Contacts of the helix formed by residues 513 - 530 (chain A) in PDB entry 1R4L
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 ILE 513 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A TRP* 5.6 3.8 - - + +
204A ARG* 6.4 0.4 - - - -
207A TYR* 3.9 14.1 - - + +
222A LEU* 4.5 10.8 - - + -
226A VAL* 4.4 20.4 - - + -
398A GLU* 3.2 19.7 - - - +
453A THR* 4.6 6.1 - - - +
454A TYR* 4.6 4.7 - - + -
457A GLU* 3.0 36.9 - - + +
461A TRP* 4.2 21.1 - - + -
511A SER* 5.3 1.6 - - - -
512A PHE* 1.3 70.6 - - - +
514A ARG* 1.3 63.7 + - - +
515A TYR 3.0 3.1 - - - -
516A TYR* 2.9 38.3 + - + +
517A THR* 3.0 15.8 + - + -
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Residues in contact with ARG 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A TYR* 3.4 4.0 - - - -
378A HIS* 5.7 1.0 + - - -
398A GLU* 3.3 34.9 + - + +
399A GLY* 3.7 0.9 - - - -
402A GLU* 2.8 38.8 + - + +
510A TYR* 4.1 10.7 - - - +
511A SER* 2.8 70.5 + - - +
513A ILE* 1.3 76.4 - - - +
515A TYR* 1.3 68.5 + - - +
517A THR* 2.8 9.2 + - - -
518A ARG* 2.6 40.8 + - - +
804A XX5 3.5 22.5 - - - +
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Residues in contact with TYR 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ARG* 3.6 7.2 - - - +
374A HIS* 5.5 0.4 - - - -
402A GLU* 3.9 21.3 - - + -
449A THR* 5.2 3.1 - - + +
450A LEU* 5.0 0.3 - - - +
453A THR* 3.5 15.9 - - + +
505A HIS* 2.7 28.2 + + - -
510A TYR* 5.8 0.2 - - - +
511A SER 4.1 0.9 - - - -
512A PHE* 2.7 54.1 - + + +
513A ILE 3.0 0.2 - - - -
514A ARG* 1.3 94.8 + - - +
516A TYR* 1.3 61.6 + - - +
518A ARG* 3.0 36.4 + - - +
519A THR* 2.8 28.8 + - - -
804A XX5 3.2 38.8 + - - +
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Residues in contact with TYR 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A VAL* 3.4 33.0 + - + -
229A THR* 2.6 43.7 + - + +
230A PHE* 3.4 20.0 + + - -
233A ILE* 4.6 3.3 - - + +
450A LEU* 3.9 38.1 - - + -
453A THR* 3.5 10.4 - - + +
454A TYR* 4.2 11.4 - - + -
513A ILE* 2.9 27.0 + - + +
515A TYR* 1.3 79.6 - - - +
517A THR* 1.3 70.2 + - + +
519A THR* 3.0 20.3 + - - -
520A LEU* 3.4 20.3 + - + +
579A MET* 4.0 10.8 - - - -
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Residues in contact with THR 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A TYR* 2.5 43.1 + - + +
222A LEU* 4.3 12.1 - - + -
226A VAL* 5.1 1.1 - - + -
399A GLY* 3.4 2.6 - - - -
513A ILE* 3.0 10.2 + - + +
514A ARG* 2.8 17.3 + - - -
516A TYR* 1.3 81.6 - - + +
518A ARG* 1.3 64.6 + - - +
520A LEU* 3.2 3.7 + - - +
521A TYR* 2.9 43.8 + - - +
579A MET* 4.3 20.9 - - - -
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Residues in contact with ARG 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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273A ARG* 4.5 5.5 - - - +
274A PHE* 5.1 11.7 - - - -
374A HIS* 3.8 13.1 - - - -
399A GLY* 3.6 2.9 - - - +
402A GLU* 3.5 8.7 + - + -
403A ALA* 3.3 42.2 - - - +
406A GLU* 2.6 48.4 + - + +
449A THR* 5.6 4.4 - - - +
514A ARG 2.6 22.6 + - - +
515A TYR* 3.0 43.4 + - - +
517A THR* 1.3 74.3 + - - +
519A THR* 1.3 73.2 + - - +
521A TYR* 4.0 0.4 - - - -
522A GLN* 2.8 31.5 + - - +
