Contacts of the helix formed by residues 251 - 260 (chain D) in PDB entry 1FM6
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 ASP 251 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249D ILE* 3.8 0.7 - - - +
250D TYR* 1.3 96.6 + - + +
252D MET* 1.3 63.6 + - - +
253D ASN* 3.4 22.9 + - - +
254D SER* 2.6 56.8 + - - -
255D LEU* 2.8 19.4 + - - +
352D PHE* 3.5 17.1 - - - -
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Residues in contact with MET 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251D ASP* 1.3 79.2 - - - +
253D ASN* 1.3 70.7 + - - +
255D LEU* 3.2 8.1 + - - +
256D MET* 3.0 52.9 + - + +
277D VAL* 3.5 29.8 - - + -
280D ARG* 5.3 5.0 + - - +
352D PHE* 3.8 10.0 - - + -
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Residues in contact with ASN 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251D ASP* 3.4 15.2 + - - +
252D MET* 1.3 85.3 - - - +
254D SER* 1.3 58.7 + - - +
256D MET* 2.8 29.2 - - + +
257D MET* 2.8 33.5 + - + +
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Residues in contact with SER 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247D PHE* 3.5 8.4 - - - -
248D VAL 4.0 7.4 - - - -
249D ILE* 4.0 2.9 - - - +
250D TYR* 3.1 33.1 + - - -
251D ASP* 2.6 52.1 + - - -
253D ASN* 1.3 72.1 - - - +
255D LEU* 1.3 64.5 + - - +
257D MET* 3.0 15.2 + - - +
258D GLY* 2.8 20.1 + - - -
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Residues in contact with LEU 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249D ILE* 3.4 30.7 - - + -
251D ASP 2.8 18.0 + - - +
252D MET* 3.4 5.8 - - - +
254D SER* 1.3 73.8 + - - +
256D MET* 1.3 54.1 - - - +
258D GLY* 3.0 2.1 + - - -
259D GLU* 2.6 62.5 + - + +
277D VAL* 3.8 31.9 - - + +
280D ARG* 4.5 11.9 - - + +
281D ILE* 3.9 21.1 - - + -
348D MET* 4.5 11.0 - - + -
352D PHE* 4.1 3.8 - - + -
503D BRL 6.2 0.7 - - + -
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Residues in contact with MET 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252D MET* 3.0 37.5 + - + +
253D ASN* 2.8 35.0 + - - +
255D LEU* 1.3 76.3 - - - +
257D MET* 1.3 54.4 + - + +
259D GLU* 4.1 5.6 - - - -
260D ASP* 2.3 63.3 + - - +
273D GLN* 4.0 20.2 - - - +
280D ARG* 4.6 5.8 - - - +
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Residues in contact with MET 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247D PHE* 3.7 26.9 - - + -
253D ASN* 2.8 23.0 + - + +
254D SER* 3.0 12.3 + - - +
256D MET* 1.3 73.7 - - + +
258D GLY* 1.3 60.9 + - - +
260D ASP* 3.9 2.4 - - - -
261D LYS* 3.0 28.5 + - - +
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Residues in contact with GLY 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247D PHE* 3.6 22.1 - - - -
249D ILE* 4.3 12.1 - - - -
254D SER 2.8 15.4 + - - -
255D LEU 3.5 2.5 - - - -
257D MET* 1.3 72.8 - - - +
259D GLU* 1.3 63.0 + - - +
261D LYS* 3.4 15.3 - - - +
262D ILE* 4.0 8.1 - - - +
265D LYS* 4.0 4.9 + - - -
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Residues in contact with GLU 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255D LEU* 2.6 37.0 + - + +
256D MET* 3.4 3.0 - - - +
258D GLY* 1.3 68.7 - - - +
260D ASP* 1.3 56.7 + - - +
261D LYS 2.6 15.1 + - - -
262D ILE* 2.7 32.1 + - + +
263D LYS 3.7 0.3 + - - -
271D GLN* 4.5 3.1 - - - +
272D GLU* 4.4 19.7 - - - +
273D GLN* 3.5 13.9 + - - +
280D ARG* 2.9 57.5 + - - +
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Residues in contact with ASP 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256D MET* 2.3 58.7 + - - +
257D MET* 3.9 2.9 - - - +
259D GLU* 1.3 66.7 - - - +
261D LYS* 1.3 60.1 + - - -
262D ILE 3.1 0.7 - - - -
263D LYS* 2.6 67.4 + - + +
264D PHE* 3.4 5.2 + - - +
272D GLU* 5.4 0.4 - - - -
273D GLN* 3.0 15.2 + - - +
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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