Contacts of the strand formed by residues 400 - 409 (chain A) in PDB entry 4EJX
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 SER 400 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363A ILE* 3.8 15.5 - - - -
364A TRP 3.8 4.5 - - - -
365A ASN* 4.3 11.1 + - - +
392A GLN* 5.2 1.7 + - - -
397A ILE* 3.3 26.3 + - - +
399A GLY* 1.3 80.0 + - - +
401A TYR* 1.3 62.7 + - - +
581A PHE* 3.4 38.6 - - - -
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Residues in contact with TYR 401 (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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362A ILE 3.3 0.9 - - - +
363A ILE* 3.5 4.6 - - - -
364A TRP* 2.6 39.2 + - - +
366A TYR* 3.6 19.3 - + - -
389A PHE 5.1 0.9 + - - -
397A ILE* 4.1 22.0 - - + +
398A GLY 4.2 11.4 + - - -
399A GLY 3.9 1.3 - - - -
400A SER* 1.3 80.7 - - - +
402A LYS* 1.3 59.8 + - - +
403A LYS* 3.8 10.4 + - + -
568A GLU* 3.4 46.0 - - + +
577A ASN* 3.5 19.3 - - + +
581A PHE* 4.9 1.8 - - - -
598A SER* 3.6 7.4 + - - -
599A ASN* 3.3 33.7 + - - -
601A MET* 3.6 29.5 - - + -
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Residues in contact with LYS 402 (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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361A GLU* 3.4 42.2 + - + +
362A ILE 3.3 13.2 - - - +
363A ILE* 4.7 6.0 - - + +
401A TYR* 1.3 70.2 - - - +
403A LYS* 1.3 67.6 + - - +
568A GLU* 4.6 1.9 - - - +
571A SER* 4.9 0.5 + - - -
573A LEU* 3.3 32.8 - - + +
576A ASP* 3.9 19.6 + - + +
577A ASN* 2.9 32.1 + - - +
580A MET* 4.3 28.7 - - - +
581A PHE* 5.2 1.9 - - + -
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Residues in contact with LYS 403 (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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360A GLU 3.7 1.0 - - - +
361A GLU* 4.4 1.1 - - - -
362A ILE* 3.1 34.9 + - + +
364A TRP* 3.4 40.4 - - + -
366A TYR* 2.7 26.6 + - - +
401A TYR* 3.8 8.7 - - + -
402A LYS* 1.3 83.4 - - - +
404A LEU* 1.3 62.9 + - - +
405A VAL* 3.5 3.9 + - + +
429A ILE* 3.8 22.4 - - + -
531A PHE 3.9 5.1 + - - -
532A THR* 3.2 16.6 + - - +
566A PHE* 3.7 20.0 - - - -
568A GLU* 2.8 26.8 + - - +
573A LEU* 3.9 3.4 - - - -
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Residues in contact with LEU 404 (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 ALA* 4.8 0.9 - - + -
360A GLU 3.3 13.0 - - - +
361A GLU* 3.7 25.8 - - + +
403A LYS* 1.3 68.9 - - - +
405A VAL* 1.3 58.5 + - - +
448A ASN* 4.2 1.3 - - - +
450A GLY* 3.8 31.2 - - - +
451A ALA 5.0 2.5 - - - +
452A TYR* 4.9 13.9 - - + +
454A LEU* 3.6 31.9 - - + -
532A THR* 3.0 24.4 + - + +
533A GLY 3.3 12.1 - - - -
534A LEU* 3.3 21.0 - - + +
573A LEU* 3.8 21.5 - - + +
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Residues in contact with VAL 405 (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 ALA 3.9 0.7 - - - +
359A ALA* 3.9 2.0 - - - -
360A GLU* 3.1 28.2 + - + +
362A ILE* 3.8 30.7 - - + -
403A LYS* 3.9 7.4 - - + +
404A LEU* 1.3 75.4 - - - +
406A TYR* 1.3 67.4 + - - +
407A ARG* 3.5 29.0 + - + +
429A ILE* 2.9 42.6 - - + +
430A LEU 4.7 1.6 - - - -
533A GLY 3.4 10.3 - - - +
534A LEU* 3.9 8.4 - - - +
535A ILE 5.2 0.2 - - - +
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Residues in contact with TYR 406 (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 ILE* 3.6 17.9 - - + -
358A ALA 4.2 2.0 - - - -
359A ALA* 5.1 4.0 - - + -
405A VAL* 1.3 75.6 - - - +
407A ARG* 1.3 84.4 + - - +
431A GLY* 3.4 23.0 - - - -
432A PRO* 3.7 9.0 - - + -
446A PHE* 3.5 27.4 - + - -
455A SER 2.7 25.5 + - - -
456A ILE* 3.2 22.2 - - + +
520A TYR* 3.6 28.9 - + - +
521A TYR 4.0 0.2 - - - -
522A SER* 3.6 11.6 + - - -
534A LEU* 3.1 44.9 - - + -
535A ILE 4.1 6.1 - - - -
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Residues in contact with ARG 407 (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 ILE* 3.6 4.9 - - - +
358A ALA 2.9 28.9 + - - +
360A GLU* 3.4 27.4 - - + +
362A ILE* 3.8 24.0 - - + +
364A TRP* 5.2 8.1 - - - -
405A VAL* 3.5 25.7 - - + +
406A TYR* 1.3 93.1 + - - +
408A GLU* 1.3 60.5 + - - +
409A TYR* 3.4 9.6 - - + -
417A ARG* 3.9 17.9 - - - +
420A ARG* 4.0 22.2 - - - +
428A GLY* 3.0 31.1 + - - -
429A ILE* 4.9 0.8 - - - +
430A LEU 3.6 6.3 + - - -
432A PRO* 4.2 2.7 - - - -
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Residues in contact with GLU 408 (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 HIS 5.1 0.5 - - - +
355A TYR* 3.6 30.3 - - + +
356A TYR* 4.0 13.6 - - - +
357A ILE* 4.0 5.8 - - + +
407A ARG* 1.3 74.6 - - - +
409A TYR* 1.3 76.6 + - - +
417A ARG* 4.7 4.0 + - - +
418A LYS* 2.9 68.0 + - + +
432A PRO* 3.3 32.8 - - + +
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Residues in contact with TYR 409 (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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356A TYR* 2.8 30.5 + - - +
358A ALA* 3.5 27.4 - - + -
360A GLU* 2.7 35.0 + - - -
407A ARG* 3.4 22.0 - - + -
408A GLU* 1.3 84.4 - - - +
410A THR* 1.3 65.5 + - - +
411A ASP 3.5 5.2 - - - +
414A PHE* 3.8 36.1 - + + -
415A THR 5.3 2.2 - - - -
416A ASN 3.4 23.8 - - - +
417A ARG* 3.5 31.5 + - + -
418A LYS* 4.2 6.7 - - - +
449A LYS* 4.6 12.2 + - - -
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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