Contacts of the strand formed by residues 321 - 325 (chain D) in PDB entry 2Y7Q
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 PHE 321 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231D PRO* 3.4 29.8 - - + -
232D PRO* 3.3 39.7 - - + -
234D VAL* 4.0 18.8 - - + -
313D GLN* 3.4 2.8 - - - +
314D VAL* 2.7 43.1 + - + +
315D THR 5.6 0.7 - - - -
319D HIS* 3.6 27.8 - - + -
320D THR* 1.3 74.9 - - - +
322D GLU* 1.3 67.7 + - - +
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Residues in contact with GLU 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D VAL* 4.5 10.2 - - - +
269D LEU* 4.7 3.5 - - - +
311D THR* 3.6 19.4 - - + +
312D CYS 3.0 17.0 - - - +
313D GLN* 3.7 24.0 + - + +
320D THR* 5.5 4.3 - - - -
321D PHE* 1.3 81.2 - - - +
323D ASP* 1.3 61.5 - - - +
324D SER* 5.4 0.9 - - - -
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Residues in contact with ASP 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B SER* 3.8 12.5 + - - -
234D VAL* 3.6 32.7 - - + +
235D LYS* 4.1 3.7 - - - +
236D ILE* 3.5 32.1 + - + +
311D THR* 3.3 0.5 - - - +
312D CYS 2.7 33.4 + - - -
322D GLU* 1.3 76.0 - - - +
324D SER* 1.3 70.5 + - - +
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Residues in contact with SER 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B SER* 4.7 0.2 + - - -
241B CYS 3.1 10.9 - - - +
242B ASP* 3.8 1.0 - - - -
243B GLY* 3.6 15.9 + - - -
236D ILE* 4.1 3.1 - - - -
309D THR* 4.3 12.6 - - - -
310D TYR 3.2 11.4 - - - -
311D THR* 2.6 37.6 + - - +
322D GLU* 5.4 1.2 - - - -
323D ASP* 1.3 80.3 + - - +
325D THR* 1.3 60.8 + - - +
393D ARG* 5.3 7.3 - - - +
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Residues in contact with THR 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B SER* 3.3 34.5 - - - -
241B CYS 3.1 10.5 - - - -
242B ASP 4.0 3.1 - - - -
236D ILE* 4.4 10.2 - - - +
238D GLN* 4.7 3.1 - - - -
253D LEU* 5.2 5.6 - - - -
304D TRP* 4.9 6.3 - - - -
309D THR* 3.7 4.3 - - - +
310D TYR* 2.9 35.2 + - - +
324D SER* 1.3 74.3 - - - +
326D LYS* 1.3 64.6 + - - +
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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