Contacts of the strand formed by residues 254 - 260 (chain G) in PDB entry 1ZMD
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 254 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164G THR* 3.6 28.9 - - - +
165G ILE* 3.6 29.6 - - + -
246G ALA* 4.2 16.2 - - + -
247G THR 3.5 10.3 - - - +
248G LYS* 4.2 13.5 - - + -
252G GLY 4.8 2.5 - - - +
253G LYS* 1.3 81.1 - - - +
255G ASP* 1.3 73.2 + - - +
256G VAL* 3.8 9.1 + - + -
269G ILE 3.7 0.7 - - - +
270G THR* 3.1 6.1 - - - -
271G CYS* 2.9 40.1 + - - +
272G ASP 4.2 6.3 - - - +
273G VAL* 4.7 0.4 - - - -
274G LEU* 4.1 16.4 - - + +
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Residues in contact with ASP 255 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246G ALA* 3.2 4.7 - - - +
247G THR* 2.9 42.1 + - - +
249G LYS* 3.0 39.4 + - + +
253G LYS 4.2 0.4 + - - -
254G ILE* 1.3 71.2 - - - +
256G VAL* 1.3 61.4 + - - +
257G SER* 3.9 2.6 + - - +
268G VAL* 3.6 19.7 - - + +
269G ILE 3.4 2.7 - - - -
270G THR* 2.8 24.1 + - - +
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Residues in contact with VAL 256 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182G VAL* 4.3 7.6 - - + -
243G VAL* 3.5 32.5 - - + -
245G GLY 3.6 5.2 - - - +
246G ALA* 4.4 0.9 - - + +
254G ILE* 4.2 7.2 - - + +
255G ASP* 1.3 75.0 - - - +
257G SER* 1.3 63.0 + - - +
258G ILE* 3.6 11.8 + - + -
268G VAL* 3.3 4.1 - - - -
269G ILE* 2.6 53.5 + - + +
271G CYS* 4.1 19.3 - - - -
274G LEU* 3.8 28.7 - - + -
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Residues in contact with SER 257 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243G VAL* 3.6 4.0 - - - +
244G THR* 2.7 46.0 + - - -
245G GLY* 2.9 19.6 + - - +
246G ALA* 5.0 0.7 + - - -
255G ASP* 3.9 3.4 + - - +
256G VAL* 1.3 71.3 - - - +
258G ILE* 1.3 55.3 + - - +
267G GLU 3.6 7.4 - - - -
268G VAL* 4.0 13.0 - - - +
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Residues in contact with ILE 258 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207G VAL* 4.3 5.6 - - + -
238G LYS* 3.8 31.6 - - + -
241G THR* 3.7 13.9 - - + -
242G LYS 3.5 5.4 - - - +
243G VAL* 4.0 15.7 - - + -
244G THR* 4.4 1.8 - - - +
256G VAL* 4.0 12.6 - - + +
257G SER* 1.3 80.3 - - - +
259G GLU* 1.3 67.8 + - - +
266G ALA* 3.4 2.1 - - - +
267G GLU* 2.8 64.5 + - + +
269G ILE* 3.8 33.2 - - + -
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Residues in contact with GLU 259 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241G THR* 3.3 8.3 - - - +
242G LYS* 2.9 34.6 + - + +
244G THR* 3.7 27.4 + - + +
258G ILE* 1.3 78.9 - - - +
260G ALA* 1.3 74.0 + - - +
263G GLY* 4.1 5.2 - - - -
264G GLY* 3.1 30.2 + - - +
265G LYS 3.6 7.9 - - - -
266G ALA* 3.8 15.7 - - - +
267G GLU* 5.9 0.2 - - - -
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Residues in contact with ALA 260 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299F ARG* 3.7 31.6 - - - +
240G ASN 3.7 7.4 - - - +
241G THR* 4.5 1.8 - - - +
242G LYS* 3.6 5.9 - - - -
259G GLU* 1.3 76.7 - - - +
261G ALA* 1.3 61.7 + - - +
262G SER* 4.1 4.3 - - - +
263G GLY* 2.8 27.9 + - - +
264G GLY 2.7 18.8 + - - +
265G LYS* 4.0 12.0 - - + +
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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