Contacts of the helix formed by residues 509 - 525 (chain A) in PDB entry 3L7A
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 GLU 509 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A SER* 3.3 31.9 + - - +
15A VAL* 3.7 26.9 - - + -
233A TYR* 4.7 5.6 + - - +
234A ARG* 4.0 17.9 + - - -
504A ALA* 4.2 5.2 - - + -
508A GLY* 1.3 73.6 - - - -
510A GLU* 1.3 64.9 + - - +
511A TYR* 3.1 10.5 + - - -
512A ILE* 3.2 26.6 + - + +
513A SER 4.8 0.2 + - - -
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Residues in contact with GLU 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A ILE 5.1 1.3 + - - +
508A GLY 3.6 1.6 - - - -
509A GLU* 1.3 77.3 - - - +
511A TYR* 1.3 61.0 + - - +
512A ILE 3.1 1.1 + - - -
513A SER* 3.4 18.1 + - - -
514A ASP* 3.3 23.5 + - - +
517A GLN* 3.0 33.3 + - - +
831A ARG* 5.7 1.7 - - - -
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Residues in contact with TYR 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A VAL* 4.7 0.2 - - - +
488A PRO* 6.4 0.2 - - + -
492A LEU* 3.7 22.7 - - + -
500A ALA* 2.9 39.7 + - - +
503A ILE* 3.7 20.2 - - + -
504A ALA* 4.2 7.1 - - + +
507A ILE* 4.3 10.9 + - + +
508A GLY 3.3 26.9 - - - -
509A GLU* 3.1 4.9 + - - -
510A GLU* 1.3 76.9 - - - +
512A ILE* 1.3 87.0 + - + +
513A SER 3.2 0.2 - - - -
514A ASP 3.1 27.8 + - - +
515A LEU* 3.2 18.8 + - + +
517A GLN* 3.9 22.5 + - + +
518A LEU* 3.7 24.5 - - + +
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Residues in contact with ILE 512 (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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15A VAL* 4.4 21.3 - - + +
233A TYR* 3.5 41.5 - - + +
488A PRO* 3.5 15.5 - - - +
489A ARG* 3.0 34.4 + - - -
493A VAL* 3.7 31.2 - - + -
509A GLU* 3.6 22.0 - - + +
510A GLU 3.1 1.6 - - - -
511A TYR* 1.3 107.0 - - + +
513A SER* 1.3 56.8 + - - +
515A LEU* 5.2 0.4 - - - -
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Residues in contact with SER 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A THR* 4.4 4.7 - - - +
150A LEU* 5.8 2.1 - - - +
233A TYR* 4.3 12.0 - - - -
489A ARG* 3.9 12.6 - - - +
509A GLU 4.8 0.2 + - - -
510A GLU* 3.4 17.2 + - - +
512A ILE* 1.3 78.7 - - - +
514A ASP* 1.3 60.5 + - - +
515A LEU 4.0 0.9 - - - -
814A ASP* 4.0 13.4 - - - +
831A ARG* 3.1 46.4 + - - +
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Residues in contact with ASP 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A GLU* 3.3 25.4 + - - +
511A TYR* 3.1 13.9 + - - -
513A SER* 1.3 81.2 - - - +
515A LEU* 1.3 65.4 + - - +
516A ASP* 4.2 15.6 + - - +
517A GLN* 3.1 39.3 + - - +
814A ASP* 6.4 0.4 - - - -
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Residues in contact with LEU 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A ILE* 5.7 0.7 - - + +
488A PRO* 3.9 26.5 - - + -
492A LEU* 4.8 0.9 - - + -
511A TYR* 3.2 26.7 + - + +
513A SER 4.0 0.2 - - - -
514A ASP* 1.3 69.3 - - - +
516A ASP* 1.3 60.7 + - - +
517A GLN 3.0 6.1 - - - -
518A LEU* 3.0 44.3 + - + +
683A LEU* 4.0 25.1 - - + -
808A SER 4.1 6.3 - - - +
809A GLY* 3.5 20.5 - - - +
811A PHE 5.0 0.7 - - - -
812A SER* 3.8 35.7 + - - +
814A ASP* 5.7 1.0 + - - +
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Residues in contact with ASP 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A ASP* 3.1 12.5 + - - +
515A LEU* 1.3 76.0 - - - +
517A GLN* 1.3 62.2 + - - +
518A LEU 3.1 0.7 + - - -
519A ARG* 3.3 29.8 + - + +
809A GLY* 3.7 24.1 + - - -
810A LYS* 3.8 6.1 + - - -
815A ARG* 5.5 7.9 - - - +
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Residues in contact with GLN 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A ILE* 3.7 13.8 - - + +
510A GLU* 3.0 48.7 + - - +
511A TYR* 3.9 13.6 + - + +
514A ASP* 3.1 31.5 + - - +
