Contacts of the helix formed by residues 552 - 567 (chain D) in PDB entry 4IVE
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 LYS 552 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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555B GLN* 4.4 11.1 + - - -
548D ALA* 4.9 0.2 - - + -
549D PRO* 2.8 35.3 + - + +
551D GLN* 1.4 91.8 + - - +
553D GLN* 1.3 62.4 + - - +
554D LYS 3.6 1.8 - - - -
555D GLN* 3.5 13.7 + - + +
556D MSE 3.1 35.9 + - + +
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Residues in contact with GLN 553 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574A GLY 5.6 0.6 + - - -
554B LYS* 6.0 1.4 - - - -
582B GLU* 4.4 16.4 + - - +
545D LEU* 3.0 46.6 + - + +
546D ALA* 4.1 9.5 + - - +
548D ALA* 3.1 17.4 + - + +
549D PRO 3.4 8.5 + - - +
550D PRO* 3.5 23.7 + - + +
552D LYS* 1.3 77.2 - - - +
554D LYS* 1.4 62.9 + - + +
556D MSE 3.3 4.5 + - - +
557D LEU* 3.1 28.9 + - - +
585D ASN* 3.4 26.2 + - - +
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Residues in contact with LYS 554 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550B PRO* 3.5 37.2 - - + +
551B GLN* 3.8 6.7 - - + +
553B GLN* 5.9 1.8 - - - -
554B LYS* 5.9 7.9 - - + +
550D PRO 4.7 2.7 + - - +
551D GLN 5.3 1.2 + - - -
552D LYS 3.6 0.2 - - - -
553D GLN* 1.4 73.2 - - + +
555D GLN* 1.3 60.0 + - - +
557D LEU* 3.3 4.2 + - + -
558D GLY* 2.9 26.5 + - - -
581D LEU* 2.9 39.3 + - + +
582D GLU* 4.4 3.3 + - - +
583D ILE 2.8 28.3 + - - -
584D ASP* 4.4 1.6 - - - +
585D ASN* 2.8 32.3 + - - +
588D LEU* 4.0 1.4 - - + +
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Residues in contact with GLN 555 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551B GLN* 3.4 40.8 + - + +
552B LYS* 4.0 12.6 + - - +
551D GLN 5.2 0.7 - - - +
552D LYS* 3.5 21.4 + - + +
553D GLN 3.3 0.4 - - - -
554D LYS* 1.3 76.4 - - - +
556D MSE 1.3 62.6 + - + +
558D GLY* 3.2 3.3 + - - -
559D GLU* 3.0 57.7 + - - +
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Residues in contact with MSE 556 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540D LEU* 3.7 29.4 - - + -
544D ARG* 3.5 34.5 - - + +
545D LEU* 4.3 12.3 - - + -
548D ALA* 3.5 29.2 - - + -
552D LYS* 3.1 23.5 + - + +
553D GLN 3.6 7.2 - - - +
555D GLN* 1.3 76.0 - - + +
557D LEU* 1.3 62.1 + - - +
559D GLU* 3.5 16.2 + - - +
560D ARG* 3.4 31.8 + - - +
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Residues in contact with LEU 557 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540D LEU* 3.8 21.1 - - + -
545D LEU* 4.0 10.8 - - + -
553D GLN 3.1 21.2 + - - +
554D LYS* 3.8 6.5 - - - +
556D MSE 1.3 73.1 - - - +
558D GLY* 1.3 58.4 + - - +
560D ARG* 3.2 5.7 + - - +
561D LEU* 2.9 32.6 + - + +
581D LEU* 3.9 10.5 - - + -
585D ASN* 3.3 38.4 - - + +
588D LEU* 3.9 27.6 - - + -
589D LEU* 3.9 16.2 - - + -
592D LEU* 3.9 17.1 - - + +
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Residues in contact with GLY 558 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551B GLN* 5.1 3.6 - - - -
554D LYS 2.9 14.8 + - - -
555D GLN* 3.2 4.7 + - - -
557D LEU* 1.3 76.1 - - - +
559D GLU* 1.3 54.7 + - - +
561D LEU* 3.8 1.1 - - - +
562D PHE* 2.9 35.5 + - - +
577D THR* 3.9 8.9 - - - +
581D LEU* 3.6 21.2 - - - +
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Residues in contact with GLU 559 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555D GLN* 3.0 43.2 + - - +
