Contacts of the helix formed by residues 246 - 253 (chain B) in PDB entry 5FLM
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 GLY 246 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1291A ASN* 4.8 2.0 - - - +
244B GLY 3.6 3.2 + - - -
245B GLN* 1.3 78.4 - - - +
247B ALA* 1.3 65.8 + - - -
248B LYS 3.4 2.7 - - - -
249B LYS* 4.0 8.7 - - - +
250B SER* 3.1 26.0 + - - -
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Residues in contact with ALA 247 (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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1287A CYS* 4.0 19.1 - - - -
1291A ASN* 6.0 0.7 - - - +
246B GLY* 1.3 74.1 - - - +
248B LYS* 1.3 65.8 + - + +
251B ALA* 3.5 20.1 + - - +
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Residues in contact with LYS 248 (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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246B GLY 3.4 0.2 - - - -
247B ALA* 1.3 79.4 - - + +
249B LYS* 1.3 77.1 + - + +
251B ALA* 3.2 4.5 + - - +
252B ILE* 3.0 36.9 + - + +
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Residues in contact with LYS 249 (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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242B ARG* 4.9 6.3 - - - +
244B GLY* 3.3 37.9 - - - +
245B GLN 4.8 1.6 - - - +
246B GLY* 3.7 10.2 + - - +
248B LYS* 1.3 87.4 - - + +
250B SER* 1.3 62.7 + - - +
252B ILE* 3.3 27.4 - - + +
253B GLY* 3.4 10.6 + - - +
255B ARG* 4.7 17.1 - - - +
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Residues in contact with SER 250 (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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1286A ARG 4.8 0.2 - - - +
1287A CYS* 3.8 6.1 + - - -
1290A SER* 3.1 43.3 + - - -
1291A ASN* 3.0 26.8 + - - -
242B ARG 5.8 1.1 - - - -
244B GLY 4.2 5.5 + - - -
246B GLY 3.1 21.3 + - - -
247B ALA 4.3 3.1 - - - -
249B LYS* 1.3 78.3 - - - +
251B ALA* 1.3 61.1 + - - +
253B GLY* 4.4 2.9 + - - -
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Residues in contact with ALA 251 (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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1283A VAL* 4.7 18.6 - - + +
1286A ARG* 5.3 11.9 - - + +
1287A CYS* 4.5 20.9 - - + +
247B ALA 3.5 15.1 + - - +
248B LYS* 3.2 6.7 + - - +
250B SER* 1.3 80.5 - - - +
252B ILE* 1.3 67.0 + - + +
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Residues in contact with ILE 252 (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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248B LYS* 3.0 28.3 + - + +
249B LYS* 3.3 23.1 - - + +
251B ALA* 1.3 82.9 - - + +
253B GLY* 1.3 79.3 + - - +
255B ARG* 3.2 39.3 - - + +
303B PRO* 3.1 34.1 - - + +
306B ASP* 6.1 4.5 - - + -
307B GLU* 5.1 6.7 - - + +
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Residues in contact with GLY 253 (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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241B ALA 5.2 1.0 - - - +
242B ARG* 4.7 14.4 - - - -
249B LYS 3.4 10.7 + - - +
250B SER 4.4 2.7 + - - -
251B ALA 3.6 1.6 - - - -
252B ILE* 1.3 97.7 - - - +
254B GLN* 1.3 66.6 + - - -
255B ARG 3.5 2.8 + - - -
303B PRO* 4.7 0.2 - - - -
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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