Contacts of the strand formed by residues 316 - 323 (chain A) in PDB entry 1EQR
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 GLY 316 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A ALA* 5.2 2.8 - - - +
310A PRO 3.4 16.8 - - - +
313A ASP* 3.0 17.7 + - - +
314A PRO 3.3 0.4 - - - +
315A LYS* 1.3 82.0 - - - +
317A ARG* 1.3 60.3 + - - -
397A ASP 3.2 15.3 - - - -
399A LYS* 3.1 18.7 + - - -
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Residues in contact with ARG 317 (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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276A GLU* 3.3 17.8 + - - +
277A ARG* 2.8 36.6 + - - +
292A LEU* 4.1 14.6 - - - +
293A THR 5.2 0.6 + - - -
294A ASP* 3.1 37.4 + - - +
296A ALA* 4.5 7.0 - - + -
310A PRO 3.7 3.4 + - - -
316A GLY* 1.3 76.3 - - - +
318A VAL* 1.3 63.0 + - - +
319A ALA* 4.2 12.7 - - - +
396A ALA* 3.7 0.2 - - - -
397A ASP 3.3 12.6 + - - -
399A LYS* 4.2 26.9 - - - +
402A VAL* 3.3 39.7 - - + +
403A ALA* 4.2 18.6 - - - +
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Residues in contact with VAL 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ASP* 3.7 4.7 + - - -
295A VAL* 3.1 46.9 + - + +
296A ALA* 3.9 23.0 - - + +
299A LEU* 4.0 11.7 - - + -
307A PHE* 4.2 18.4 - - + +
310A PRO* 4.0 12.8 - - + -
311A ALA* 4.4 4.0 - - + +
317A ARG* 1.3 75.3 - - - +
319A ALA* 1.3 57.5 + - - +
394A PHE* 4.2 13.2 - - + -
395A GLY 3.2 6.5 - - - +
396A ALA* 3.6 29.4 - - + -
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Residues in contact with ALA 319 (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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292A LEU* 4.4 14.1 - - + -
293A THR 3.1 8.5 - - - +
294A ASP* 4.2 0.7 - - - -
317A ARG* 3.9 19.1 - - - +
318A VAL* 1.3 72.6 - - - +
320A ALA* 1.3 59.5 + - - +
394A PHE* 3.3 3.8 - - - -
395A GLY 2.8 36.5 + - - -
402A VAL* 3.6 24.9 - - + +
406A MET* 3.4 12.7 - - + +
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Residues in contact with ALA 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A GLU 4.3 0.3 - - - +
292A LEU* 3.4 5.4 - - - -
293A THR* 2.7 44.6 + - - +
295A VAL* 4.4 7.4 - - + -
318A VAL 3.9 0.8 + - - -
319A ALA* 1.3 73.4 - - - +
321A LEU* 1.3 61.2 + - - +
322A ARG 4.0 1.5 + - - -
384A THR* 4.0 17.4 - - + +
392A ILE* 3.9 12.8 - - + -
393A PHE 3.2 5.2 - - - -
394A PHE* 3.7 26.5 - - + -
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Residues in contact with LEU 321 (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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290A MET* 4.1 25.8 - - + -
291A GLU 4.1 17.7 - - - +
292A LEU* 4.0 12.3 - - + -
319A ALA 4.1 0.2 + - - -
320A ALA* 1.3 73.1 - - - +
322A ARG* 1.3 74.8 + - - +
323A VAL* 3.2 13.7 + - + +
392A ILE* 4.3 2.0 - - - +
393A PHE* 2.9 32.9 + - + +
406A MET* 4.1 12.8 - - + +
409A LEU* 3.4 32.3 - - + -
410A ARG* 3.5 28.7 - - + +
413A VAL* 5.2 0.7 - - + -
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Residues in contact with ARG 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A MET* 4.0 7.7 - - - +
291A GLU 4.6 7.8 + - - +
320A ALA 4.0 2.4 + - - -
321A LEU* 1.3 78.0 - - - +
323A VAL* 1.3 57.9 - - - +
324A PRO* 3.4 25.8 - - - +
384A THR* 2.9 36.0 + - + +
385A ALA* 2.5 29.3 + - - +
386A ALA* 3.8 5.1 - - + +
387A GLN* 2.8 37.4 + - - +
390A ASP* 3.3 22.4 + - + +
391A MET 3.5 8.3 - - - +
392A ILE* 4.6 7.9 - - + +
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Residues in contact with VAL 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A MET* 3.9 6.5 - - - -
321A LEU* 3.4 14.4 - - + +
322A ARG* 1.3 73.6 - - - +
324A PRO* 1.3 60.6 - - + +
326A GLY* 2.9 23.1 + - - -
329A LEU* 5.3 2.0 - - + -
391A MET* 2.9 32.3 + - + +
393A PHE* 3.7 27.6 - - + -
413A VAL* 3.6 24.0 - - + -
417A LEU* 3.5 30.3 - - + -
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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