556D MSE 3.7 24.2 - - - +
557D LEU 3.4 0.2 - - - -
558D GLY* 1.3 73.7 - - - +
560D ARG* 1.3 62.9 + - - +
562D PHE* 4.6 2.3 - - - +
563D PRO* 3.2 22.2 - - - +
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Residues in contact with ARG 560 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538D GLU* 2.8 37.4 + - - +
539D THR* 4.0 3.2 - - - +
540D LEU* 3.5 51.4 - - + +
544D ARG* 5.8 1.8 - - - +
556D MSE 3.4 20.2 + - - +
557D LEU 3.2 3.9 + - - +
559D GLU* 1.3 81.3 - - - +
561D LEU* 1.3 65.8 + - - +
563D PRO* 3.3 10.2 - - - +
564D LEU* 3.8 17.7 - - + +
592D LEU* 3.7 20.6 - - + -
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Residues in contact with LEU 561 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557D LEU* 2.9 14.9 + - + +
558D GLY* 3.3 4.0 + - - +
560D ARG* 1.3 75.2 - - - +
562D PHE* 1.3 65.2 + - - +
564D LEU* 3.2 6.5 + - - +
565D ILE* 3.0 41.9 + - + +
577D THR* 4.2 9.2 - - + +
580D LEU* 4.1 17.7 - - + -
581D LEU* 4.0 21.3 - - + -
588D LEU* 4.0 34.5 - - + +
591D MSE 5.0 1.1 - - + -
592D LEU* 3.6 29.1 - - + +
598D LEU* 4.5 16.8 - - + -
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Residues in contact with PHE 562 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558D GLY 2.9 17.9 + - - +
559D GLU* 4.6 2.7 - - - +
561D LEU* 1.3 76.9 - - - +
563D PRO* 1.4 67.4 - - + +
565D ILE* 3.3 1.2 + - - +
566D GLN* 2.9 66.5 + - + +
570D PRO 5.6 0.9 - - - -
573D ALA* 3.7 10.8 - - + -
574D GLY* 3.6 28.3 - - - -
577D THR* 3.6 25.6 - - + +
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Residues in contact with PRO 563 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559D GLU 3.2 23.1 - - - +
560D ARG* 3.3 13.5 - - - +
562D PHE* 1.4 94.8 - - + +
564D LEU* 1.3 57.0 + - + +
566D GLN* 3.5 20.5 + - - +
567D ALA* 3.1 26.9 + - - +
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Residues in contact with LEU 564 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560D ARG 3.8 17.0 - - - +
561D LEU 3.2 7.1 + - - +
563D PRO* 1.3 76.7 - - + +
565D ILE* 1.3 66.4 + - - +
567D ALA* 3.3 18.1 + - + +
568D MSE 3.7 16.5 + - + +
592D LEU* 3.8 36.3 - - + +
598D LEU* 3.7 25.4 - - + -
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Residues in contact with ILE 565 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561D LEU* 3.0 29.8 + - + +
562D PHE 3.9 2.9 - - - +
564D LEU* 1.3 74.8 - - - +
566D GLN* 1.3 52.4 + - - +
568D MSE 2.9 12.1 + - - +
569D HIS 2.9 31.5 + - - +
573D ALA* 3.8 20.6 - - + -
576D ILE* 3.8 22.9 - - + -
577D THR* 3.4 31.4 - - - +
580D LEU* 3.8 24.9 - - + -
598D LEU* 4.1 9.9 - - + -
602D VAL* 3.8 22.2 - - + -
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Residues in contact with GLN 566 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562D PHE* 2.9 45.8 + - + +
563D PRO* 3.5 20.2 + - - +
565D ILE* 1.3 76.3 - - - +
567D ALA* 1.3 59.6 + - - +
568D MSE 3.2 0.2 - - - -
570D PRO* 3.3 40.3 - - + +
573D ALA* 3.7 13.5 - - + +
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Residues in contact with ALA 567 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563D PRO 3.1 13.1 + - - +
564D LEU* 3.6 14.4 - - + +
565D ILE 3.2 0.8 - - - -
566D GLN* 1.3 76.7 - - - +
568D MSE 1.3 61.7 + - + +
570D PRO* 5.0 0.7 - - - -
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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