Contacts of the strand formed by residues 277 - 282 (chain F) in PDB entry 1M54
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 ILE 277 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251F LEU* 3.8 16.4 - - + +
261F ILE* 3.3 37.7 - - + +
264F ILE* 4.8 1.1 - - + -
265F ALA* 3.4 38.4 - - + +
268F LEU* 3.8 26.9 - - + -
269F LYS* 4.6 12.6 - - + -
275F CYS* 4.5 6.7 - - + -
276F ARG* 1.3 75.4 - - - +
278F ILE* 1.3 70.8 + - - +
319F VAL 3.5 11.9 - - - +
320F VAL* 4.3 3.8 - - - -
321F ASP* 3.4 25.2 + - - +
322F LYS 3.7 2.6 + - - -
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Residues in contact with ILE 278 (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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250F MET* 3.9 29.6 - - + -
251F LEU 3.2 6.3 + - - +
252F VAL* 4.0 13.2 - - + -
253F ALA 3.1 24.9 + - - +
261F ILE* 3.5 8.6 - - - +
276F ARG* 3.9 22.0 - - - +
277F ILE* 1.3 86.7 - - - +
279F GLY* 1.3 67.0 + - - +
280F VAL* 5.2 0.2 - - - -
322F LYS* 3.4 21.3 - - + +
324F PHE* 3.5 32.5 - - + -
356F VAL* 4.3 11.2 - - + -
360F ALA* 4.4 7.4 - - + +
363F GLU* 5.9 1.1 - - - +
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Residues in contact with GLY 279 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253F ALA 3.6 4.0 - - - -
255F VAL* 4.2 0.2 - - - -
261F ILE* 3.7 12.3 - - - -
278F ILE* 1.3 74.5 - - - +
280F VAL* 1.3 58.1 + - - +
320F VAL* 3.9 3.1 - - - +
322F LYS 2.6 16.3 + - - -
323F TRP* 3.2 21.6 - - - -
324F PHE* 2.7 33.6 + - - +
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Residues in contact with VAL 280 (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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252F VAL* 3.6 24.9 - - + -
253F ALA 3.1 12.5 + - - +
254F SER* 3.3 25.1 - - - -
255F VAL* 3.0 25.7 + - - +
279F GLY* 1.3 75.1 - - - +
281F ASP* 1.3 65.0 + - - +
282F PRO* 4.5 0.5 - - - +
306F ILE* 4.9 1.8 - - + -
323F TRP* 4.8 0.2 - - - -
324F PHE 3.3 2.9 - - - -
326F SER* 3.6 27.4 - - - +
352F SER* 4.3 12.8 - - - +
353F THR* 4.1 4.0 - - - -
356F VAL* 3.3 25.1 - - + -
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Residues in contact with ASP 281 (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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255F VAL 4.8 0.7 - - - +
279F GLY 4.1 0.2 - - - -
280F VAL* 1.3 77.5 - - - +
282F PRO* 1.3 68.4 - - - +
285F SER* 2.7 27.8 + - - -
287F LEU* 3.3 13.8 + - - +
288F ALA* 3.0 24.2 + - + -
307F GLY* 3.1 5.9 + - - -
323F TRP* 4.2 11.2 - - + -
324F PHE 3.0 7.9 + - - +
325F LYS* 2.6 39.0 + - + +
326F SER* 2.7 30.4 + - - -
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Residues in contact with PRO 282 (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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281F ASP* 1.3 95.4 - - - +
283F GLU* 1.3 61.0 + - - +
285F SER* 2.8 31.9 + - - -
301F TYR* 3.6 28.3 - - + -
303F VAL* 5.2 5.6 - - + +
306F ILE* 3.5 28.2 - - + +
307F GLY* 3.2 31.9 - - - +
325F LYS* 4.0 2.4 + - - -
326F SER* 3.1 14.4 - - - +
327F ASN* 5.8 0.7 - - - -
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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