Contacts of the helix formed by residues 302 - 315 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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284B ILE* 4.3 12.1 - - + -
285B PRO* 4.3 15.5 - - + -
286B ALA* 6.0 2.2 - - + +
300B GLU 4.3 3.8 - - - +
301B ILE* 1.3 93.1 - - + +
303B ALA* 1.3 66.0 + - - +
304B THR* 3.4 4.0 + - - +
305B ILE* 3.5 24.3 + - + +
306B SER* 3.1 23.4 + - - -
215D GLU* 3.5 34.8 - - + +
244D ASN* 5.4 2.7 - - - +
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Residues in contact with ALA 303 (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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178B SER 4.7 5.8 - - - +
180B PHE* 3.8 24.9 - - + -
301B ILE 3.7 1.0 + - - -
302B PRO* 1.3 71.6 - - - +
304B THR* 1.3 64.0 + - - +
306B SER* 3.3 2.3 + - - -
307B LYS* 3.0 44.0 + - - +
215D GLU* 3.2 15.2 + - - +
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Residues in contact with THR 304 (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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302B PRO* 3.4 2.9 - - - +
303B ALA* 1.3 79.3 - - - +
305B ILE* 1.3 69.9 + - + +
307B LYS* 3.3 17.4 + - - +
308B SER* 3.3 15.2 + - - +
215D GLU* 5.0 3.2 + - - -
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Residues in contact with ILE 305 (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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282B PHE* 3.7 34.8 - - + -
283B LEU 3.4 28.3 - - - +
284B ILE* 4.6 4.5 - - + -
285B PRO* 4.3 6.1 - - + -
301B ILE* 3.9 14.8 - - + -
302B PRO* 3.5 31.2 + - + +
303B ALA 3.4 0.4 - - - -
304B THR* 1.3 80.0 - - + +
306B SER* 1.3 64.3 + - - +
308B SER* 3.0 18.6 + - - -
309B ILE* 3.1 16.8 + - + +
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Residues in contact with SER 306 (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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180B PHE* 3.1 47.3 - - - +
226B LEU* 5.0 4.1 - - - +
301B ILE* 3.2 13.3 - - - +
302B PRO 3.1 16.1 + - - -
303B ALA 3.5 4.7 - - - -
305B ILE* 1.3 79.1 - - - +
307B LYS* 1.3 57.5 + - - +
309B ILE* 3.1 10.9 + - - +
310B LEU* 2.8 33.1 + - - +
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Residues in contact with LYS 307 (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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174B VAL* 4.1 40.2 + - + +
175B PRO 5.8 0.8 + - - -
176B ASP* 5.6 5.7 + - - +
180B PHE* 4.7 5.2 - - + -
303B ALA* 3.0 38.7 + - - +
304B THR* 3.7 9.1 + - - +
305B ILE 3.2 0.4 - - - -
306B SER* 1.3 76.4 - - - +
308B SER* 1.3 60.3 + - - +
310B LEU* 3.5 9.0 + - - +
311B LYS* 3.2 27.8 + - - +
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Residues in contact with SER 308 (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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282B PHE* 3.7 27.7 - - - -
304B THR* 3.3 12.0 + - - +
305B ILE* 3.0 11.3 + - - -
307B LYS* 1.3 77.9 - - - +
309B ILE* 1.3 60.9 + - - +
311B LYS* 3.2 11.4 + - - +
312B LEU* 3.1 22.9 + - - +
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Residues in contact with ILE 309 (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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226B LEU* 4.1 22.0 - - + -
235B PHE* 6.1 1.3 - - + -
279B LEU* 4.0 16.8 - - + -
282B PHE* 3.7 26.2 - - + -
292B VAL* 4.2 25.8 - - + -
301B ILE* 4.9 1.6 - - + -
305B ILE* 3.1 28.3 + - + +
306B SER* 3.1 13.4 + - - +
308B SER* 1.3 74.3 - - - +
310B LEU* 1.3 66.0 + - - +
312B LEU* 2.9 18.1 + - - +
313B PHE* 3.1 32.5 + - + -
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Residues in contact with LEU 310 (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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172B ILE* 4.1 33.3 - - + +
174B VAL* 3.9 28.5 - - + -
180B PHE* 4.3 16.2 - - + -
224B TYR* 4.7 7.4 - - + -
226B LEU* 4.1 13.2 - - + -
238B VAL* 3.8 38.1 - - + -
306B SER 2.8 18.2 + - - +
307B LYS* 3.9 7.6 - - - +
308B SER 3.3 0.2 - - - -
309B ILE* 1.3 76.3 - - - +
311B LYS* 1.3 65.3 + - + +
313B PHE* 3.0 21.4 + - + +
314B LYS* 3.5 6.1 + - - +
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Residues in contact with LYS 311 (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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172B ILE 5.7 4.9 - - - -
307B LYS 3.2 18.1 + - - +
308B SER* 3.3 13.2 - - - +
309B ILE 3.1 0.2 - - - -
310B LEU* 1.3 78.9 - - + +
312B LEU* 1.3 57.7 + - + +
314B LYS* 2.9 18.4 + - + -
315B TYR* 3.2 41.8 + - + +
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Residues in contact with LEU 312 (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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272B ARG* 4.5 3.8 - - - -
274B VAL* 4.2 15.5 - - + +
278B SER* 3.3 36.8 - - - +
279B LEU* 3.6 20.9 - - + -
281B GLN* 4.2 5.2 - - - +
282B PHE* 4.1 11.9 - - + -
308B SER 3.1 14.4 + - - +
309B ILE 2.9 12.4 + - - +
311B LYS* 1.3 77.1 - - + +
313B PHE* 1.3 61.7 + - - +
314B LYS 3.2 0.3 + - - -
315B TYR* 3.3 27.6 + - + +
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Residues in contact with PHE 313 (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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168B ILE* 3.2 8.8 - - - +
172B ILE* 5.5 1.1 - - + -
226B LEU* 4.6 6.5 - - + -
235B PHE* 4.1 22.7 - + + -
236B CYS 4.5 0.2 - - - -
237B GLY* 3.9 19.3 - - - -
238B VAL* 3.7 26.2 - - + -
270B VAL* 3.8 29.2 - - + -
272B ARG* 3.1 50.8 + - + -
274B VAL* 3.6 24.0 - - + -
279B LEU* 5.8 0.7 - - + -
309B ILE* 3.1 40.9 + - + -
310B LEU* 3.0 16.3 + - + +
312B LEU* 1.3 78.4 - - + +
314B LYS* 1.3 57.8 + - - +
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Residues in contact with LYS 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ILE* 2.6 44.3 + - + +
169B PRO* 2.5 36.7 + - + +
170B PRO* 3.7 13.7 - - - +
172B ILE* 5.9 5.8 - - + -
272B ARG* 3.9 7.7 + - - -
310B LEU 3.5 5.3 + - - +
311B LYS* 2.9 11.1 + - + +
313B PHE* 1.3 80.5 - - - +
315B TYR* 1.3 90.5 + - + +
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Residues in contact with TYR 315 (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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170B PRO 5.5 2.6 + - - -
272B ARG* 4.0 16.6 + - - +
311B LYS* 3.2 47.0 + - + +
312B LEU* 3.3 27.2 + - + +
313B PHE 3.6 0.4 + - - -
314B LYS* 1.3 111.9 - - + +
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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