Contacts of the helix formed by residues 511 - 523 (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 511 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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510A LYS* 1.3 74.6 - - - +
512A GLU* 1.3 59.1 + - - +
513A VAL* 3.7 6.2 + - - +
514A CYS* 3.2 27.3 + - - +
515A ILE* 2.8 32.6 + - - +
562A LYS* 6.5 0.4 - - - -
566A ASN* 3.8 16.4 - - - -
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Residues in contact with GLU 512 (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* 1.3 73.9 - - - +
513A VAL* 1.3 58.4 + - - +
515A ILE* 3.8 10.6 - - - +
516A LEU* 2.9 33.6 + - - +
566A ASN* 3.4 38.5 - - + +
569A ALA* 3.5 2.6 - - + +
570A ARG* 2.5 59.6 + - - +
573A LEU* 3.7 3.5 - - - +
580A PHE* 4.2 12.8 - - - -
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Residues in contact with VAL 513 (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* 3.2 7.5 + - - +
512A GLU* 1.3 78.3 - - - +
514A CYS* 1.3 62.6 + - - +
516A LEU* 3.7 2.1 - - - +
517A HIS* 2.9 30.2 + - + +
528A PRO* 5.8 0.2 - - - +
530A TYR* 3.8 18.3 + - + +
565A LYS* 3.4 55.9 - - + +
566A ASN* 3.3 17.2 + - - +
569A ALA* 3.7 6.3 - - - -
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Residues in contact with CYS 514 (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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510A LYS* 4.1 13.2 - - + -
511A SER* 3.2 27.5 + - - +
513A VAL* 1.3 82.0 - - - +
515A ILE* 1.3 61.1 + - - +
517A HIS* 2.9 10.2 + - - +
518A GLU* 2.7 31.4 + - - +
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Residues in contact with ILE 515 (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* 5.0 2.5 - - - -
505A ILE* 4.0 21.6 - - + +
507A PRO* 3.4 33.9 - - + -
510A LYS* 3.9 26.0 - - + +
511A SER 2.8 26.5 + - - +
512A GLU* 3.8 14.8 - - - +
514A CYS* 1.3 73.6 - - - +
516A LEU* 1.3 57.9 + - - +
518A GLU* 3.3 9.9 + - - +
519A TYR* 2.8 29.5 + - + +
573A LEU* 4.6 14.6 - - + -
577A ILE* 5.8 1.1 - - + -
580A PHE* 4.6 17.0 - - + -
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Residues in contact with LEU 516 (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 2.9 19.5 + - - +
513A VAL 3.7 2.2 - - - +
515A ILE* 1.3 73.1 - - - +
517A HIS* 1.3 63.8 + - - +
519A TYR* 3.3 5.8 + - + -
520A MET* 2.9 42.9 + - + +
528A PRO* 3.5 34.3 - - + -
530A TYR* 3.8 13.7 - - + +
546A VAL* 5.1 4.3 - - + -
569A ALA* 4.1 10.3 - - + +
572A THR* 3.9 22.7 - - + -
573A LEU* 3.2 34.7 - - + +
576A LEU* 4.7 1.6 - - + -
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Residues in contact with HIS 517 (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* 2.9 17.9 + - + +
514A CYS* 3.1 14.1 - - - +
516A LEU* 1.3 82.3 - - - +
518A GLU* 1.3 68.1 + - + +
520A MET* 3.9 1.4 - - - +
521A GLN* 3.1 40.5 + - + +
527A ARG* 4.7 23.1 - - + +
528A PRO* 4.2 19.8 - - + +
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Residues in contact with GLU 518 (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 ILE* 4.0 15.7 - - + +
506A ASN 4.7 0.5 + - - -
510A LYS* 2.6 40.5 + - - +
514A CYS 2.7 15.1 + - - +
515A ILE* 3.5 7.5 - - - +
517A HIS* 1.3 76.2 - - + +
519A TYR* 1.3 58.9 + - - +
521A GLN* 3.7 12.6 - - - +
522A ARG* 2.8 73.4 + - + +
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Residues in contact with TYR 519 (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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494A VAL* 4.0 22.0 - - + +
505A ILE* 4.9 13.5 - - + -
515A ILE* 2.8 22.6 + - + +
516A LEU* 3.5 12.3 - - + +
518A GLU* 1.3 73.7 - - - +
520A MET* 1.3 67.6 + - + +
522A ARG* 4.3 3.4 - - - -
523A VAL* 2.7 68.8 + - + +
524A LEU* 4.0 16.7 - - + +
573A LEU* 4.5 4.3 - - + -
576A LEU* 3.8 43.9 + - + +
577A ILE* 3.8 31.5 - - + +
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Residues in contact with MET 520 (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* 2.9 40.8 + - + +
517A HIS 3.9 2.0 - - - +
519A TYR* 1.3 78.1 - - + +
521A GLN* 1.3 51.4 + - - +
524A LEU* 3.1 24.2 + - + +
525A LYS 2.6 32.6 + - - -
526A VAL* 3.1 27.8 + - + +
527A ARG 3.5 6.5 - - - +
528A PRO* 3.2 43.7 - - + -
546A VAL* 5.2 1.6 - - - -
548A ILE* 3.2 33.9 - - + -
572A THR* 5.5 0.9 - - - -
576A LEU* 4.8 4.3 - - + -
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Residues in contact with GLN 521 (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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517A HIS* 3.1 28.8 + - + +
518A GLU* 3.7 22.3 - - - +
520A MET* 1.3 76.1 - - - +
522A ARG* 1.3 74.3 + - - +
525A LYS* 3.2 25.5 - - - +
526A VAL 3.5 9.3 + - - +
527A ARG* 6.1 0.7 - - - -
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Residues in contact with ARG 522 (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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503A PHE* 4.3 29.7 - - - +
504A VAL 2.5 33.8 + - - +
505A ILE* 3.4 16.8 - - + +
506A ASN 5.1 0.8 - - - +
518A GLU* 2.8 47.8 + - + +
519A TYR* 3.6 3.1 - - - +
521A GLN* 1.3 90.5 - - - +
523A VAL* 1.3 68.5 + - + +
525A LYS* 4.0 14.9 - - - +
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Residues in contact with VAL 523 (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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494A VAL* 5.1 1.6 - - + -
496A ASP* 3.9 15.7 - - - +
503A PHE* 3.7 53.2 - - + -
505A ILE* 5.3 2.0 - - + -
519A TYR* 2.7 56.7 + - + +
522A ARG* 1.3 79.3 - - + +
524A LEU* 1.3 71.2 + - + +
525A LYS* 3.5 7.3 - - - +
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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