Contacts of the strand formed by residues 254 - 260 (chain E) in PDB entry 1ZMC
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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164E THR* 3.2 35.9 - - - +
165E ILE* 4.1 8.7 - - + -
246E ALA* 4.2 10.3 - - + -
247E THR 3.5 11.2 - - - +
248E LYS* 3.8 15.9 - - + +
252E GLY 4.3 0.4 - - - +
253E LYS* 1.3 80.5 - - - +
255E ASP* 1.3 73.4 + - - +
256E VAL* 3.9 13.9 + - + -
269E ILE 3.5 1.6 - - - +
270E THR* 3.2 5.2 - - - -
271E CYS* 2.9 37.3 + - - +
272E ASP 3.5 17.9 - - - +
273E VAL 4.1 0.2 - - - -
274E LEU* 3.7 22.0 - - + +
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Residues in contact with ASP 255 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246E ALA* 3.0 5.2 - - - +
247E THR* 2.9 49.5 + - - +
249E LYS* 3.2 32.7 + - + +
254E ILE* 1.3 70.2 - - - +
256E VAL* 1.3 62.1 + - - +
257E SER 4.0 0.6 + - - -
268E VAL* 3.7 20.6 - - + +
269E ILE 3.4 1.6 - - - -
270E THR* 2.9 26.9 + - - +
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Residues in contact with VAL 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182E VAL* 4.6 12.1 - - + -
184E ILE* 5.3 0.2 - - + -
243E VAL* 3.8 31.2 - - + -
245E GLY 3.5 5.4 - - - +
246E ALA* 4.2 4.7 - - + -
254E ILE* 4.1 12.6 - - + -
255E ASP* 1.3 75.0 - - - +
257E SER* 1.3 61.8 + - - +
258E ILE* 3.7 14.0 + - + +
268E VAL* 3.4 2.4 - - - -
269E ILE* 2.8 43.3 + - + +
271E CYS* 4.3 9.4 - - - -
274E LEU* 3.7 31.4 - - + -
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Residues in contact with SER 257 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243E VAL* 3.7 1.6 - - - +
244E THR* 2.5 50.1 + - - -
245E GLY* 2.9 17.9 + - - +
255E ASP 4.0 2.2 + - - -
256E VAL* 1.3 73.1 - - - +
258E ILE* 1.3 62.7 + - - +
267E GLU 3.4 5.8 - - - -
268E VAL* 3.9 18.4 - - - -
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Residues in contact with ILE 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207E VAL* 4.1 9.9 - - + -
238E LYS* 4.1 22.9 - - + -
241E THR* 4.7 9.6 - - + -
242E LYS 3.2 8.3 - - - +
243E VAL* 3.9 23.1 - - + -
244E THR* 4.4 1.3 - - - +
256E VAL* 4.1 13.7 - - + +
257E SER* 1.3 80.9 - - - +
259E GLU* 1.3 67.9 + - - +
265E LYS 4.6 0.2 - - - -
266E ALA* 3.3 7.1 - - - +
267E GLU* 2.8 69.5 + - + +
268E VAL 4.8 0.2 - - - +
269E ILE* 4.2 23.3 - - + -
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Residues in contact with GLU 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241E THR* 3.2 9.2 - - - -
242E LYS* 2.7 44.3 + - + +
244E THR* 3.3 25.0 - - + +
258E ILE* 1.3 76.2 - - - +
260E ALA* 1.3 60.9 + - - +
263E GLY* 4.5 4.3 - - - -
264E GLY* 3.1 37.0 + - - +
265E LYS* 4.1 3.8 - - - -
266E ALA* 4.3 14.3 - - - +
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Residues in contact with ALA 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240E ASN 3.7 7.6 - - - +
241E THR* 4.0 6.3 - - + -
242E LYS* 4.7 1.7 - - - +
259E GLU* 1.3 75.2 - - - +
261E ALA* 1.3 67.4 + - - +
262E SER* 4.4 7.4 - - - +
263E GLY* 2.8 32.6 + - - +
264E GLY 2.8 8.5 + - - -
265E LYS* 3.5 28.2 - - + +
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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