515A LEU 3.0 1.0 - - - -
516A ASP* 1.3 74.6 - - + +
518A LEU* 1.3 60.1 + - - +
519A ARG* 3.0 6.1 - - - -
520A LYS* 2.9 58.5 + - - +
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Residues in contact with LEU 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A LEU* 5.2 1.6 - - + -
503A ILE* 3.9 27.4 - - + -
507A ILE* 4.4 4.0 - - + -
511A TYR* 3.7 26.2 - - + +
515A LEU* 3.0 40.6 + - + +
517A GLN* 1.3 76.2 - - - +
519A ARG* 1.3 61.6 + - - +
520A LYS 3.1 0.2 - - - -
521A LEU* 3.0 31.6 + - + +
683A LEU* 3.8 9.6 - - + -
805A ILE* 3.4 23.3 - - + +
806A ALA* 3.3 16.8 - - - +
808A SER* 3.4 13.9 - - - +
809A GLY 4.8 2.5 - - - +
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Residues in contact with ARG 519 (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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516A ASP* 3.3 20.4 + - - +
517A GLN 3.0 0.8 - - - -
518A LEU* 1.3 75.9 - - - +
520A LYS* 1.3 63.5 + - + +
521A LEU 3.0 0.2 - - - -
522A LEU* 2.9 41.2 + - + +
702A GLU* 3.2 40.0 + - - +
806A ALA* 3.2 15.1 + - - +
807A THR* 3.9 24.2 - - - +
809A GLY* 6.3 1.3 - - - +
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Residues in contact with LYS 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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507A ILE* 3.8 31.5 + - + -
517A GLN* 2.9 58.4 + - - +
519A ARG* 1.3 77.4 - - + +
521A LEU* 1.3 60.0 + - - +
522A LEU 3.2 1.3 + - - -
523A SER* 3.3 22.4 + - - -
524A TYR* 3.8 8.1 - - + -
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Residues in contact with LEU 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A ILE* 4.1 24.0 - - + -
506A ARG* 4.7 5.2 - - + -
507A ILE* 4.3 23.6 - - + -
518A LEU* 3.0 39.4 + - + +
520A LYS* 1.3 73.7 - - - +
522A LEU* 1.3 62.5 + - - +
523A SER 3.0 2.7 - - - -
524A TYR* 2.9 29.1 + - + +
525A VAL 3.8 3.5 + - - -
530A PHE* 3.8 32.1 - - + -
802A ILE* 4.0 9.9 - - + +
805A ILE* 4.2 17.0 - - + -
806A ALA* 4.0 10.8 - - + +
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Residues in contact with LEU 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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519A ARG* 2.9 43.0 + - + +
521A LEU* 1.3 77.4 - - - +
523A SER* 1.3 59.9 + - - +
524A TYR 3.1 1.7 + - - -
525A VAL* 3.5 25.0 + - + +
802A ILE 4.8 0.9 - - - +
803A ARG* 4.3 31.0 - - + +
806A ALA* 3.4 23.3 - - + +
807A THR* 4.5 11.7 - - + -
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Residues in contact with SER 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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520A LYS* 3.3 15.1 + - - -
521A LEU 3.0 0.6 - - - -
522A LEU* 1.3 77.6 - - - +
524A TYR* 1.3 70.0 + - - +
525A VAL* 3.6 1.1 + - - -
526A ASP* 5.1 1.4 + - - +
527A ASP* 5.1 2.3 + - - +
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Residues in contact with TYR 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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506A ARG* 3.9 46.1 + - + +
507A ILE* 4.3 9.1 - - + +
520A LYS 3.8 19.3 - - - -
521A LEU* 2.9 21.7 + - + +
523A SER* 1.3 87.8 - - - +
525A VAL* 1.3 60.3 + - - +
526A ASP 3.1 3.1 - - - -
527A ASP* 2.9 53.6 + - + +
530A PHE* 3.7 29.4 - + + -
802A ILE* 4.5 1.7 - - - +
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Residues in contact with VAL 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A LEU 3.8 1.6 + - - -
522A LEU* 3.5 19.7 + - + +
523A SER 3.6 0.4 - - - -
524A TYR* 1.3 76.7 - - - +
526A ASP* 1.3 72.6 + - - +
531A ILE* 3.4 7.0 - - - +
799A ARG* 3.1 61.2 + - + +
802A ILE* 4.2 18.2 - - + -
803A ARG* 3.9 43.3 - - + +
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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