Contacts of the strand formed by residues 254 - 260 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A THR* 4.5 17.7 - - - +
165A ILE* 4.6 10.5 - - + -
246A ALA* 3.5 14.8 - - + -
247A THR 3.3 10.8 - - - +
248A LYS* 4.3 10.3 - - + -
252A GLY 4.1 6.7 - - - +
253A LYS* 1.3 80.3 - - - +
255A ASP* 1.3 64.5 + - - +
256A VAL* 3.4 28.2 + - + -
270A THR* 3.4 4.4 - - - -
271A CYS* 3.0 47.1 + - - +
272A ASP 4.4 10.1 - - - +
274A LEU* 3.5 25.4 - - + -
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Residues in contact with ASP 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A ALA* 3.3 4.0 - - - -
247A THR* 2.8 45.0 + - + +
249A LYS* 3.0 41.7 + - - +
254A ILE* 1.3 73.2 - - - +
256A VAL* 1.3 60.5 + - - +
257A SER 4.0 0.7 + - - -
268A VAL* 3.5 18.6 - - + -
269A ILE 3.4 2.2 - - - -
270A THR* 2.6 28.1 + - - -
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Residues in contact with VAL 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A VAL* 3.8 29.2 - - + -
243A VAL* 3.5 32.5 - - + -
245A GLY 3.6 4.3 - - - +
246A ALA* 4.9 1.6 - - + -
254A ILE* 3.4 26.9 - - + -
255A ASP* 1.3 72.9 - - - +
257A SER* 1.3 62.7 + - - +
258A ILE* 3.6 13.1 + - + -
268A VAL* 3.3 4.8 - - - -
269A ILE* 2.7 50.4 + - + +
271A CYS* 4.4 2.2 - - - -
274A LEU* 4.1 7.2 - - + -
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Residues in contact with SER 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A VAL* 3.5 1.4 - - - +
244A THR* 2.7 52.5 + - - -
245A GLY* 2.9 24.5 + - - +
255A ASP 4.0 2.0 + - - -
256A VAL* 1.3 71.7 - - - +
258A ILE* 1.3 57.5 + - - +
267A GLU 3.3 8.5 - - - -
268A VAL* 4.3 12.3 - - - +
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Residues in contact with ILE 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A VAL* 4.3 7.0 - - + -
238A LYS* 3.5 33.4 - - + -
241A THR* 3.8 11.0 - - + -
242A LYS 3.2 9.4 - - - +
243A VAL* 3.9 24.7 - - + -
244A THR* 4.3 2.2 + - - +
256A VAL* 3.9 11.2 - - + +
257A SER* 1.3 80.5 - - - +
259A GLU* 1.3 67.0 + - - +
266A ALA* 3.3 1.9 - - - +
267A GLU* 2.8 60.6 + - + +
269A ILE* 3.8 22.2 - - + -
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Residues in contact with GLU 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A THR* 3.4 7.4 - - - +
242A LYS* 2.8 50.5 + - + +
244A THR* 3.8 20.2 + - + +
258A ILE* 1.3 82.8 - - - +
260A ALA* 1.3 70.5 + - - +
263A GLY* 3.4 4.0 - - - -
264A GLY 2.8 38.1 + - - +
265A LYS 4.1 4.9 - - - -
266A ALA* 3.5 18.5 - - - +
267A GLU* 5.7 0.2 - - - -
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Residues in contact with ALA 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A ASN 3.7 9.2 - - - +
241A THR* 4.4 2.0 - - - +
242A LYS* 3.7 2.3 + - - -
259A GLU* 1.3 83.3 - - - +
261A ALA* 1.3 60.8 + - - +
262A SER* 4.2 7.6 - - - +
263A GLY* 2.9 39.9 + - - +
264A GLY 3.3 3.0 + - - -
265A LYS* 4.0 23.5 - - + +
97H LYS* 5.3 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