Contacts of the strand formed by residues 354 - 364 (chain A) in PDB entry 4EGA
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 ILE 354 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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345A TRP* 4.0 29.8 - - + +
348A LEU* 3.8 36.7 + - + +
349A GLU* 4.4 27.6 - - + +
352A GLY* 3.5 3.5 - - - -
353A ASP* 1.3 86.8 + - - +
355A TYR* 1.3 64.4 + - - +
405A TYR* 3.9 33.1 - - + -
406A MET 3.2 11.4 - - - +
407A PHE* 4.3 6.3 - - + -
408A ARG* 5.4 0.8 + - - -
449A VAL* 4.0 17.7 - - + -
807A GOL 5.6 0.4 - - - +
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Residues in contact with TYR 355 (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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354A ILE* 1.3 75.2 - - - +
356A LEU* 1.3 70.2 + - - +
357A GLY* 3.4 6.5 + - - -
405A TYR* 3.5 7.0 - - - -
406A MET* 2.6 75.4 + - + +
407A PHE 4.7 0.2 - - - -
408A ARG* 3.8 47.3 - - + +
446A ASP* 2.6 39.0 + - - +
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Residues in contact with LEU 356 (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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355A TYR* 1.3 79.5 - - - +
357A GLY* 1.3 59.6 + - - +
403A GLU* 3.9 35.0 - - + +
404A ASN 4.0 9.9 - - - +
405A TYR* 3.7 42.0 - - + +
466A ASN* 5.4 1.1 - - - +
469A HIS* 4.2 10.5 - - + +
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Residues in contact with GLY 357 (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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355A TYR* 3.4 9.7 + - - -
356A LEU* 1.3 74.7 - - - +
358A ARG* 1.3 57.7 + - - -
403A GLU* 3.2 15.1 - - - +
404A ASN 2.8 36.1 + - - +
406A MET* 3.9 11.6 - - - +
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Residues in contact with ARG 358 (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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357A GLY* 1.3 77.7 - - - +
359A TYR* 1.3 61.4 + - - +
360A GLU* 2.9 32.8 + - + +
401A SER* 2.9 40.6 + - - -
402A GLU* 3.2 11.9 - - - +
403A GLU* 3.9 22.9 + - + +
404A ASN 4.1 0.4 - - - +
406A MET* 4.2 15.7 - - - +
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Residues in contact with TYR 359 (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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358A ARG* 1.3 73.5 - - - +
360A GLU* 1.3 63.2 + - - +
361A GLY* 3.4 32.0 - - - -
362A TRP 2.7 23.0 + - - -
370A PHE* 3.3 46.8 - + + +
371A LEU 3.4 14.7 + - - -
400A VAL* 3.2 18.5 - - + +
401A SER* 3.4 0.2 - - - -
402A GLU 2.9 30.1 + - - -
404A ASN* 4.0 19.6 - - - +
406A MET* 4.7 10.3 - - + -
446A ASP 5.8 2.5 - - - -
448A SER* 4.2 13.2 - - - -
813A DMS 5.9 2.9 - - + -
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Residues in contact with GLU 360 (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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358A ARG* 2.9 35.1 + - + +
359A TYR* 1.3 80.3 - - - +
361A GLY* 1.3 57.5 + - - +
399A TRP* 3.6 22.2 + - + +
400A VAL 3.2 6.1 - - - +
401A SER* 3.4 24.2 + - - +
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Residues in contact with GLY 361 (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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359A TYR* 3.4 18.4 - - - -
360A GLU* 1.3 75.2 - - - +
362A TRP* 1.3 65.0 + - - -
371A LEU 5.3 0.2 - - - -
399A TRP* 3.5 22.8 - - - -
400A VAL* 2.9 30.7 + - - +
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Residues in contact with TRP 362 (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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359A TYR* 2.7 29.8 + - - -
361A GLY* 1.3 72.6 - - - -
363A TYR* 1.3 62.6 + - - +
370A PHE* 3.8 0.9 - - - -
371A LEU* 3.4 24.0 + - + +
373A PRO* 4.3 27.1 - - + +
376A ILE* 3.4 40.7 - - + +
388A LYS* 3.7 23.3 - - + -
397A VAL* 3.7 23.1 - - + -
398A THR* 3.5 25.6 - - - -
399A TRP* 3.5 47.9 - + + -
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Residues in contact with TYR 363 (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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291A GLN* 4.6 3.8 - - - -
362A TRP* 1.3 76.1 - - - +
364A SER* 1.3 71.4 + - - +
365A ILE* 3.9 18.0 + - + -
368A GLU* 2.8 47.4 + - - +
369A SER 3.5 21.1 - - - -
370A PHE* 3.3 45.1 - + + -
371A LEU* 4.8 0.9 - - - +
397A VAL* 3.2 6.2 - - - -
398A THR* 2.8 39.5 + - - +
400A VAL* 3.9 18.4 - - + -
451A ARG* 3.7 24.6 + - - -
472A TYR* 3.5 11.8 - - - -
473A VAL* 4.8 0.3 - - - +
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Residues in contact with SER 364 (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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363A TYR* 1.3 74.3 - - - +
365A ILE* 1.3 53.4 + - - +
366A SER 3.8 2.6 + - - -
367A ASP* 2.8 36.0 + - - -
368A GLU* 2.7 32.2 + - - -
369A SER* 2.9 20.9 + - - -
371A LEU* 4.2 8.7 - - - +
390A SER* 4.6 0.9 - - - -
395A HIS* 4.0 13.3 - - - +
396A VAL 4.1 6.1 + - - -
397A VAL* 4.2 14.6 - - - -
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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