Contacts of the helix formed by residues 316 - 322 (chain A) in PDB entry 5T4S
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 GLY 316 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226A ASP 3.2 15.7 - - - -
229A ALA* 3.3 6.1 - - - -
231A TYR 3.1 23.4 + - - -
232A ILE* 4.3 0.6 - - - +
314A ALA 3.6 0.8 + - - -
315A LEU* 1.3 72.1 - - - +
317A ALA* 1.3 60.8 + - - -
318A THR 3.2 2.9 - - - -
319A PHE* 2.9 21.4 + - - +
320A ILE* 2.9 20.2 + - - +
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Residues in contact with ALA 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ASP 4.3 1.6 - - - +
20A TYR* 3.7 31.0 - - + -
162A TYR* 3.8 19.5 - - + -
226A ASP 4.4 0.2 + - - -
229A ALA 2.9 14.2 + - - +
230A SER* 3.3 18.4 + - - +
316A GLY* 1.3 71.8 - - - -
318A THR* 1.3 55.7 - - - +
320A ILE* 4.2 0.8 - - - +
321A ARG* 2.9 42.4 + - - +
403A DMS 4.3 1.1 - - + -
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Residues in contact with THR 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A SER 3.2 13.1 + - - -
231A TYR* 3.3 1.4 - - - -
232A ILE* 4.0 14.4 - - + -
279A LEU* 3.9 21.2 - - + +
283A ASP* 3.3 27.3 - - - +
284A TYR* 4.1 6.7 - - + -
299A ALA* 2.9 43.8 + - + +
316A GLY 3.2 0.4 - - - -
317A ALA* 1.3 78.2 - - - +
319A PHE* 1.3 61.4 + - - +
321A ARG* 3.5 20.5 + - - +
322A LYS* 4.1 4.5 + - - +
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Residues in contact with PHE 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A VAL* 5.8 0.2 - - + -
232A ILE* 4.0 13.2 - - + +
270A PHE* 3.9 23.8 - + + -
272A LEU* 3.7 14.6 - - + -
277A TYR* 3.6 29.6 - + + -
279A LEU* 4.5 6.5 - - + -
315A LEU* 3.9 39.7 - - + +
316A GLY 2.9 9.7 + - - +
318A THR* 1.3 78.0 - - - +
320A ILE* 1.3 63.0 + - + +
322A LYS* 3.1 5.2 + - - +
323A PHE* 3.0 50.7 + + + -
336A PHE* 3.6 37.9 - + - -
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Residues in contact with ILE 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A PHE* 4.2 20.2 - - + +
161A TYR* 5.5 0.2 - - - -
162A TYR* 3.7 37.3 + - + +
225A VAL* 4.9 7.6 - - + -
226A ASP 4.2 0.2 - - - -
227A THR* 3.8 37.0 - - + +
315A LEU 3.9 11.0 - - - +
316A GLY 2.9 27.6 + - - +
319A PHE* 1.3 75.0 - - + +
321A ARG* 1.3 65.7 + - - +
323A PHE 2.9 29.2 + - - +
324A TYR* 3.9 1.4 + - - -
325A THR* 3.8 18.6 - - - +
339A ALA* 4.7 1.4 - - - +
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Residues in contact with ARG 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ASP* 2.8 45.7 + - - +
20A TYR* 3.1 28.4 + - - +
161A TYR* 5.3 0.5 - - - -
162A TYR* 3.4 26.8 - - + +
163A ASN 3.5 8.1 - - - +
164A ARG* 3.8 33.4 + - - +
230A SER 4.8 1.0 + - - -
283A ASP 5.1 0.4 + - - -
286A PHE* 5.2 1.6 - - - -
299A ALA* 4.5 2.8 - - - +
317A ALA* 2.9 25.5 + - - +
318A THR* 3.5 30.2 + - - +
319A PHE 3.3 0.4 - - - -
320A ILE* 1.3 78.1 - - - +
322A LYS* 1.3 60.3 + - - +
339A ALA* 3.4 14.9 - - - +
404A DMS 2.7 34.6 + - - +
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Residues in contact with LYS 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A ARG* 4.4 10.7 - - - +
278A THR* 2.7 29.1 + - - +
279A LEU* 4.1 9.8 - - + +
283A ASP* 3.5 30.7 + - + +
318A THR 4.1 3.3 + - - +
319A PHE 3.1 9.3 + - - +
321A ARG* 1.3 78.9 - - - +
323A PHE* 1.3 85.1 + - + +
338A LEU* 3.8 19.1 - - + +
339A ALA* 3.0 22.1 + - - +
23B GLU* 2.5 39.4 + - - -
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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