Contacts of the helix formed by residues 560 - 577 (chain A) in PDB entry 2YT4
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 560 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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542A PHE* 3.3 11.0 - - - -
558A ALA 2.9 2.2 + - - +
559A SER* 1.3 81.1 + - - +
561A LYS* 1.3 64.3 + - - +
562A LYS* 3.9 6.9 + - - +
563A LEU* 3.0 37.0 + - - +
564A ALA* 3.0 22.5 + - - +
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Residues in contact with LYS 561 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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532A PHE* 3.3 53.9 - - + -
542A PHE* 3.4 29.2 - - + -
543A GLY 6.0 0.2 - - - -
560A SER* 1.3 72.6 - - - +
562A LYS* 1.3 57.6 + - - +
564A ALA* 3.4 4.7 + - - +
565A LYS* 3.0 28.5 + - + +
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Residues in contact with LYS 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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560A SER* 3.1 8.4 - - - +
561A LYS* 1.3 80.2 - - - +
563A LEU* 1.3 68.8 + - + +
565A LYS* 3.2 19.5 - - + +
566A ASN* 3.1 28.7 + - - +
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Residues in contact with LEU 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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558A ALA* 3.5 17.0 - - + -
559A SER* 3.2 26.0 - - - +
560A SER* 3.0 23.2 + - - +
562A LYS* 1.3 86.7 - - + +
564A ALA* 1.3 64.2 + - - +
566A ASN* 3.4 12.3 + - - +
567A LYS* 3.1 29.0 + - - +
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Residues in contact with ALA 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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542A PHE 3.6 26.7 - - - +
543A GLY 4.1 0.4 - - - -
544A ALA* 3.5 18.1 - - + +
556A GLY* 3.7 2.5 - - - -
557A THR* 3.8 20.0 - - - +
558A ALA* 3.9 2.8 - - - +
560A SER 3.0 10.4 + - - +
561A LYS* 3.8 7.4 - - - +
563A LEU* 1.3 74.6 - - - +
565A LYS* 1.3 60.4 + - - +
567A LYS* 3.3 2.7 + - - +
568A ALA* 2.8 32.2 + - - +
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Residues in contact with LYS 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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513A VAL* 3.4 34.0 - - + +
530A TYR* 3.7 36.2 - - + -
532A PHE* 3.5 30.3 - - + -
544A ALA* 3.8 6.9 - - - +
561A LYS* 3.0 12.8 + - + +
562A LYS* 3.2 17.7 - - + +
564A ALA* 1.3 78.1 - - - +
566A ASN* 1.3 57.2 + - - +
568A ALA* 3.5 3.7 + - - +
569A ALA* 3.1 26.3 + - - +
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Residues in contact with ASN 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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511A SER* 3.8 15.8 - - - -
512A GLU* 3.4 24.4 - - + +
513A VAL* 3.3 25.7 + - - +
562A LYS* 3.1 35.4 + - - +
563A LEU* 3.9 12.3 - - - +
564A ALA 3.3 0.2 - - - -
565A LYS* 1.3 73.3 - - - +
567A LYS* 1.3 58.2 + - + +
570A ARG* 2.6 37.3 + - - +
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Residues in contact with LYS 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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540A GLU* 3.8 13.3 + - - -
555A SER 3.9 3.3 - - - +
556A GLY* 3.7 10.3 - - - -
557A THR* 2.8 33.0 + - + +
558A ALA* 3.1 21.5 - - + +
563A LEU* 3.1 15.2 + - - +
564A ALA 3.3 6.7 + - - +
566A ASN* 1.3 76.9 - - + +
568A ALA* 1.3 57.6 + - - +
570A ARG* 3.8 6.1 - - - +
571A ALA* 2.8 34.3 + - - +
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Residues in contact with ALA 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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530A TYR* 4.6 1.8 - - + -
544A ALA* 3.6 29.2 - - + +
545A SER* 4.0 3.8 - - - +
546A VAL* 4.1 8.7 - - + -
554A GLY* 3.6 12.6 - - - +
555A SER 3.7 12.1 - - - -
556A GLY* 3.7 1.4 - - - +
564A ALA 2.8 17.3 + - - +
565A LYS 3.6 5.2 - - - +
567A LYS* 1.3 77.6 - - - +
569A ALA* 1.3 56.5 + - - +
572A THR* 2.9 32.0 + - - -
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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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512A GLU 3.5 29.8 - - - +
513A VAL 3.6 2.0 - - - +
516A LEU* 4.1 5.4 - - + -
530A TYR* 3.6 19.7 - - - +
