Contacts of the helix formed by residues 523 - 534 (chain B) in PDB entry 1LD8
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 523 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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521B GLU* 3.7 13.9 - - + +
522B PRO* 1.3 81.9 - - - +
524B TYR* 1.3 65.3 + - - +
526B LEU* 3.1 41.7 + - + +
527B ARG* 3.3 16.1 + - - +
562B TYR* 5.0 1.3 - - + -
568B VAL* 4.0 11.5 - - + +
569B PRO 5.5 0.9 - - - +
571B LEU* 4.0 19.7 - - + -
833B GLN* 4.2 0.2 - - - -
837B GLU* 3.5 24.0 - - + +
841B MET* 3.7 30.7 - - + -
887B LEU* 3.9 24.7 - - + -
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Residues in contact with TYR 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A THR* 2.6 32.0 + - - -
351A ILE* 3.3 37.0 + - + +
353A LYS* 6.1 0.4 - - + -
523B LEU* 1.3 70.9 - - - +
525B SER* 1.3 66.9 + - - +
526B LEU 3.2 1.0 + - - -
527B ARG* 3.3 59.0 + - - +
530B HIS* 3.8 29.3 - + - -
533B GLU* 5.5 2.1 - - - +
783B ARG 4.8 2.9 + - - -
786B GLY* 6.1 0.4 - - - -
831B HIS* 3.4 30.5 - + + -
833B GLN* 3.4 12.0 - - - +
834B ALA* 3.8 16.2 - - + -
837B GLU* 2.8 17.6 + - - +
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Residues in contact with SER 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B TYR* 1.3 76.5 - - - +
526B LEU* 1.3 62.7 + - - +
527B ARG 3.5 0.4 - - - +
530B HIS* 3.2 33.4 + - - +
556B GLN* 5.3 2.9 + - - +
559B PHE* 3.6 45.4 - - - +
784B PHE 4.8 0.7 + - - -
785B GLU 4.9 2.6 + - - -
786B GLY* 5.6 0.7 - - - -
834B ALA* 4.9 3.3 + - - +
837B GLU* 2.6 33.3 + - - +
841B MET* 4.3 5.8 - - - -
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Residues in contact with LEU 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B LEU* 3.1 31.4 + - + +
525B SER* 1.3 79.9 - - - +
527B ARG* 1.3 67.0 + - - +
528B PRO* 3.6 3.1 - - - +
556B GLN* 5.6 1.1 - - - +
559B PHE* 3.3 41.3 - - + +
560B SER* 4.4 1.8 - - - +
562B TYR* 4.2 4.7 - - + +
563B LYS* 3.6 53.0 + - + +
568B VAL* 3.7 29.2 - - + -
841B MET* 5.3 2.0 - - + -
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Residues in contact with ARG 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A THR* 6.0 1.6 - - - +
353A LYS* 5.5 6.9 - - - +
523B LEU 3.3 10.1 + - - +
524B TYR* 3.3 55.4 + - - +
525B SER 4.5 0.2 - - - +
526B LEU* 1.3 80.4 - - - +
528B PRO* 1.3 69.8 - - + +
529B GLU* 3.1 29.6 + - - +
530B HIS* 3.0 20.2 + - + +
531B ALA 4.3 0.7 + - - -
831B HIS* 6.0 0.6 - - - -
833B GLN* 5.3 6.7 + - - +
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Residues in contact with PRO 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526B LEU 3.6 3.5 - - - +
527B ARG* 1.3 83.4 - - + +
529B GLU* 1.3 79.5 + - + +
530B HIS 3.1 1.4 + - - -
531B ALA* 3.3 19.2 + - - +
532B ARG* 4.7 4.8 + - - +
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Residues in contact with GLU 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527B ARG* 3.1 28.8 + - + +
528B PRO* 1.3 98.0 - - + +
530B HIS* 1.3 63.1 + - - +
531B ALA 3.1 0.4 - - - -
532B ARG* 3.0 56.2 + - - +
533B GLU* 4.2 6.2 + - - +
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Residues in contact with HIS 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B TYR* 3.8 38.9 - + - +
525B SER* 3.2 27.6 + - - +
527B ARG* 3.0 19.2 + - + +
529B GLU* 1.3 79.5 - - - +
531B ALA* 1.3 55.6 + - - +
533B GLU* 2.9 34.3 + - + +
556B GLN* 5.2 1.6 + - - +
559B PHE* 3.9 10.8 - + - -
783B ARG 3.4 15.5 + - - -
784B PHE* 2.8 57.8 + + - -
786B GLY* 6.1 0.2 - - - -
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Residues in contact with ALA 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527B ARG 4.3 0.8 + - - -
528B PRO 3.3 13.7 + - - +
529B GLU 3.1 0.6 - - - -
530B HIS* 1.3 77.8 - - - +
532B ARG* 1.3 62.2 + - - +
533B GLU 3.1 1.4 + - - -
534B ARG* 3.3 28.8 + - + +
556B GLN* 5.0 9.1 - - - +
784B PHE* 4.9 3.6 - - - -
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Residues in contact with ARG 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A GLU* 6.0 4.4 - - - +
528B PRO 4.7 3.7 + - - -
529B GLU* 3.0 49.3 + - - +
531B ALA* 1.3 79.3 - - - +
533B GLU* 1.3 65.5 + - - +
534B ARG 3.2 7.9 + - - +
536B GLN* 4.6 9.7 - - - +
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Residues in contact with GLU 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A GLU 4.4 12.6 - - - +
348A LYS 5.0 2.4 - - - +
350A THR* 4.6 15.0 + - - +
351A ILE 5.9 0.6 + - - -
524B TYR* 5.5 1.8 - - - +
529B GLU 4.4 4.5 - - - +
530B HIS* 2.9 31.4 + - + +
532B ARG* 1.3 82.6 - - - +
534B ARG* 1.3 66.7 + - - +
535B LEU 3.7 0.5 + - - -
552B GLU* 4.8 0.9 - - - +
783B ARG* 3.0 81.1 + - - +
784B PHE* 3.6 13.4 - - + +
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Residues in contact with ARG 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531B ALA* 3.3 20.2 - - + +
532B ARG 3.2 7.1 - - - +
533B GLU* 1.3 82.5 - - - +
535B LEU* 1.3 69.0 + - - +
536B GLN* 3.5 10.2 + - - +
549B ALA* 4.8 2.4 + - - +
552B GLU* 3.3 29.7 + - - +
553B GLU* 3.4 38.0 + - - +
556B GLN* 3.9 26.9 - - - +
783B ARG* 5.5 1.1 - - - -
784B PHE* 3.4 29.8 - - + -
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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