Contacts of the strand formed by residues 246 - 253 (chain A) in PDB entry 1ZD4
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 VAL 246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241A THR* 3.6 2.3 - - - -
242A VAL* 2.9 48.1 + - + +
243A LYS* 2.7 29.5 + - + +
244A PRO 3.7 0.2 - - - -
245A ARG* 1.3 82.6 - - + +
247A ARG* 1.3 62.8 + - - +
248A LEU* 4.9 6.5 - - + -
292A LYS* 3.9 21.3 - - + -
298A SER* 3.4 10.3 - - - -
300A PRO* 5.0 3.6 - - + -
305A GLU* 3.8 19.1 - - - +
314A GLU* 3.5 21.5 - - - +
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Residues in contact with ARG 247 (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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239A TYR* 3.4 45.0 - - + +
240A VAL 3.3 26.2 - - - +
241A THR* 3.9 14.6 - - + +
245A ARG 4.2 0.4 - - - -
246A VAL* 1.3 73.4 - - - +
248A LEU* 1.3 62.3 + - - +
296A GLU* 3.7 17.5 + - - +
297A SER* 3.3 5.4 - - - -
298A SER* 2.5 39.7 + - - +
455A LYS* 6.2 2.0 - - - +
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Residues in contact with LEU 248 (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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238A GLY 3.9 0.2 - - - +
239A TYR* 3.4 5.3 - - - -
240A VAL* 2.9 34.2 + - - +
242A VAL* 3.3 34.5 - - + -
246A VAL* 4.2 4.7 - - + -
247A ARG* 1.3 75.8 - - - +
249A HIS* 1.3 60.0 + - - +
250A PHE* 4.7 2.5 - - - -
289A MET* 4.2 14.1 - - + -
290A ASP 4.3 1.8 - - - +
291A MET 4.6 0.2 - - - -
292A LYS* 3.7 42.0 - - + +
296A GLU 4.9 0.2 - - - -
297A SER* 3.4 7.2 - - - +
298A SER 5.7 0.4 - - - +
314A GLU* 4.4 7.0 - - + +
315A MET* 3.1 34.3 - - + -
318A PHE* 4.4 9.2 - - + -
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Residues in contact with HIS 249 (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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237A HIS* 3.0 30.6 + - + +
238A GLY 3.3 7.9 - - - +
239A TYR* 3.4 22.7 - + + -
248A LEU* 1.3 74.5 - - - +
250A PHE* 1.3 76.6 + - - +
251A VAL* 4.1 0.4 - - + -
269A TRP* 3.8 25.8 - + - -
289A MET* 4.0 3.2 - - - +
290A ASP* 2.9 41.8 + - + +
296A GLU* 3.4 58.1 - - + +
297A SER* 2.8 8.9 + - - +
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Residues in contact with PHE 250 (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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237A HIS* 3.6 3.6 - - - -
238A GLY* 2.9 63.5 + - - -
239A TYR 3.9 2.9 - - - -
240A VAL* 4.2 7.2 - - + -
248A LEU 4.7 0.9 - - - -
249A HIS* 1.3 85.0 + - - +
251A VAL* 1.3 69.1 + - - +
252A GLU* 3.6 21.1 - - + -
269A TRP* 5.6 0.2 - - - -
287A LEU* 3.5 36.6 - - + +
288A ALA 3.2 14.1 - - - +
289A MET* 3.7 15.5 - - - -
290A ASP 4.6 0.2 - - - +
318A PHE* 3.5 29.8 - + - -
322A LEU* 4.2 19.7 - - + -
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Residues in contact with VAL 251 (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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235A MET* 3.4 41.3 - - + -
236A SER 3.4 3.1 - - - +
237A HIS* 3.8 19.1 - - + +
249A HIS* 4.1 1.1 - - + -
250A PHE* 1.3 75.7 - - - +
252A GLU* 1.3 63.1 + - - +
253A LEU 4.3 0.2 + - - -
269A TRP* 3.3 54.3 - - + +
276A ILE* 4.4 7.3 - - + +
286A VAL* 3.6 2.1 - - - +
287A LEU* 3.5 2.9 - - - -
288A ALA* 2.8 34.9 + - + +
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Residues in contact with GLU 252 (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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235A MET* 5.0 0.2 - - - +
236A SER* 3.1 41.7 + - - +
238A GLY 5.9 0.2 - - - +
250A PHE* 3.6 24.2 - - + -
251A VAL* 1.3 75.6 - - - +
253A LEU* 1.3 69.7 + - - +
254A GLY 5.3 1.8 - - - +
285A ARG* 2.7 47.7 + - + +
286A VAL 3.3 3.4 - - - +
287A LEU* 3.0 20.4 - - + +
322A LEU* 5.9 0.6 - - - +
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Residues in contact with LEU 253 (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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145A MET* 6.4 2.2 - - + -
230A CYS* 5.4 0.9 - - + -
235A MET* 4.0 19.1 - - + -
251A VAL 4.3 0.2 + - - -
252A GLU* 1.3 78.2 - - - +
254A GLY* 1.3 67.5 + - - +
276A ILE* 3.8 37.0 - - + +
277A PRO* 4.1 16.2 - - + -
280A ALA* 3.7 11.7 - - + +
284A TYR 3.6 1.7 - - - +
285A ARG* 4.6 0.2 - - - -
286A VAL* 3.0 34.9 + - - +
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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