Contacts of the helix formed by residues 553 - 567 (chain A) in PDB entry 3EPZ
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 HIS 553 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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504A GLU* 3.2 40.6 - - + +
505A LYS* 3.5 43.0 + - + +
508A ILE* 5.3 2.1 - - + +
549A SER 3.0 18.8 + - - +
550A LEU 3.0 8.6 + - - +
552A ARG* 1.3 97.6 + - - +
554A ALA* 1.3 67.1 + - - +
555A GLN 3.2 2.9 - - - -
556A PHE* 3.1 9.1 + - + +
557A VAL* 2.8 29.5 + - + +
595A ARG* 4.9 0.2 - - - -
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Residues in contact with ALA 554 (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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550A LEU 3.1 7.7 + - - +
551A LEU* 3.2 16.4 + - - +
552A ARG 3.6 0.6 - - - -
553A HIS* 1.3 76.7 - - - +
555A GLN* 1.3 57.3 + - - +
557A VAL* 3.3 3.6 + - - +
558A VAL* 2.9 34.5 + - - +
584A LEU* 3.8 26.2 - - + -
587A LEU* 4.5 2.7 - - + -
588A ALA* 3.9 21.5 - - + +
595A ARG* 3.6 12.2 - - - +
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Residues in contact with GLN 555 (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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553A HIS 3.2 0.8 - - - -
554A ALA* 1.3 69.8 - - - +
556A PHE* 1.3 67.7 + - - +
558A VAL* 3.2 8.1 + - + +
559A GLU* 3.0 37.4 + - - +
588A ALA* 3.4 35.1 + - + +
592A LEU* 5.3 1.7 - - - +
595A ARG* 3.2 21.6 + - - +
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Residues in contact with PHE 556 (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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505A LYS* 3.5 58.8 - - + +
506A ILE* 3.6 23.8 - - + -
509A SER* 3.4 22.9 - - - -
553A HIS* 3.1 12.1 + - + +
555A GLN* 1.3 78.4 - - - +
557A VAL* 1.3 64.5 + - + +
559A GLU* 3.2 10.0 + - + +
560A GLN* 2.9 49.5 + - + +
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Residues in contact with VAL 557 (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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505A LYS 4.6 1.8 - - - +
508A ILE* 3.9 24.0 - - + -
509A SER* 3.8 20.9 - - - +
512A VAL* 4.0 28.5 - - + -
550A LEU* 4.0 10.5 - - + -
553A HIS* 2.8 31.2 + - + +
554A ALA 3.7 4.7 - - - +
556A PHE* 1.3 72.4 - - - +
558A VAL* 1.3 56.6 + - - +
560A GLN* 3.1 4.0 + - - +
561A VAL* 3.0 31.5 + - + +
584A LEU* 3.9 21.3 - - + -
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Residues in contact with VAL 558 (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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554A ALA 2.9 22.5 + - - +
555A GLN* 3.4 15.0 - - + +
557A VAL* 1.3 68.7 - - - +
559A GLU* 1.3 67.1 + - + +
561A VAL* 3.9 0.2 - - - +
562A GLU* 2.9 32.3 + - - +
576A PHE* 3.8 7.9 - - + -
581A MSE 3.8 28.0 - - + -
584A LEU* 3.9 19.3 - - + +
585A ILE* 4.0 27.1 - - + +
588A ALA* 4.4 7.9 - - + -
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Residues in contact with GLU 559 (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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555A GLN* 3.0 29.3 + - - +
556A PHE* 3.6 12.7 - - + +
558A VAL* 1.3 81.7 - - + +
560A GLN* 1.3 59.1 + - + +
562A GLU* 3.4 15.7 + - - +
563A SER* 2.9 31.0 + - - -
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Residues in contact with GLN 560 (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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428A GLU* 5.9 5.9 + - - +
506A ILE* 6.1 1.8 - - - +
509A SER* 3.4 33.4 - - - +
510A LYS* 5.3 12.1 - - - +
513A VAL* 4.7 5.7 - - + +
556A PHE* 2.9 44.1 + - + +
557A VAL 3.1 6.7 + - - +
559A GLU* 1.3 78.0 - - - +
561A VAL* 1.3 59.1 + - + +
563A SER* 3.5 9.4 + - - -
564A TYR* 3.0 28.1 + - - +
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Residues in contact with VAL 561 (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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509A SER 5.4 0.4 - - - +
512A VAL* 4.0 26.5 - - + -
513A VAL* 4.2 13.2 - - + -
516A LEU* 5.1 0.7 - - + -
557A VAL* 3.0 22.1 + - + +
558A VAL 3.9 0.7 - - - +
560A GLN* 1.3 72.9 - - + +
562A GLU* 1.3 65.5 + - - +
564A TYR* 3.3 8.3 + - - +
565A ASP* 3.1 22.5 + - - +
575A ILE* 3.7 26.4 - - + +
576A PHE* 4.1 13.5 - - + +
581A MSE 3.8 35.4 - - + -
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Residues in contact with GLU 562 (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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558A VAL 2.9 16.7 + - - +
559A GLU* 3.7 17.0 - - - +
561A VAL* 1.3 75.0 - - - +
563A SER* 1.3 58.7 + - - +
565A ASP* 3.2 5.6 + - + +
566A GLU* 2.9 46.7 + - + +
576A PHE* 3.7 30.0 - - + -
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Residues in contact with SER 563 (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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559A GLU 2.9 18.4 + - - -
560A GLN* 3.5 13.9 - - - -
562A GLU* 1.3 77.5 - - - +
564A TYR* 1.3 62.8 + - - +
566A GLU* 3.4 6.3 + - - +
567A ALA* 3.2 24.5 + - - +
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Residues in contact with TYR 564 (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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463A GLU* 4.4 17.0 - - - -
513A VAL* 3.8 25.6 - - + -
517A GLN* 2.5 41.2 + - + +
560A GLN 3.0 14.7 + - - +
561A VAL* 3.5 10.1 - - - +
562A GLU 3.3 0.2 - - - -
563A SER* 1.3 75.9 - - - +
565A ASP* 1.3 67.1 + - - +
567A ALA* 3.4 13.9 + - + +
568A GLY* 3.7 9.4 + - - -
569A ASP 5.1 7.1 + - - -
575A ILE* 3.6 27.8 - - + -
702A BGC 4.5 3.0 + - - -
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Residues in contact with ASP 565 (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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561A VAL 3.1 14.0 + - - +
562A GLU* 3.2 9.8 + - + +
564A TYR* 1.3 83.0 - - - +
566A GLU* 1.3 64.7 + - + +
567A ALA 3.1 1.5 + - - -
568A GLY 3.8 12.8 + - - +
574A PRO* 3.3 18.7 - - + +
575A ILE* 3.1 24.7 + - - +
576A PHE* 2.7 40.2 + - + +
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Residues in contact with GLU 566 (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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562A GLU* 2.9 37.5 + - + +
563A SER* 3.9 6.7 - - - +
565A ASP* 1.3 79.4 - - + +
567A ALA* 1.3 59.4 + - - +
568A GLY 5.4 0.2 - - - -
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Residues in contact with ALA 567 (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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563A SER 3.2 15.8 + - - +
564A TYR* 3.7 8.7 - - + +
565A ASP 3.1 1.2 - - - -
566A GLU* 1.3 80.5 - - - +
568A GLY* 1.3 61.0 + - - +
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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