Contacts of the strand formed by residues 241 - 248 (chain B) 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 THR 241 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B VAL* 3.5 13.6 - - + +
208B GLU 3.0 7.9 + - - -
209B PHE* 3.4 4.0 + - - +
238B LYS* 3.4 23.8 + - + +
239B LEU 3.3 12.0 + - - -
240B ASN* 1.3 76.5 + - - +
242B LYS* 1.3 58.0 + - - +
258B ILE* 3.5 37.0 - - + -
259B GLU 3.1 19.1 - - - +
260B ALA* 5.2 0.9 - - - -
265B LYS* 6.2 0.2 - - - -
481B NAD 3.2 23.0 - - - -
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Residues in contact with LYS 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B PHE* 4.0 25.6 - - + -
241B THR* 1.3 72.7 - - - +
243B VAL* 1.3 70.4 + - - +
244B THR* 3.4 5.1 + - - +
258B ILE* 3.3 5.0 - - - +
259B GLU* 2.8 62.2 + - - +
260B ALA 4.0 11.9 + - - -
261B ALA* 4.0 17.3 + - - +
263B GLY* 4.6 6.3 - - - -
481B NAD 3.9 9.2 - - - +
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Residues in contact with VAL 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B PHE* 3.1 25.0 - - + -
158B ILE* 4.8 1.1 - - + -
184B ILE* 4.0 26.7 - - + -
207B VAL* 3.3 36.6 - - + -
242B LYS* 1.3 75.8 - - - +
244B THR* 1.3 62.6 + - - +
245B GLY* 4.1 9.6 - - - +
256B VAL* 3.5 28.3 - - + -
257B SER 3.4 6.3 - - - +
258B ILE* 4.0 5.6 - - + -
481B NAD 3.3 22.8 + - - +
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Residues in contact with THR 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B PHE* 4.2 9.7 - - - -
242B LYS* 3.4 8.3 + - - +
243B VAL* 1.3 74.4 - - - +
245B GLY* 1.3 59.8 + - - +
257B SER* 2.8 27.1 + - - -
258B ILE 4.4 0.2 + - - -
259B GLU* 3.6 32.6 + - - +
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Residues in contact with GLY 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B PHE* 5.4 0.7 - - - -
158B ILE* 4.4 14.4 - - - -
243B VAL* 3.5 1.3 - - - -
244B THR* 1.3 83.8 - - - +
246B ALA* 1.3 59.0 - - - +
256B VAL* 3.7 2.9 - - - +
257B SER* 2.7 34.3 + - - +
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Residues in contact with ALA 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B GLY 5.2 3.8 - - - +
158B ILE* 4.1 23.2 - - + +
165B ILE* 5.8 4.5 - - + +
245B GLY* 1.3 74.5 - - - +
247B THR* 1.3 69.0 + - - +
254B ILE* 4.6 2.9 - - + -
255B ASP 3.1 14.4 - - - +
256B VAL* 3.9 9.6 - - + -
257B SER* 5.5 0.9 - - - -
274B LEU* 3.9 28.3 - - + -
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Residues in contact with THR 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B ILE* 5.8 1.3 - - - -
246B ALA* 1.3 81.5 - - - +
248B LYS* 1.3 64.3 + - - +
249B LYS* 3.6 7.3 + - - +
254B ILE* 3.5 6.5 - - - -
255B ASP* 2.8 47.9 + - - +
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Residues in contact with LYS 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B ASP* 4.7 5.4 - - - +
163B ASP* 4.9 3.7 + - - -
164B THR* 3.2 38.2 + - + +
165B ILE* 4.8 14.7 - - + +
247B THR* 1.3 75.5 - - - +
249B LYS* 1.3 67.2 + - - +
252B GLY* 3.4 26.5 + - - +
253B LYS 3.7 8.3 - - - +
254B ILE* 4.4 9.6 - - + -
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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