Contacts of the helix formed by residues 552 - 572 (chain A) in PDB entry 5I35
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 VAL 552 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550A TYR 3.8 0.8 + - - -
551A GLU* 1.3 73.0 - - - +
553A LYS* 1.3 70.2 + - + +
554A VAL* 3.1 19.1 + - + +
555A MSE 3.2 17.4 + - + +
556A GLU* 3.0 17.5 + - - +
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Residues in contact with LYS 553 (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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551A GLU 3.4 4.5 + - - -
552A VAL* 1.3 74.4 - - + +
554A VAL* 1.3 58.8 + - + +
556A GLU* 2.9 19.8 + - - +
557A ASP* 2.7 67.9 + - - +
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Residues in contact with VAL 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552A VAL* 3.1 13.0 + - + +
553A LYS* 1.3 81.1 - - + +
555A MSE 1.3 58.6 + - - +
557A ASP* 3.4 6.7 + - - +
558A ALA* 3.0 27.1 + - + +
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Residues in contact with MSE 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A LEU* 5.6 2.7 - - - -
551A GLU* 4.1 24.7 - - + -
552A VAL* 3.2 19.1 + - + +
554A VAL* 1.3 77.7 - - - +
556A GLU* 1.3 68.1 + - - +
558A ALA* 3.1 15.6 + - + +
559A HIS* 3.2 14.0 + - - +
589A ASN* 6.1 0.7 - - - +
592A PRO* 4.1 23.7 - - + +
594A MSE 3.1 34.3 - - + +
595A LEU* 4.0 14.1 - - + -
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Residues in contact with GLU 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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538A ARG* 3.0 48.3 + - - -
547A LEU* 4.0 24.3 - - + +
549A GLY* 4.8 5.5 - - - -
551A GLU* 4.5 19.9 - - + +
552A VAL 3.0 12.6 + - - +
553A LYS* 2.9 27.7 + - - +
555A MSE 1.3 81.1 - - - +
557A ASP* 1.3 63.5 + - - +
559A HIS* 3.2 5.5 + - - +
560A LEU* 3.0 39.5 + - + +
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Residues in contact with ASP 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A ARG* 2.8 26.1 + - - +
553A LYS* 2.7 58.7 + - - +
554A VAL* 3.8 6.3 - - - +
556A GLU* 1.3 74.0 - - - +
558A ALA* 1.3 57.5 + - - +
560A LEU* 3.4 6.8 + - - +
561A ASP* 2.9 40.2 + - - +
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Residues in contact with ALA 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 VAL* 3.0 15.1 + - + +
555A MSE 3.1 11.8 + - + +
557A ASP* 1.3 78.5 - - - +
559A HIS* 1.3 56.1 + - - +
561A ASP* 3.6 10.4 + - - +
562A ALA* 3.2 20.4 + - - +
589A ASN* 3.3 38.6 + - - +
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Residues in contact with HIS 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A SER* 4.5 5.6 + - - -
546A PHE* 3.2 26.3 - + - -
547A LEU* 4.1 29.7 - - + +
555A MSE 3.2 11.4 + - - +
556A GLU* 3.2 8.6 + - - +
558A ALA* 1.3 73.1 - - - +
560A LEU* 1.3 70.8 + - + +
562A ALA* 3.3 4.3 + - - +
563A ILE* 3.1 52.1 + - + +
589A ASN* 3.0 28.3 + - - +
590A LEU* 3.1 21.1 + - - -
592A PRO* 3.7 14.9 - - + +
610A HIS* 3.9 6.5 + - - -
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Residues in contact with LEU 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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534A ARG* 3.6 39.7 - - + +
537A VAL* 3.8 26.0 - - + +
538A ARG* 3.8 32.3 - - + +
541A SER* 5.0 0.7 - - - +
547A LEU* 4.8 4.3 - - + -
556A GLU* 3.0 44.4 + - + +
557A ASP* 4.3 3.4 - - - +
559A HIS* 1.3 81.4 - - + +
561A ASP* 1.3 66.3 + - - +
563A ILE* 3.2 6.5 + - + +
564A LEU* 3.1 31.5 + - + +
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Residues in contact with ASP 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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534A ARG* 2.4 36.4 + - - +
557A ASP* 2.9 27.1 + - - +
558A ALA* 3.7 9.5 - - - +
559A HIS 3.3 0.2 - - - -
560A LEU* 1.3 73.8 - - - +
562A ALA* 1.3 63.1 + - - +
564A LEU* 3.2 7.2 + - - +
565A ILE* 3.1 28.5 + - + +
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Residues in contact with ALA 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 ALA 3.2 11.1 + - - +
559A HIS 3.6 6.5 - - - +
560A LEU 3.3 0.4 - - - -
561A ASP* 1.3 76.1 - - - +
563A ILE* 1.3 68.4 + - - +
565A ILE* 3.3 15.0 + - - +
566A LEU* 3.6 12.5 + - - +
586A LYS 4.5 10.1 - - - +
587A ILE* 4.2 18.7 - - - +
589A ASN* 3.8 5.2 - - + -
590A LEU* 3.5 33.3 - - + +
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Residues in contact with ILE 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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525A ILE* 3.9 21.1 - - + -
526A ILE* 5.1 7.9 - - + -
529A ALA* 4.1 13.5 - - + +
537A VAL* 4.0 24.9 - - + -
541A SER* 4.2 8.1 - - - +
559A HIS* 3.1 44.5 + - + +
560A LEU* 3.2 6.5 + - - +
