Contacts of the helix formed by residues 530 - 537 (chain A) in PDB entry 1IEV
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 VAL 530 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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392A LEU* 4.7 1.6 - - + -
522A LEU* 4.2 16.6 - - + -
528A VAL 2.9 8.5 + - - +
529A VAL* 1.3 74.4 - - - +
531A GLN* 1.3 63.1 + - - +
532A PRO* 3.4 3.6 - - - -
533A LEU* 3.1 17.1 + - + -
534A LEU* 2.8 40.5 + - + +
540A LEU* 4.3 13.0 - - + -
571A TRP* 3.1 36.6 - - + +
572A PHE 5.9 0.6 + - - -
590A LEU* 3.5 25.6 - - + -
591A PHE* 4.6 1.6 - - + -
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Residues in contact with GLN 531 (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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529A VAL* 4.2 8.3 - - - +
530A VAL* 1.3 79.2 + - - +
532A PRO* 1.3 61.2 - - + +
534A LEU* 3.4 8.5 + - + +
535A ALA* 2.8 34.2 + - - +
572A PHE 5.1 1.3 - - - +
573A LYS* 3.0 42.1 + - - +
590A LEU* 3.9 29.8 - - + +
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Residues in contact with PRO 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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506A LEU* 3.7 37.0 - - + +
510A GLN* 5.0 3.4 + - - +
529A VAL* 4.5 14.6 - - + +
530A VAL* 3.5 5.2 - - - -
531A GLN* 1.3 95.6 - - + +
533A LEU* 1.3 65.6 + - + +
535A ALA* 3.0 16.2 + - + +
536A ALA* 3.2 11.3 + - - +
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Residues in contact with LEU 533 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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484A VAL* 4.3 4.5 - - + -
501A ILE* 3.5 28.0 - - + -
505A GLY 4.2 1.8 - - - +
506A LEU* 4.1 22.2 - - + -
509A VAL* 3.7 37.7 - - + -
520A THR* 4.8 4.0 - - + -
522A LEU* 3.8 26.7 - - + -
529A VAL 4.9 8.1 - - - +
530A VAL* 3.1 13.2 + - + +
532A PRO* 1.3 79.9 - - + +
534A LEU* 1.3 60.7 + - - +
536A ALA* 3.6 1.4 + - - +
537A SER* 2.8 31.2 + - - -
540A LEU* 3.7 15.1 - - + +
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Residues in contact with LEU 534 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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392A LEU* 4.5 5.2 - - + -
393A LYS* 2.5 52.8 + - + +
530A VAL* 2.8 29.1 + - + +
531A GLN* 3.5 7.2 - - + +
533A LEU* 1.3 76.4 - - - +
535A ALA* 1.3 62.0 + - - +
536A ALA 3.3 0.5 + - - -
537A SER* 3.4 3.3 + - - +
540A LEU* 3.5 39.9 - - + -
590A LEU* 4.1 7.6 - - + -
591A PHE* 3.7 35.2 - - + -
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Residues in contact with ALA 535 (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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393A LYS* 4.2 1.4 + - - -
396A LYS* 3.9 12.1 - - - -
531A GLN 2.8 16.0 + - - +
532A PRO* 3.0 13.6 + - + +
534A LEU* 1.3 79.2 - - - +
536A ALA* 1.3 60.4 + - - +
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Residues in contact with ALA 536 (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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396A LYS* 3.1 20.5 + - - +
509A VAL* 3.8 23.1 - - + -
510A GLN* 3.9 30.1 - - + -
513A CYS* 3.1 18.4 - - + +
518A CYS* 4.0 0.2 - - - -
532A PRO 3.2 9.1 + - - +
535A ALA* 1.3 79.3 - - - +
537A SER* 1.3 58.7 + - - +
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Residues in contact with SER 537 (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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393A LYS* 2.4 32.1 + - - -
396A LYS* 3.4 7.5 - - - -
509A VAL* 3.8 5.5 - - - +
518A CYS* 3.7 7.4 - - - -
520A THR* 2.8 26.3 + - - -
533A LEU 2.8 19.8 + - - -
534A LEU 3.4 3.2 + - - -
536A ALA* 1.3 78.1 - - - +
538A ASP* 1.3 59.2 + - - +
539A ALA 3.3 21.8 - - - -
540A LEU* 4.1 5.6 - - - +
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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