546A VAL* 4.4 3.3 - - - +
565A LYS 3.1 17.5 + - - +
566A ASN 3.7 2.2 - - - +
568A ALA* 1.3 74.3 - - - +
570A ARG* 1.3 60.9 + - - +
572A THR* 2.9 7.3 + - - -
573A LEU* 2.8 35.1 + - - +
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Residues in contact with ARG 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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512A GLU* 2.5 54.9 + - - +
566A ASN 2.6 22.1 + - - +
567A LYS* 3.8 6.1 - - - +
569A ALA* 1.3 71.9 - - - +
571A ALA* 1.3 58.4 + - - +
573A LEU* 3.0 10.0 + - - +
574A GLU* 2.9 47.8 + - - +
580A PHE* 4.1 26.6 + - + -
581A VAL* 6.0 0.4 - - - +
582A LYS* 5.5 10.1 - - - +
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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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554A GLY* 3.7 14.6 - - - -
555A SER 3.9 11.4 - - - +
567A LYS 2.8 22.4 + - - +
568A ALA 3.7 4.5 - - - +
570A ARG* 1.3 72.8 - - - +
572A THR* 1.3 60.2 + - - +
574A GLU* 3.4 14.1 + - - +
575A ILE* 2.8 30.8 + - - +
701A GLU* 5.1 6.1 - - - +
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Residues in contact with THR 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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516A LEU* 3.9 20.4 - - + -
520A MET* 5.5 2.2 - - - -
546A VAL* 3.5 20.9 - - + +
548A ILE* 5.9 0.7 - - + -
553A TYR* 4.0 14.8 - - + -
554A GLY* 2.8 25.9 + - - +
568A ALA 2.9 14.4 + - - -
569A ALA* 2.9 11.9 + - - -
571A ALA* 1.3 74.4 - - - +
573A LEU* 1.3 64.5 + - - +
575A ILE* 3.2 6.0 + - - +
576A LEU* 3.0 37.1 + - + +
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Residues in contact with LEU 573 (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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512A GLU* 3.7 11.0 - - - +
515A ILE* 4.6 4.5 - - + -
516A LEU* 3.2 48.0 - - + +
519A TYR* 4.5 7.9 - - + -
569A ALA 2.8 34.0 + - - +
570A ARG* 3.3 9.9 - - - +
572A THR* 1.3 71.8 - - - +
574A GLU* 1.3 57.0 + - - +
576A LEU* 4.9 1.1 - - - -
577A ILE* 2.7 65.2 + - + +
580A PHE* 3.8 33.7 - - + -
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Residues in contact with GLU 574 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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570A ARG* 2.9 42.2 + - - +
571A ALA* 3.4 14.6 - - - +
572A THR 3.2 0.2 - - - -
573A LEU* 1.3 77.6 - - - +
575A ILE* 1.3 61.1 + - + +
577A ILE 3.5 11.6 - - - +
580A PHE* 4.2 26.0 - - + +
696A ARG* 3.5 17.1 + - - -
700A ARG* 4.4 22.2 + - - -
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Residues in contact with ILE 575 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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553A TYR* 3.9 19.7 - - + -
554A GLY 5.2 4.5 - - - +
571A ALA 2.8 21.5 - - - +
572A THR* 3.2 10.2 + - - +
574A GLU* 1.3 76.5 - - + +
576A LEU* 1.3 66.3 + - + +
693A SER* 3.4 15.7 + - - +
696A ARG* 2.4 48.9 + - + +
697A MET* 3.3 44.9 - - + -
701A GLU* 4.4 15.7 - - - +
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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
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516A LEU* 4.7 4.9 - - + -
519A TYR* 3.8 39.3 + - + +
520A MET* 4.8 4.7 - - + -
524A LEU* 4.1 18.4 - - + -
548A ILE* 5.9 3.6 - - + -
553A TYR* 4.3 9.2 - - + -
572A THR* 3.0 35.2 + - + +
573A LEU* 4.1 2.2 - - - +
575A ILE* 1.3 97.2 - - + +
577A ILE* 1.3 63.1 + - + +
578A PRO* 3.4 11.2 - - - +
687A HIS 5.3 1.1 - - - +
688A VAL* 4.1 23.6 - - + -
690A ASN* 5.7 1.7 + - - -
693A SER* 4.2 11.1 + - - +
696A ARG* 4.4 0.2 - - - -
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Residues in contact with ILE 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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492A MET* 4.8 13.9 - - + -
494A VAL* 4.2 26.2 - - + -
505A ILE* 5.7 1.6 - - + -
515A ILE* 5.8 1.1 - - + -
519A TYR* 3.8 37.9 - - + +
573A LEU* 2.7 47.8 + - + +
574A GLU 3.5 14.5 - - - +
576A LEU* 1.3 75.2 - - + +
578A PRO* 1.3 79.3 - - + +
579A ASP 3.5 0.5 + - - -
580A PHE* 3.4 31.9 + - + +
583A GLN 6.1 0.2 - - - +
696A ARG* 4.6 0.4 - - - -
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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