562A ALA* 1.3 76.1 - - - +
564A LEU* 1.3 56.1 + - - +
566A LEU* 3.1 24.3 + - + +
567A GLY* 3.1 8.5 + - - -
590A LEU* 3.5 24.7 - - + -
610A HIS* 3.9 14.1 - - + -
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Residues in contact with LEU 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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529A ALA* 4.0 22.2 - - + +
532A ARG* 2.8 55.2 + - - +
533A ASP 4.8 0.7 - - - +
534A ARG* 3.7 42.4 - - + +
537A VAL* 4.8 10.8 - - + -
560A LEU* 3.1 19.4 + - + +
561A ASP* 3.2 7.8 + - - +
563A ILE* 1.3 74.1 - - + +
565A ILE* 1.3 59.2 + - - +
567A GLY* 4.0 1.6 - - - +
568A GLU* 2.8 24.7 + - - +
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Residues in contact with ILE 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 ASP* 3.1 17.4 + - + +
562A ALA* 3.3 9.3 + - - +
564A LEU* 1.3 75.0 - - - +
566A LEU* 1.3 63.1 + - + +
568A GLU* 3.2 36.0 + - - +
569A ALA 3.5 4.3 + - - -
576A PHE* 3.9 15.1 - - + -
581A GLN* 3.3 22.2 - - + +
582A SER* 4.7 2.2 - - - +
586A LYS* 3.4 43.7 - - + +
587A ILE* 4.0 13.5 - - + -
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Residues in contact with LEU 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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522A TYR* 4.7 2.2 - - - +
526A ILE* 4.7 13.9 - - + -
562A ALA 3.6 8.5 + - - +
563A ILE* 3.1 13.6 + - + +
565A ILE* 1.3 77.3 - - - +
567A GLY* 1.3 62.6 + - - +
568A GLU 3.4 0.2 + - - -
569A ALA* 3.5 4.5 + - - +
570A PHE* 3.3 31.9 + - + -
587A ILE* 4.6 16.6 - - + -
590A LEU* 4.1 28.3 - - + -
613A MSE 3.5 26.5 - - + -
614A GLY* 5.2 0.4 - - - -
617A PHE* 3.4 47.8 - - + -
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Residues in contact with GLY 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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526A ILE* 5.9 0.2 - - - -
529A ALA* 3.3 31.9 - - - +
530A ALA* 3.7 5.6 - - - -
532A ARG* 3.5 6.5 - - - -
563A ILE 3.1 8.1 + - - -
564A LEU 3.1 6.3 + - - -
566A LEU* 1.3 75.4 - - - +
568A GLU* 1.3 53.4 + - - +
570A PHE* 3.1 5.3 + - - -
571A ALA* 2.7 37.2 + - - +
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Residues in contact with GLU 568 (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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532A ARG* 3.4 25.3 + - - +
564A LEU 2.8 10.3 + - - +
565A ILE* 3.2 33.5 + - - +
567A GLY* 1.3 70.9 - - - +
569A ALA* 1.3 65.9 + - - +
571A ALA* 3.1 5.8 + - - +
572A SER* 3.1 26.4 + - - -
576A PHE* 4.1 7.8 - - + -
581A GLN* 3.1 30.0 + - - +
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Residues in contact with ALA 569 (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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565A ILE 3.5 3.0 + - - -
566A LEU 3.7 8.5 - - - +
567A GLY 3.3 0.4 - - - -
568A GLU* 1.3 82.4 - - - +
570A PHE* 1.3 61.9 + - - +
572A SER* 3.6 16.5 + - - +
574A GLU 5.4 0.3 - - - +
576A PHE* 3.6 46.2 - - + +
617A PHE* 3.9 14.4 - - + -
629A CYS* 3.4 27.6 + - + +
630A LYS 3.8 0.5 + - - -
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Residues in contact with PHE 570 (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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472A LEU* 4.7 7.9 - - + -
476A LEU* 4.3 18.4 - - + -
526A ILE* 3.7 29.8 - - + -
530A ALA* 4.1 15.6 - - + +
566A LEU* 3.3 19.4 + - + -
567A GLY* 3.1 6.4 + - - +
569A ALA* 1.3 76.4 - - - +
571A ALA* 1.3 57.8 + - - +
613A MSE 4.0 21.1 - - + -
617A PHE* 3.9 31.6 - + - -
629A CYS* 3.5 26.0 - - + -
630A LYS* 3.4 24.0 - - - +
632A MSE 4.5 2.9 - - + -
633A PHE* 3.4 34.9 - + + +
634A GLU* 5.0 2.8 - - - +
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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
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530A ALA* 3.2 26.9 + - - +
532A ARG* 4.0 13.2 - - + -
567A GLY 2.7 17.7 + - - +
568A GLU* 3.1 5.8 + - - +
570A PHE* 1.3 72.6 - - - +
572A SER* 1.3 59.8 - - - +
573A ASP 4.1 0.3 + - - -
630A LYS* 3.9 17.5 - - - +
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Residues in contact with SER 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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568A GLU 3.1 16.0 + - - -
569A ALA* 3.6 9.9 + - - +
570A PHE 3.5 1.0 - - - -
571A ALA* 1.3 78.4 - - - +
573A ASP* 1.3 61.3 + - - +
574A GLU* 2.9 39.8 + - - +
575A PRO 6.2 0.2 - - - -
576A PHE* 5.9 4.0 - - - -
629A CYS 4.4 1.6 + - - -
630A LYS* 3.3 21.1 + - - +
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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
------------------------------------------------------------
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