Contacts of the helix formed by residues 526 - 534 (chain A) in PDB entry 1ULT
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 LEU 526 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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517A ILE* 5.2 0.4 - - - +
518A PRO* 2.6 36.8 + - + +
519A ARG 3.5 19.3 - - - +
520A THR* 4.0 12.8 - - + -
524A LYS 3.2 0.8 + - - -
525A PHE* 1.3 68.2 - - - +
527A LYS* 1.3 57.2 + - - +
528A ARG* 2.9 51.2 + - + +
529A ALA* 3.1 24.7 + - + +
530A LEU* 3.7 8.6 + - - +
1001A CIT 3.6 7.2 - - - +
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Residues in contact with LYS 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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435A LYS 4.4 6.5 + - - +
447A SER* 3.2 16.5 + - - +
448A VAL* 4.7 5.1 - - - +
451A GLU* 2.6 35.8 + - - -
464A ALA* 4.6 1.1 - - - -
465A VAL 2.8 18.8 + - - +
466A VAL* 3.6 20.4 - - + -
525A PHE* 3.0 29.9 + - + +
526A LEU* 1.3 71.8 - - - +
528A ARG* 1.3 64.0 + - - +
529A ALA 3.2 0.2 - - - -
530A LEU* 3.3 13.4 + - + +
531A ARG* 2.9 51.1 + - - +
1001A CIT 3.6 17.9 + - - +
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Residues in contact with ARG 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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520A THR* 6.3 0.4 - - - +
526A LEU* 2.9 17.0 + - + +
527A LYS* 1.3 78.9 - - - +
529A ALA* 1.3 62.8 + - - +
531A ARG* 3.2 21.9 + - - +
532A GLU* 3.5 13.0 + - - +
1001A CIT 2.6 59.7 + - - +
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Residues in contact with ALA 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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518A PRO* 4.8 8.7 - - + -
526A LEU* 3.1 25.7 + - + +
528A ARG* 1.3 78.6 - - - +
530A LEU* 1.3 60.4 + - - +
532A GLU* 3.0 10.4 + - - +
533A GLN* 2.9 44.8 + - + +
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Residues in contact with LEU 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A ALA* 4.0 18.6 - - + -
466A VAL* 4.3 19.1 - - + -
468A ILE* 4.4 0.9 - - - +
480A VAL* 3.8 31.2 - - + -
517A ILE* 3.9 22.9 - - + -
518A PRO* 4.7 13.5 - - + -
526A LEU 4.2 6.1 - - - +
527A LYS* 3.3 21.2 + - + +
529A ALA* 1.3 77.0 - - - +
531A ARG* 1.3 63.9 + - - +
533A GLN* 4.4 13.9 - - - +
534A TYR* 3.1 41.7 + - + +
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Residues in contact with ARG 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A LEU 4.1 7.1 + - - -
435A LYS* 3.8 20.6 + - - +
466A VAL* 4.3 14.2 - - + +
467A ALA* 4.2 24.6 + - - +
468A ILE* 4.1 11.0 - - - +
469A PRO* 5.2 2.4 - - - +
527A LYS* 2.9 57.0 + - - +
528A ARG* 3.2 13.1 - - - +
530A LEU* 1.3 76.2 - - - +
532A GLU* 1.3 58.3 + - - +
534A TYR 4.0 0.9 - - - -
535A LYS* 3.3 24.1 + - - +
1001A CIT 2.9 42.9 + - - -
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Residues in contact with GLU 532 (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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528A ARG 3.5 8.7 + - - +
529A ALA* 3.0 11.0 + - - +
531A ARG* 1.3 80.3 - - - +
533A GLN* 1.3 66.6 + - - +
535A LYS* 3.1 45.9 + - - +
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Residues in contact with GLN 533 (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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518A PRO* 4.7 10.7 - - - +
529A ALA* 2.9 35.2 + - + +
530A LEU* 3.3 10.4 + - - +
532A GLU* 1.3 79.4 - - - +
534A TYR* 1.3 88.7 + - + +
535A LYS* 3.3 2.6 + - - +
536A ASN 4.9 0.9 + - - -
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Residues in contact with TYR 534 (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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466A VAL* 6.1 0.2 - - + -
468A ILE* 3.2 24.0 - - + +
478A LEU* 3.4 32.3 - - + -
480A VAL* 4.2 12.7 - - + +
512A VAL* 3.3 41.6 - - + +
513A PHE 4.9 1.6 + - - -
514A ALA* 5.6 1.9 - - - +
530A LEU* 3.1 32.8 + - + +
533A GLN* 1.3 99.1 + - + +
535A LYS* 1.3 64.2 + - - +
536A ASN 3.2 2.7 - - - -
537A TYR* 3.1 32.4 + + + +
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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