Contacts of the helix formed by residues 280 - 289 (chain B) in PDB entry 5FHH
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 280 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279B ALA* 1.3 86.2 - - + +
281B LEU* 1.3 70.7 + - + +
282B ALA* 4.3 7.9 - - + +
283B GLN* 2.9 25.2 + - + +
284B CYS* 2.9 19.4 + - - -
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Residues in contact with LEU 281 (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 ALA 3.7 1.2 + - - -
280B PRO* 1.3 74.3 - - + +
282B ALA* 1.3 64.5 + - + +
284B CYS* 2.9 12.7 + - + -
285B VAL* 2.4 50.7 + - + +
318B LYS* 5.7 5.4 - - + +
321B ALA* 4.2 26.7 - - + -
322B VAL* 5.5 3.4 - - + -
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Residues in contact with ALA 282 (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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280B PRO* 3.1 7.3 - - + -
281B LEU* 1.3 85.4 - - + +
283B GLN* 1.3 66.5 + - - +
285B VAL* 4.1 6.5 - - - +
286B ALA* 3.0 21.7 + - - +
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Residues in contact with GLN 283 (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 ALA* 3.8 18.4 - - + -
280B PRO* 2.9 29.7 + - + +
282B ALA* 1.3 75.0 - - - +
284B CYS* 1.3 55.6 + - - +
286B ALA* 2.6 29.3 + - - +
287B LEU* 2.9 29.4 + - + +
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Residues in contact with CYS 284 (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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274B ILE* 3.1 48.2 - - + +
276B SER 4.3 1.8 - - - -
277B GLY* 4.6 3.6 - - - -
278B GLN 3.9 9.4 - - - -
279B ALA* 3.6 18.6 - - - -
280B PRO 2.9 19.9 + - - -
281B LEU* 2.9 13.9 + - - +
283B GLN* 1.3 75.8 - - - +
285B VAL* 1.3 51.2 + - - +
287B LEU* 3.2 8.4 + - - -
288B ALA 2.6 32.2 + - - -
318B LYS* 6.1 4.7 - - + -
322B VAL* 4.4 8.1 - - + -
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Residues in contact with VAL 285 (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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281B LEU* 2.4 46.9 + - + +
282B ALA* 4.1 6.5 - - - +
284B CYS* 1.3 67.3 - - - +
286B ALA* 1.3 61.1 + - - +
288B ALA* 3.2 8.7 + - - +
289B GLN* 3.1 28.7 + - + +
321B ALA 4.7 1.1 - - - +
322B VAL* 4.1 26.7 - - + +
325B ALA* 4.3 19.7 - - + -
326B VAL* 4.1 18.4 - - + +
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Residues in contact with ALA 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B ALA 3.0 15.2 + - - +
283B GLN* 2.6 18.6 + - - +
285B VAL* 1.3 69.5 - - - +
287B LEU* 1.3 64.7 + - + +
288B ALA 3.1 1.1 - - - -
289B GLN* 3.1 21.9 + - - +
290B ARG* 4.2 4.9 + - - +
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Residues in contact with LEU 287 (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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273B GLY 3.7 17.2 - - - +
274B ILE* 4.4 6.7 - - + +
279B ALA* 5.5 3.4 - - + -
283B GLN* 2.9 56.7 + - + +
284B CYS* 3.8 8.1 - - - +
286B ALA* 1.3 75.1 - - + +
288B ALA* 1.3 61.7 + - - +
289B GLN 3.2 9.3 - - - +
290B ARG* 5.0 1.7 - - - +
293B VAL* 3.8 8.8 - - - +
534B THR* 4.0 29.6 - - + +
535B GLY* 3.9 12.6 - - - -
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Residues in contact with ALA 288 (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 ALA 4.2 11.2 - - - +
273B GLY 4.2 0.9 + - - -
274B ILE* 3.7 10.1 - - + -
284B CYS 2.6 21.6 + - - +
285B VAL 3.3 7.4 - - - +
286B ALA 3.1 0.2 - - - -
287B LEU* 1.3 73.1 - - - +
289B GLN* 1.3 58.8 + - - +
293B VAL* 3.1 25.4 - - - +
294B ARG* 3.3 7.8 + - - +
297B TRP* 4.3 4.0 - - + +
322B VAL* 3.6 28.3 - - + -
326B VAL* 4.3 9.1 - - + +
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Residues in contact with GLN 289 (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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525A HIS* 4.5 18.5 + - - -
285B VAL* 3.1 18.5 + - + +
286B ALA* 3.1 10.2 + - - +
287B LEU 3.2 8.5 - - - +
288B ALA* 1.3 81.7 - - - +
290B ARG* 1.3 80.6 + - - +
291B PRO 4.2 1.4 - - - +
293B VAL* 3.9 5.9 - - - +
294B ARG* 4.0 15.6 - - - +
325B ALA 5.6 0.8 + - - -
326B VAL* 3.9 33.3 + - + +
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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