Contacts of the helix formed by residues 566 - 582 (chain A) in PDB entry 5E2Q
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 GLN 566 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A SER 5.4 2.1 + - - +
109A PHE* 3.3 52.6 - - + +
110A GLY 4.1 9.2 - - - +
318A TYR* 5.7 2.8 - - - -
556A PHE* 3.9 25.2 + - + -
564A TRP* 4.6 1.4 - - - -
565A ARG* 1.3 79.1 - - - +
567A ALA* 1.3 68.4 + - - +
568A HIS* 2.7 43.6 + - - +
569A MET* 2.8 20.0 + - + +
570A GLN* 3.0 25.7 + - - +
4B TYR* 4.0 7.3 - - - -
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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
----------------------------------------------------------
318A TYR* 4.0 19.5 - - + -
504A SER* 3.9 15.9 - - - -
505A SER* 2.8 51.3 + - - +
508A GLU* 4.4 1.3 - - + -
565A ARG 4.2 1.2 + - - -
566A GLN* 1.3 75.9 + - - +
568A HIS* 1.3 60.4 + - - +
570A GLN* 3.4 2.1 + - - -
571A ALA* 3.0 16.1 + - - +
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Residues in contact with HIS 568 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A TYR* 3.5 31.6 - + - -
450A HIS* 4.4 7.9 - + - -
508A GLU* 2.9 25.5 + - + -
512A GLU* 4.6 8.8 - - - +
566A GLN* 2.7 25.9 + - - +
567A ALA* 1.3 74.1 - - - +
569A MET* 1.3 62.0 + - - +
571A ALA* 3.3 9.2 - - - +
572A ARG* 3.1 35.2 + - - +
2B ARG 2.6 27.5 + - - -
3B VAL* 4.4 1.6 - - - -
4B TYR* 3.4 42.3 - + + -
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Residues in contact with MET 569 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A PHE* 3.7 22.9 - - + -
549A ALA* 3.8 19.1 - - + +
552A LEU* 4.3 0.9 - - + -
553A ALA* 3.2 42.6 - - + +
556A PHE* 3.6 27.6 - - + -
564A TRP* 4.8 0.2 - - + -
566A GLN* 2.8 23.1 + - + +
568A HIS* 1.3 77.9 - - - +
570A GLN* 1.3 64.8 + - - +
571A ALA 3.1 0.2 - - - -
572A ARG* 3.2 14.2 + - - +
573A PHE 3.0 17.7 + - - -
6B HIS* 3.6 36.3 - - + -
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Residues in contact with GLN 570 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A ILE* 5.5 6.7 - - - +
505A SER* 3.2 25.7 + - - +
564A TRP* 3.2 55.9 - - + +
566A GLN 3.0 16.2 + - - +
567A ALA* 4.8 1.4 - - - -
569A MET* 1.3 76.0 - - - +
571A ALA* 1.3 61.3 + - - +
573A PHE* 3.3 3.5 + - - +
574A VAL* 3.1 22.9 + - - +
641A TYR* 3.3 24.9 - - + +
642A GLU* 5.8 2.0 - - - +
645A ALA* 3.5 18.6 - - + +
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Residues in contact with ALA 571 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A SER 3.7 3.8 - - - +
508A GLU* 3.9 6.5 - - + +
509A CYS* 3.4 35.5 - - + +
512A GLU* 4.8 4.3 - - + -
567A ALA 3.0 14.4 + - - +
568A HIS 3.3 11.9 - - - +
569A MET 3.1 0.2 - - - -
570A GLN* 1.3 78.9 - - - +
572A ARG* 1.3 56.8 + - - +
574A VAL* 3.5 3.8 + - - +
575A ILE* 3.2 31.3 + - - +
641A TYR* 3.3 10.3 + - - -
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Residues in contact with ARG 572 (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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446A GLN* 5.9 3.2 - - - +
512A GLU* 2.7 32.7 + - + +
545A ASN* 4.4 11.9 - - - +
546A MET* 3.6 31.1 - - - +
549A ALA* 3.6 24.1 - - + +
550A GLY* 3.6 16.4 - - - +
568A HIS* 3.1 17.8 + - - +
569A MET* 3.2 18.9 + - - +
571A ALA* 1.3 74.7 - - - +
573A PHE* 1.3 60.2 + - - +
575A ILE* 3.5 2.4 + - - +
576A LEU* 3.0 27.5 + - - +
3B VAL* 5.9 0.6 - - - +
4B TYR* 3.0 29.0 + - - +
5B ILE* 4.5 2.2 - - - +
6B HIS* 3.6 33.5 + - - +
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Residues in contact with PHE 573 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550A GLY* 3.4 27.1 - - - +
553A ALA* 4.1 0.2 - - + -
554A LEU* 3.6 22.2 - - + -
564A TRP* 3.4 30.5 - + + -
569A MET 3.0 8.1 + - - +
570A GLN 3.3 6.0 + - - +
572A ARG* 1.3 75.2 - - - +
574A VAL* 1.3 59.5 + - - +
576A LEU* 3.3 6.4 - - + +
577A ARG* 3.0 35.0 + - + +
644A TYR 3.5 21.5 - - - -
645A ALA* 4.2 6.7 - - - -
646A THR 3.9 6.3 - - - -
647A VAL* 3.9 23.6 - - + -
655A PHE* 3.6 42.6 - + - -
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Residues in contact with VAL 574 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A CYS* 3.7 8.5 - - - -
