP* 3.9 18.4 - - + -
314B ASP* 4.4 10.2 - - + +
315B ASP 3.0 19.3 + - - +
316B PRO 3.8 4.7 - - - +
318B VAL* 1.3 84.6 - - - +
320B HIS* 1.3 63.0 + - - +
322B LYS* 4.0 15.6 + - - +
323B TRP* 3.1 53.2 + - + +
346B TYR* 5.4 1.0 + - - -
402B 1BG 3.8 23.0 - - + +
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Residues in contact with HIS 320 (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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287B ALA 2.8 29.1 + - - -
289B PHE* 3.5 18.3 - + + -
300B CYS* 3.4 13.3 - - - +
303B CYS* 3.8 0.8 - - - -
307B LEU* 4.5 0.6 - - - +
316B PRO 2.9 17.0 + - - +
317B TRP* 3.4 22.6 - + + +
319B GLU* 1.3 77.0 - - - +
321B ALA* 1.3 56.7 + - - +
324B PHE* 2.9 55.0 + + + +
327B CYS* 3.5 10.8 - - + -
329B PHE* 4.6 3.1 - + - -
330B LEU* 4.0 9.2 - - + -
401B ZN 2.1 36.7 - - - -
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Residues in contact with ALA 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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317B TRP 3.1 15.9 + - - +
318B VAL 3.2 3.6 + - - +
320B HIS* 1.3 74.3 - - - +
322B LYS* 1.3 62.1 + - - +
325B PRO* 3.6 11.0 - - - +
330B LEU* 3.6 18.3 - - + +
338B PHE* 3.8 15.9 - - + -
339B VAL* 4.3 10.5 - - - -
342B ILE* 3.8 21.1 - - + -
343B GLN* 2.9 23.6 + - - +
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Residues in contact with LYS 322 (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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318B VAL* 2.8 17.3 + - + +
319B GLU* 3.3 20.0 + - - +
321B ALA* 1.3 77.2 - - - +
323B TRP* 1.3 103.9 + - + +
325B PRO* 4.3 0.3 - - - +
342B ILE* 3.7 12.1 - - + +
343B GLN* 3.0 20.7 + - - +
346B TYR* 3.7 51.5 + - + +
402B 1BG 5.3 2.2 + - - -
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Residues in contact with TRP 323 (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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307B LEU* 3.5 23.0 - - + +
319B GLU* 3.1 42.9 + - - +
322B LYS* 1.3 114.1 - - + +
324B PHE* 1.3 86.7 + - + +
325B PRO* 3.3 12.0 - - - +
402B 1BG 3.4 66.1 + - + -
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Residues in contact with PHE 324 (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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289B PHE* 4.7 2.7 - + - -
303B CYS* 3.9 19.5 - - - -
305B GLY* 3.5 37.2 - - - -
306B GLY 3.5 18.4 - - - -
307B LEU* 3.7 25.8 - - + -
320B HIS* 2.9 36.2 + + + +
323B TRP* 1.3 100.4 - - + +
325B PRO* 1.3 66.2 - - - +
326B ARG 3.2 2.5 - - - -
327B CYS* 3.1 18.7 + - + +
330B LEU* 3.5 2.6 - - - +
402B 1BG 4.2 13.5 - - - -
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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