Contacts of the helix formed by residues 299 - 308 (chain F) in PDB entry 5UH8
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 ASN 299 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241F LEU* 5.0 3.4 - - - +
246F GLU* 4.5 4.6 + - - +
295F LEU* 3.1 30.9 + - - +
296F LEU 3.6 3.4 - - - -
298F ALA* 1.3 79.4 - - - +
300F LEU* 1.3 57.8 + - - +
301F ARG 3.1 6.1 - - - -
302F LEU* 3.3 21.4 + - + +
303F VAL 3.8 2.1 + - - -
328F LEU* 3.5 16.3 - - + +
343F PHE* 3.2 41.4 - - + +
344F SER* 4.9 0.2 - - - -
6H T 2.4 47.7 + - - +
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Residues in contact with LEU 300 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365D ILE* 4.0 36.3 - - + -
366D ILE* 4.3 13.0 - - + -
231F TYR* 3.4 19.1 - - + +
235F ILE* 3.6 19.9 - - + +
296F LEU 3.1 8.9 + - - +
297F GLU* 3.3 25.6 - - + +
298F ALA 3.0 2.6 + - - -
299F ASN* 1.3 75.4 - - - +
301F ARG* 1.3 60.1 + - - +
303F VAL* 4.2 2.3 + - + +
304F VAL* 3.3 22.5 + - - +
325F ASN* 3.2 34.3 - - - +
328F LEU* 4.8 4.3 - - + -
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Residues in contact with ARG 301 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235F ILE* 3.6 24.5 + - + +
236F GLY* 3.7 21.6 + - - -
238F VAL 4.1 10.7 + - - +
239F ALA* 5.4 1.6 - - - +
240F LEU* 3.6 39.9 - - + +
298F ALA 4.6 2.9 - - - +
299F ASN 3.1 0.2 - - - -
300F LEU* 1.3 78.4 - - - +
302F LEU* 1.3 65.3 + - - +
303F VAL 3.2 0.4 - - - -
304F VAL* 3.1 7.1 + - - +
305F SER* 3.0 22.2 + - - -
6H T 3.5 26.2 - - - +
7H G 3.1 63.3 + - - +
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Residues in contact with LEU 302 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299F ASN* 3.3 20.2 + - + +
301F ARG* 1.3 79.7 - - - +
303F VAL* 1.3 61.2 + - - +
305F SER* 2.3 28.8 + - - +
306F LEU* 3.4 13.0 - - + +
344F SER* 3.8 34.8 - - - +
347F ALA* 4.0 17.9 - - + -
348F THR* 4.3 9.4 - - - +
351F ILE* 4.5 9.6 - - + -
5H A 4.1 22.4 - - + -
6H T 3.2 37.1 + - + +
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Residues in contact with VAL 303 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299F ASN 3.8 2.1 + - - +
300F LEU* 4.5 4.3 - - + +
301F ARG 3.2 0.4 - - - -
302F LEU* 1.3 77.8 - - - +
304F VAL* 1.3 62.9 + - + +
305F SER 3.2 0.5 + - - -
306F LEU* 3.2 5.9 + - - +
307F ALA* 3.0 21.6 + - + +
321F ILE* 3.5 24.2 - - + +
324F GLY* 3.8 9.4 - - - -
325F ASN* 3.2 35.0 - - - +
328F LEU* 3.6 25.1 - - + -
351F ILE* 3.6 34.8 - - + -
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Residues in contact with VAL 304 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231F TYR* 3.8 2.0 - - + +
232F LEU* 3.9 25.4 - - + -
235F ILE* 3.6 20.2 - - + -
300F LEU 3.3 21.3 - - - +
301F ARG* 3.1 5.8 + - - +
303F VAL* 1.3 76.3 - - + +
305F SER* 1.3 63.3 + - - +
306F LEU 3.4 0.3 + - - -
307F ALA* 3.5 13.0 + - - +
308F LYS* 3.6 15.9 + - - +
317F PHE* 4.2 18.3 - - + -
321F ILE* 3.8 24.2 - - + -
7H G 4.5 11.2 - - - -
8H G 4.7 5.3 - - - +
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Residues in contact with SER 305 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301F ARG 3.0 7.4 + - - -
302F LEU* 2.3 36.2 + - - +
304F VAL* 1.3 78.4 - - - +
306F LEU* 1.3 60.4 + - - +
308F LYS* 3.2 37.2 - - - +
309F ARG* 3.9 11.4 + - - -
6H T 3.6 28.7 - - - -
7H G 4.0 13.0 + - - -
8H G 5.9 0.9 - - - -
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Residues in contact with LEU 306 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302F LEU* 3.4 23.1 - - + +
303F VAL 3.2 5.8 + - - +
305F SER* 1.3 82.1 + - - +
307F ALA* 1.3 59.5 + - - +
308F LYS 3.4 1.1 - - - -
309F ARG* 3.9 29.1 + - - +
310F TYR* 3.2 27.1 - - + -
348F THR* 3.7 39.0 - - + +
351F ILE* 3.6 34.1 - - + -
352F ARG* 4.5 17.3 - - + +
355F ILE* 4.6 4.9 - - + -
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Residues in contact with ALA 307 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303F VAL* 3.0 17.2 + - + +
304F VAL 3.5 4.5 + - - +
305F SER 3.4 0.2 - - - -
306F LEU* 1.3 76.4 - - - +
308F LYS* 1.3 62.6 + - - +
309F ARG 3.1 6.5 + - - -
310F TYR* 3.2 11.5 + - - +
317F PHE* 4.0 2.2 - - + -
320F LEU* 3.5 20.3 - - + +
321F ILE* 4.1 34.3 - - + +
355F ILE* 3.9 21.3 - - + -
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Residues in contact with LYS 308 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398C ARG* 3.6 6.4 + - - -
304F VAL 3.6 8.5 + - - +
305F SER* 3.2 28.6 + - - +
307F ALA* 1.3 79.1 - - - +
309F ARG* 1.3 68.4 + - + +
310F TYR 3.2 0.4 - - - -
311F THR* 3.2 29.3 - - - +
317F PHE* 3.7 23.3 - - + -
7H G 5.2 4.6 + - - -
8H G 3.6 37.4 + - - +
9H G 3.9 25.3 + - - +
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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