Contacts of the helix formed by residues 279 - 287 (chain B) in PDB entry 5FLZ
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 SER 279 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181B GLU* 3.8 14.0 - - - +
185B LEU* 4.7 1.2 - - - +
277B VAL 4.3 1.0 + - - -
278B VAL* 1.3 79.3 - - - +
280B LEU* 1.3 69.2 + - - +
281B LYS* 3.2 31.5 + - - +
282B SER* 3.3 19.3 + - - -
283B LEU* 3.0 22.3 + - - +
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Residues in contact with LEU 280 (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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181B GLU* 3.5 27.1 - - + +
184B ILE* 4.6 16.4 - - + -
185B LEU* 4.4 13.0 - - + -
188B VAL* 4.0 38.4 - - + -
220B LEU* 4.1 28.7 - - + -
224B ILE* 4.9 6.1 - - + -
279B SER* 1.3 76.7 + - - +
281B LYS* 1.4 56.4 + - - +
283B LEU* 3.0 17.4 + - + +
284B TYR* 2.7 41.1 + - + +
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Residues in contact with LYS 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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68A ILE* 2.5 41.4 - - + +
70A LEU* 5.7 0.2 - - + -
151A LEU* 5.1 2.1 - - - +
154A LEU* 5.5 5.8 - - + +
155A VAL* 5.5 7.4 - - + -
158A LEU* 3.4 35.1 - - + +
216B PHE* 4.8 11.0 - - + -
220B LEU* 4.1 16.2 - - + -
279B SER* 3.6 20.0 - - - +
280B LEU* 1.4 74.8 - - + +
282B SER* 1.4 64.0 + - - +
284B TYR* 3.3 15.4 + - - +
285B ARG* 3.3 22.5 + - - +
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Residues in contact with SER 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A VAL* 4.1 15.8 - - - +
277B VAL 5.4 0.2 + - - -
278B VAL* 3.5 12.8 - - - -
279B SER* 3.3 31.8 + - - -
281B LYS* 1.4 77.2 - - - +
283B LEU* 1.4 64.9 + - - +
285B ARG* 3.2 33.9 + - - +
286B GLU* 3.1 24.4 + - - +
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Residues in contact with LEU 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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185B LEU* 5.1 9.9 - - + -
188B VAL* 5.3 5.8 - - + -
192B LEU* 3.9 35.2 - - + -
224B ILE* 5.6 1.6 - - + -
271B LEU* 3.5 35.9 - - + -
278B VAL* 4.3 8.7 - - + -
279B SER 3.0 14.8 + - - +
280B LEU* 3.0 17.7 + - + +
282B SER* 1.4 75.2 - - - +
284B TYR* 1.4 82.9 + - + +
286B GLU* 3.7 3.2 + - - +
287B ILE* 3.2 38.1 + - + +
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Residues in contact with TYR 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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220B LEU* 2.6 45.5 + - + +
223B LEU* 3.6 40.8 - - + -
224B ILE* 3.5 24.7 + - + +
280B LEU* 2.7 37.4 + - + +
281B LYS* 3.4 11.2 - - - +
282B SER 3.1 0.2 - - - -
283B LEU* 1.4 89.5 - - + +
285B ARG* 1.4 67.0 - - - +
287B ILE* 3.4 6.0 + - + +
288B TYR* 3.1 44.9 + + + +
291B ILE* 5.4 12.0 - - + +
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Residues in contact with ARG 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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151A LEU* 3.1 52.2 + - + +
152A LYS* 4.7 10.5 - - - +
155A VAL* 4.0 30.8 - - + +
278B VAL* 5.6 2.8 - - - +
281B LYS 3.4 11.9 - - - +
282B SER* 3.2 36.7 + - - +
284B TYR* 1.4 63.8 - - - +
286B GLU* 1.4 97.6 + - - +
287B ILE 3.4 0.2 + - - -
288B TYR* 3.3 25.9 + - - +
289B GLU* 4.0 4.0 - - - +
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Residues in contact with GLU 286 (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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267B PHE* 5.0 7.8 - - - -
271B LEU* 4.2 24.2 - - + -
278B VAL* 5.8 1.8 - - + -
282B SER* 3.1 17.6 + - - +
283B LEU 4.1 3.1 - - - +
285B ARG* 1.4 119.3 + - - +
287B ILE* 1.3 56.3 + - - +
289B GLU* 2.9 21.9 - - - +
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Residues in contact with ILE 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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192B LEU* 5.4 2.0 - - + -
264B TYR* 3.6 41.1 - - + +
267B PHE* 4.3 21.1 - - + -
271B LEU* 4.8 14.1 - - + -
283B LEU* 3.2 35.3 + - + +
284B TYR* 3.6 7.2 - - + +
285B ARG 3.4 0.4 + - - -
286B GLU* 1.3 78.2 - - + +
288B TYR* 1.4 62.4 + - - +
289B GLU* 3.3 5.3 + - - -
290B ASN* 3.5 21.7 + - + +
291B ILE* 3.7 23.2 + - + +
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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