570A GLN 3.1 15.0 + - - +
571A ALA 3.6 7.9 - - - +
573A PHE* 1.3 74.7 - - - +
575A ILE* 1.3 61.4 + - - +
577A ARG* 2.9 9.3 + - - +
578A VAL* 2.8 28.1 + - + +
621A PHE* 3.7 29.6 - - + -
641A TYR* 3.8 25.4 - - + +
644A TYR* 3.7 15.7 - - + -
645A ALA* 3.9 30.3 - - + +
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Residues in contact with ILE 575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A CYS* 4.0 9.6 - - - +
512A GLU* 3.7 27.8 - - + -
513A SER* 3.4 29.8 - - - +
516A LEU* 3.8 22.2 - - + -
546A MET* 3.8 24.2 - - + -
571A ALA 3.2 15.1 + - - +
572A ARG 3.8 7.0 - - - +
573A PHE 3.4 0.2 - - - -
574A VAL* 1.3 75.3 - - - +
576A LEU* 1.3 62.9 + - - +
578A VAL* 3.2 10.1 + - - +
579A LEU* 3.0 34.5 + - + +
618A LEU* 4.8 8.7 - - + -
621A PHE* 4.7 2.5 - - + -
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Residues in contact with LEU 576 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546A MET* 5.5 0.6 - - - +
547A VAL* 3.6 37.2 - - + +
550A GLY* 3.5 34.1 - - - +
551A LEU* 3.8 6.5 - - + +
572A ARG 3.0 14.7 + - - +
573A PHE* 3.3 11.7 - - + +
574A VAL 3.2 0.2 - - - -
575A ILE* 1.3 77.2 - - - +
577A ARG* 1.3 56.4 + - - +
579A LEU* 3.3 7.4 + - - +
580A LEU* 2.9 48.5 + - + +
587A VAL* 4.0 8.7 - - + -
589A ILE* 4.3 6.7 - - + -
655A PHE* 4.1 25.8 - - + -
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Residues in contact with ARG 577 (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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573A PHE* 3.0 27.3 + - + +
574A VAL 2.9 9.3 + - - +
576A LEU* 1.3 72.5 - - - +
578A VAL* 1.3 60.3 + - - +
580A LEU* 3.3 8.9 + - - +
581A GLU* 2.8 32.0 + - - +
643A GLY 3.3 23.8 + - - -
644A TYR* 3.3 40.7 + - + +
646A THR* 3.6 21.8 + - - -
648A THR* 5.9 4.2 - - - +
655A PHE* 3.6 29.7 - - + -
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Residues in contact with VAL 578 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574A VAL 2.8 18.8 + - - +
575A ILE* 3.2 8.9 + - + +
577A ARG* 1.3 75.2 - - - +
579A LEU* 1.3 68.4 + - + +
581A GLU* 3.3 21.0 + - - +
582A ALA* 3.3 12.6 + - - +
617A ALA* 4.1 17.7 - - + +
618A LEU* 5.0 3.1 - - + -
621A PHE* 3.9 57.0 - - + -
644A TYR* 4.0 18.4 - - + +
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Residues in contact with LEU 579 (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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516A LEU* 5.1 2.5 - - + -
543A TRP* 4.0 37.9 - - + +
546A MET* 5.5 1.1 - - + -
547A VAL* 4.1 22.4 - - + -
575A ILE* 3.0 36.6 + - + +
576A LEU* 3.8 4.3 - - - +
578A VAL* 1.3 83.7 - - + +
580A LEU* 1.3 63.9 + - - +
582A ALA* 3.5 15.9 + - - +
583A GLY* 4.0 3.5 + - - +
586A LEU* 4.1 17.0 - - + +
587A VAL* 4.1 18.3 + - + +
614A GLY* 4.2 19.5 - - - +
617A ALA* 5.1 2.2 - - + -
618A LEU* 4.9 7.9 - - + +
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Residues in contact with LEU 580 (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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576A LEU* 2.9 35.9 + - + +
577A ARG* 3.3 10.5 + - - +
579A LEU* 1.3 74.1 - - - +
581A GLU* 1.3 63.4 + - - +
583A GLY* 3.2 14.3 + - - +
587A VAL* 3.2 39.9 - - + +
588A THR* 4.5 1.1 - - - -
589A ILE* 4.4 8.5 - - + -
653A GLU* 3.4 28.9 - - + +
655A PHE* 3.7 31.4 - - + -
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Residues in contact with GLU 581 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A ARG* 2.8 19.1 + - - +
578A VAL* 3.4 11.7 - - - +
579A LEU 3.3 0.2 - - - -
580A LEU* 1.3 78.9 - - - +
582A ALA* 1.3 61.7 + - - +
583A GLY* 3.2 1.0 + - - -
644A TYR* 2.5 42.3 + - + -
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Residues in contact with ALA 582 (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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578A VAL 3.3 4.6 + - - +
579A LEU* 3.7 13.5 - - - +
580A LEU 3.2 0.6 - - - -
581A GLU* 1.3 79.0 - - - +
583A GLY* 1.3 61.5 + - - +
584A GLU* 3.3 16.1 - - - +
586A LEU* 5.0 1.3 - - + -
613A VAL* 3.8 19.5 - - + +
617A ALA* 3.8 29.2 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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