804A XX5 5.3 8.7 + - - -
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Residues in contact with THR 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A ILE* 3.6 29.7 - - + +
449A THR* 4.4 10.6 - - - +
450A LEU* 3.5 24.3 - - + +
515A TYR 2.8 15.5 + - - -
516A TYR 3.0 12.4 + - - -
518A ARG* 1.3 86.4 + - - +
520A LEU* 1.3 58.5 + - + +
522A GLN* 3.1 27.6 + - - +
523A PHE* 3.3 12.0 - - - -
584A LEU* 3.8 12.8 - - + -
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Residues in contact with LEU 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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229A THR* 2.8 29.2 - - - +
233A ILE* 5.3 0.7 - - + -
450A LEU* 4.3 15.0 - - + -
516A TYR* 3.6 28.9 - - + +
517A THR 3.2 3.6 + - - +
519A THR* 1.3 78.3 - - + +
521A TYR* 1.3 67.5 + - - +
523A PHE* 3.3 12.1 + - - +
524A GLN* 3.2 18.0 + - - +
579A MET* 3.3 31.9 - - + -
580A ASN 4.0 8.8 - - - +
581A VAL* 3.5 30.1 - - + +
583A PRO* 4.7 0.2 - - - +
584A LEU* 4.8 8.1 - - + -
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Residues in contact with TYR 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A TYR* 3.4 13.5 - - - -
397A ASN* 2.9 20.4 + - - -
399A GLY* 3.3 40.8 - - - -
400A PHE* 3.5 17.5 - + - -
403A ALA* 3.6 9.6 - - + -
517A THR* 2.9 28.1 + - - +
520A LEU* 1.3 73.4 - - - +
522A GLN* 1.3 68.6 + - - +
524A GLN* 2.7 32.5 + - - +
525A PHE* 3.0 34.7 + + + -
566A TRP* 4.1 12.9 - + - -
570A LEU* 4.0 23.8 - - + -
579A MET* 4.6 17.6 - - + +
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Residues in contact with GLN 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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403A ALA* 4.2 2.9 - - - +
406A GLU* 3.5 51.5 + - + +
407A ILE* 4.0 14.5 - - - +
410A LEU* 3.1 23.0 - - + +
446A ILE* 3.8 12.6 - - - +
518A ARG* 2.8 13.9 + - - +
519A THR* 3.1 25.5 + - - +
521A TYR* 1.3 76.7 - - - +
523A PHE* 1.3 92.2 + - + +
525A PHE* 3.7 4.3 + - - +
526A GLN* 3.3 20.3 + - - +
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Residues in contact with PHE 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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410A LEU* 3.4 20.4 - - + -
446A ILE* 3.8 23.3 - - + -
519A THR 3.3 24.0 - - - -
520A LEU 3.3 4.0 + - - +
521A TYR 2.9 2.4 + - - -
522A GLN* 1.3 98.5 - - - +
524A GLN* 1.3 60.2 + - - +
526A GLN* 3.6 4.9 - - + +
527A GLU* 2.9 30.0 + - - +
539A LEU* 4.0 6.4 - - + +
583A PRO* 3.8 10.6 - - + +
584A LEU* 3.4 58.1 - - + +
587A TYR* 3.8 35.2 - + + -
588A PHE* 4.7 1.1 - + - -
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Residues in contact with GLN 524 (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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520A LEU 3.2 18.8 + - - +
521A TYR* 2.7 27.8 + - - +
523A PHE* 1.3 71.6 - - - +
525A PHE* 1.3 63.7 + - + +
526A GLN 3.2 0.5 + - - -
527A GLU* 3.2 12.9 + - - +
528A ALA* 3.4 5.2 + - - +
570A LEU* 4.2 9.0 - - + +
574A VAL* 3.3 28.2 - - + +
576A ALA* 4.1 9.7 - - - +
578A ASN 3.5 10.0 + - - +
579A MET* 3.5 12.1 - - - +
580A ASN* 3.0 42.2 - - - +
583A PRO* 3.8 19.1 - - + -
