Contacts of the helix formed by residues 302 - 314 (chain A) in PDB entry 4U8T
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 PRO 302 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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284A ILE* 4.0 19.1 - - + -
285A PRO* 4.1 22.2 - - + -
286A ALA* 5.9 2.2 - - + +
300A GLU* 4.2 3.8 - - - +
301A ILE* 1.3 91.5 - - + +
303A ALA* 1.3 60.2 + - - +
304A THR* 3.5 4.9 - - + +
305A ILE* 3.4 15.0 + - + +
306A SER* 2.9 27.4 + - - -
215E GLU* 3.5 34.1 - - + +
244E ASN* 5.3 1.3 - - - +
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Residues in contact with ALA 303 (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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178A SER 4.7 6.5 - - - +
180A PHE* 3.8 25.0 - - + -
301A ILE 3.7 0.8 + - - -
302A PRO* 1.3 71.2 - - - +
304A THR* 1.3 65.8 + - - +
306A SER* 3.2 2.8 + - - -
307A LYS* 3.1 36.9 + - - +
215E GLU* 3.3 12.1 + - - +
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Residues in contact with THR 304 (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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302A PRO* 5.0 6.3 - - + -
303A ALA* 1.3 79.9 - - - +
305A ILE* 1.3 72.1 + - + +
307A LYS* 3.5 10.4 + - - +
308A SER* 3.4 22.2 + - - -
311A LYS* 5.8 0.2 + - - -
215E GLU* 4.7 8.4 + - - +
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Residues in contact with ILE 305 (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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282A PHE* 3.9 32.9 - - + -
283A LEU 3.5 26.2 - - - +
284A ILE* 4.4 3.1 - - + -
285A PRO* 4.2 16.2 - - + -
301A ILE* 3.9 17.5 - - + -
302A PRO* 3.4 19.2 + - + +
303A ALA 3.3 0.2 - - - -
304A THR* 1.3 84.7 - - + +
306A SER* 1.3 62.5 + - - +
308A SER* 3.2 8.4 + - - -
309A ILE* 3.2 24.1 + - + +
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Residues in contact with SER 306 (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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180A PHE* 3.1 48.5 - - - +
226A LEU* 5.4 3.8 - - - +
301A ILE* 3.3 15.7 - - - +
302A PRO 2.9 17.1 + - - -
303A ALA 3.2 8.7 + - - -
305A ILE* 1.3 77.9 - - - +
307A LYS* 1.3 57.1 + - - +
309A ILE* 3.1 9.5 + - - +
310A LEU* 2.8 32.8 + - - +
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Residues in contact with LYS 307 (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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174A VAL* 3.8 47.5 + - + +
175A PRO 5.6 1.2 + - - -
176A ASP* 4.9 10.3 + - - +
180A PHE* 4.8 6.1 - - + -
303A ALA* 3.1 26.2 + - - +
304A THR* 3.9 8.5 - - - +
305A ILE 3.3 0.2 - - - -
306A SER* 1.3 76.7 - - - +
308A SER* 1.3 62.2 + - - +
310A LEU* 3.3 9.5 + - + +
311A LYS* 3.0 36.4 + - - +
314A LYS* 5.8 0.2 + - - -
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Residues in contact with SER 308 (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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282A PHE* 3.6 27.2 - - - -
304A THR* 3.4 9.8 + - - -
305A ILE* 3.2 11.2 + - - -
306A SER 3.2 0.6 - - - -
307A LYS* 1.3 80.3 - - - +
309A ILE* 1.3 61.4 + - - +
311A LYS* 3.2 36.2 + - - +
312A LEU* 3.3 10.9 + - - +
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Residues in contact with ILE 309 (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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226A LEU* 4.2 18.2 - - + -
235A PHE* 6.3 1.3 - - + -
279A LEU* 3.8 17.7 - - + -
282A PHE* 3.8 22.4 - - + -
292A VAL* 4.2 31.6 - - + -
301A ILE* 4.5 4.5 - - + -
305A ILE* 3.4 27.6 - - + +
306A SER* 3.1 13.4 + - - +
308A SER* 1.3 73.1 - - - +
310A LEU* 1.3 67.0 + - - +
312A LEU* 3.0 17.2 + - - +
313A PHE* 3.2 31.4 + - + -
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Residues in contact with LEU 310 (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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172A ILE* 4.3 26.2 - - + -
174A VAL* 3.8 28.7 - - + -
180A PHE* 4.3 17.3 - - + -
224A TYR* 4.8 5.4 - - + -
226A LEU* 4.3 13.2 - - + -
238A VAL* 4.1 35.7 - - + -
306A SER 2.8 19.1 + - - +
307A LYS* 3.6 9.9 - - - +
308A SER 3.2 0.2 - - - -
309A ILE* 1.3 78.0 - - - +
311A LYS* 1.3 61.0 + - - +
313A PHE* 3.2 15.7 + - + +
314A LYS* 3.3 25.8 + - - +
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Residues in contact with LYS 311 (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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304A THR 5.8 0.2 + - - -
307A LYS* 3.0 26.8 + - - +
308A SER* 3.2 28.8 + - - +
309A ILE 3.1 0.2 - - - -
310A LEU* 1.3 76.1 - - - +
312A LEU* 1.3 65.5 + - + +
314A LYS* 3.2 28.7 + - - +
315A TYR* 3.7 12.3 + - - +
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Residues in contact with LEU 312 (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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272A ARG* 3.7 13.3 + - - -
274A VAL* 4.1 16.5 - - + +
278A SER* 3.2 37.9 - - - +
279A LEU* 4.1 13.7 - - + -
281A GLN* 4.8 5.2 - - - +
282A PHE* 4.4 9.9 - - + -
308A SER 3.3 8.7 + - - +
309A ILE* 3.0 10.8 + - - +
311A LYS* 1.3 80.7 - - + +
313A PHE* 1.3 61.2 + - + +
314A LYS 3.4 0.3 + - - -
315A TYR* 3.6 24.9 + - + +
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Residues in contact with PHE 313 (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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168A ILE* 3.8 8.0 - - - +
226A LEU* 5.0 8.3 - - + -
235A PHE* 3.7 28.0 - + + -
236A CYS 4.4 0.2 - - - -
237A GLY* 3.7 23.3 - - - -
238A VAL* 3.8 19.7 - - + -
270A VAL* 3.8 32.6 - - + +
272A ARG* 3.2 44.7 + - + -
274A VAL* 3.7 22.2 - - + -
279A LEU* 5.7 0.7 - - + -
309A ILE* 3.2 41.2 + - + -
310A LEU* 3.2 13.4 + - + +
312A LEU* 1.3 77.6 - - + +
314A LYS* 1.3 56.9 + - - +
315A TYR 3.4 0.9 - - - -
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Residues in contact with LYS 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ILE* 3.7 15.8 - - + +
169A PRO* 4.2 13.2 - - + +
170A PRO 4.5 4.0 - - - +
171A TRP* 4.2 9.1 - - - +
172A ILE* 3.5 64.5 + - + +
270A VAL* 5.4 0.4 - - + -
307A LYS 5.8 0.2 + - - -
310A LEU* 3.3 24.2 + - - +
311A LYS* 3.2 19.2 + - - +
313A PHE* 1.3 77.2 - - - +
315A TYR* 1.3 59.9 + - - +
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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