Contacts of the strand formed by residues 324 - 330 (chain A) in PDB entry 5DVX
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 TYR 324 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A LEU* 3.4 29.4 - - + +
178A ARG 2.6 30.6 + - - -
180A LEU* 3.6 23.7 - - + +
214A LEU 4.5 4.7 + - - -
321A PHE 3.7 20.4 - - - -
322A SER 3.9 3.1 - - - -
323A ARG* 1.3 75.9 - - - +
325A PHE* 1.3 70.2 + - - +
326A GLN* 3.9 19.2 + - + -
343A THR* 3.6 23.3 - - + -
344A VAL 3.4 14.6 - - - +
345A PHE* 4.2 6.7 - + + -
346A ASN 4.0 2.9 - - - +
388A ALA* 3.5 2.4 - - - -
389A SER* 2.9 51.6 + - - -
390A PHE* 3.7 6.4 - - - -
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Residues in contact with PHE 325 (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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166A ILE* 4.0 30.1 - - + -
168A PRO* 3.8 40.4 - - + -
171A ALA* 4.2 7.2 - - + -
241A VAL* 5.8 4.9 - - + -
278A PHE* 6.5 0.2 - + - -
324A TYR* 1.3 74.9 - - - +
326A GLN* 1.3 62.1 + - - +
327A TYR* 5.7 1.3 - - + -
343A THR* 3.3 7.3 - - - +
344A VAL* 2.8 47.8 + - + +
345A PHE 4.8 1.8 - - - -
346A ASN* 3.6 26.7 - - + -
386A ILE* 3.9 11.0 - - + -
387A GLU 3.2 15.5 - - - +
388A ALA* 4.0 15.0 - - + -
390A PHE* 3.7 25.1 - + - -
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Residues in contact with GLN 326 (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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177A LEU* 3.4 20.3 - - + +
214A LEU* 3.9 19.0 - - - +
218A ARG* 2.9 36.4 + - - +
324A TYR* 3.9 21.1 + - + -
325A PHE* 1.3 76.9 - - - +
327A TYR* 1.3 63.9 + - - +
341A ILE* 4.0 10.3 - - + -
342A TRP 3.2 15.0 - - - +
343A THR* 2.9 19.5 + - - +
385A VAL 4.2 0.3 - - - +
386A ILE* 3.7 1.0 - - - +
387A GLU* 2.8 34.7 + - + +
404A GOL 3.4 15.5 + - - +
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Residues in contact with TYR 327 (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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162A SER* 2.9 33.4 + - - -
164A VAL* 3.5 28.5 + - + +
166A ILE* 5.6 2.0 - - + -
239A HIS* 2.7 34.0 + + - -
325A PHE* 5.7 1.1 - - + -
326A GLN* 1.3 79.9 - - - +
328A GLU* 1.3 72.9 + - - +
329A GLY* 4.0 0.7 - - - -
341A ILE* 3.8 3.1 - - - +
342A TRP* 2.9 51.9 + - + +
344A VAL* 4.7 7.6 - - + -
381A LEU* 5.1 2.9 - - + -
384A ARG* 3.8 20.0 - - + -
385A VAL 3.8 16.4 - - - +
386A ILE* 4.0 20.2 - - + -
404A GOL 3.6 12.9 - - - -
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Residues in contact with GLU 328 (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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160A PHE* 4.8 1.8 - - + +
269A PRO* 4.1 18.5 - - - +
270A GLY 5.3 1.3 - - - -
327A TYR* 1.3 78.4 - - - +
329A GLY* 1.3 59.8 + - - +
339A GLY* 3.4 29.5 + - - +
340A VAL 3.4 10.8 - - - +
341A ILE* 4.8 2.5 - - + +
384A ARG* 2.9 32.7 + - + +
385A VAL 5.1 0.8 + - - -
404A GOL 2.3 43.8 + - - +
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Residues in contact with GLY 329 (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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160A PHE* 3.3 19.3 - - - +
162A SER* 3.3 13.2 - - - -
327A TYR* 4.0 2.1 + - - -
328A GLU* 1.3 74.7 - - - +
330A SER* 1.3 56.8 + - - -
338A GLN* 3.4 1.7 - - - +
339A GLY 3.0 12.5 + - - -
340A VAL* 2.8 33.8 + - - -
342A TRP* 4.0 1.8 - - - -
384A ARG* 3.5 4.5 - - - -
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Residues in contact with SER 330 (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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160A PHE 3.7 1.5 + - - -
161A GLN* 3.3 34.9 + - - -
162A SER* 2.9 32.0 + - - -
329A GLY* 1.3 75.8 - - - -
331A LEU* 1.3 81.5 + - - +
336A CYS 3.5 2.2 - - - -
337A ALA 3.1 14.8 - - - -
338A GLN* 4.0 1.6 - - - -
340A VAL* 3.8 8.1 - - - -
342A TRP* 2.8 21.0 + - - +
376A ARG* 3.7 0.5 + - - -
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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