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Residues in contact with PHE 525 (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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400A PHE* 3.6 40.2 - + - -
403A ALA* 5.0 3.8 - - + -
407A ILE* 3.4 31.2 - - + -
521A TYR* 3.0 54.0 + + + -
522A GLN 3.9 3.1 - - - +
524A GLN* 1.3 84.7 - - + +
526A GLN* 1.3 56.6 + - - +
528A ALA* 3.6 1.3 + - - +
529A LEU* 2.8 39.3 + - + +
554A LEU* 4.7 9.2 - - + -
557A MET* 4.8 6.7 - - + -
570A LEU* 4.8 11.4 - - + -
573A VAL* 4.1 32.3 - - + -
574A VAL* 3.5 9.8 - - + +
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Residues in contact with GLN 526 (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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407A ILE* 3.2 39.8 + - - +
410A LEU* 4.4 24.3 - - + +
411A SER* 4.2 16.3 - - - -
522A GLN 3.3 15.0 + - - +
523A PHE* 3.7 9.4 - - + +
524A GLN 3.1 0.8 - - - -
525A PHE* 1.3 78.0 - - - +
527A GLU* 1.3 59.6 + - - +
528A ALA 3.0 6.6 + - - -
529A LEU* 4.2 5.6 - - - +
530A CYS* 2.7 39.7 + - - -
539A LEU* 4.6 13.2 - - + +
542A CYS* 3.5 22.2 - - - +
543A ASP 4.4 0.5 - - - +
544A ILE* 4.5 5.6 - - - +
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Residues in contact with GLU 527 (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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523A PHE 2.9 17.0 + - - +
524A GLN* 3.2 5.8 + - - +
526A GLN* 1.3 76.1 - - - +
528A ALA* 1.3 58.2 + - - +
530A CYS* 4.6 4.3 - - - +
531A GLN* 3.4 26.3 + - - +
539A LEU* 4.0 28.0 - - + +
583A PRO* 3.9 21.1 - - + +
586A ASN* 3.8 19.1 - - - +
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Residues in contact with ALA 528 (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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524A GLN 3.4 2.3 + - - +
525A PHE 3.8 2.0 - - - +
526A GLN 3.0 0.4 - - - -
527A GLU* 1.3 80.3 - - - +
529A LEU* 1.3 60.9 + - + +
530A CYS 3.3 1.1 - - - -
531A GLN* 3.3 10.6 + - - +
532A ALA* 3.0 24.7 + - - +
553A LYS* 3.9 21.3 + - - +
573A VAL* 4.3 0.9 - - + +
574A VAL* 3.3 36.8 - - + -
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Residues in contact with LEU 529 (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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407A ILE* 3.7 29.8 - - + -
408A MET* 6.0 0.2 - - + -
525A PHE* 2.8 30.2 + - + +
526A GLN* 3.6 5.8 + - - +
528A ALA* 1.3 74.3 - - + +
530A CYS* 1.3 59.6 + - - +
532A ALA* 2.7 24.6 + - - +
533A ALA* 2.9 15.6 + - - +
544A ILE* 4.3 22.4 - - + -
550A ALA* 3.9 26.9 - - + +
553A LYS* 4.3 16.4 - - + -
554A LEU* 4.3 26.5 - - + +
573A VAL* 5.6 4.9 - - + -
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Residues in contact with CYS 530 (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 GLN* 2.7 36.5 + - - +
527A GLU* 4.8 3.4 - - - +
529A LEU* 1.3 74.4 - - - +
531A GLN* 1.3 56.4 + - - +
533A ALA* 2.8 27.3 + - - +
534A LYS 2.9 9.5 + - - -
535A HIS* 3.1 29.0 + - + +
539A LEU* 4.4 6.5 - - + -
542A CYS* 2.0 52.5 - - + -
544A ILE* 5.4 0.9 - - - -
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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