Contacts of the helix formed by residues 496 - 508 (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 ASN 496 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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492A LEU* 2.8 22.4 + - + +
495A CYS* 1.3 79.4 - - - +
497A PRO* 1.4 65.5 - - - +
498A GLY* 4.2 1.7 + - - -
499A LEU* 3.2 35.4 + - - +
500A ALA* 3.1 18.0 + - - +
537A VAL* 3.9 1.8 - - - +
541A ASN* 3.1 34.1 + - - +
658A PRO* 3.8 8.1 - - + +
684A ASN* 2.9 36.9 + - - +
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Residues in contact with PRO 497 (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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13A ILE* 3.6 25.0 - - + +
15A VAL* 5.1 1.3 - - + -
16A ARG* 3.6 29.6 - - + +
493A VAL 3.7 13.6 - - - +
494A LEU 3.8 9.6 - - - +
495A CYS 3.5 7.0 - - - +
496A ASN* 1.4 88.9 - - - +
498A GLY* 1.3 57.5 + - - +
500A ALA* 3.3 6.4 + - + +
501A GLU* 2.9 31.9 + - - +
544A LYS* 6.3 1.6 - - - +
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Residues in contact with GLY 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ILE* 4.8 1.8 - - - +
496A ASN* 3.3 2.2 + - - -
497A PRO* 1.3 82.1 - - - +
499A LEU* 1.3 58.6 + - - +
501A GLU* 3.5 4.6 + - - +
502A ILE* 3.2 29.6 + - - +
537A VAL* 3.8 18.3 - - - +
540A GLU* 5.7 2.7 - - - -
541A ASN* 6.0 0.4 - - - -
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Residues in contact with LEU 499 (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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492A LEU* 3.8 9.6 - - + -
496A ASN* 3.2 38.5 + - - +
498A GLY* 1.3 72.8 - - - +
500A ALA* 1.3 67.1 + - - +
502A ILE* 3.3 24.5 - - + +
503A ILE* 3.1 43.3 + - + +
530A PHE* 6.0 0.2 - - + -
534A VAL* 4.9 11.0 - - + +
537A VAL* 3.6 11.7 - - + +
683A LEU 3.5 24.9 - - - +
684A ASN* 4.0 11.0 - - - +
685A GLY* 5.3 0.2 - - - -
805A ILE* 4.2 19.3 - - + -
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Residues in contact with ALA 500 (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* 4.0 14.9 - - + +
492A LEU* 4.4 8.8 - - + +
493A VAL* 4.2 24.2 - - + -
496A ASN 3.1 13.4 + - - +
497A PRO 3.3 8.7 + - - +
499A LEU* 1.3 76.5 - - - +
501A GLU* 1.3 57.3 + - - +
503A ILE* 3.6 3.5 + - - -
504A ALA* 3.0 22.0 + - - +
511A TYR* 2.9 30.0 + - - +
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Residues in contact with GLU 501 (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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13A ILE* 4.0 19.3 - - + +
14A SER* 3.0 34.7 + - - -
15A VAL* 3.0 31.6 + - - +
497A PRO 2.9 17.3 + - - +
498A GLY* 3.8 6.5 - - - +
499A LEU 3.2 0.2 - - - -
500A ALA* 1.3 74.9 - - - +
502A ILE* 1.3 60.8 + - + +
504A ALA* 3.2 4.4 + - - +
505A GLU* 2.9 54.4 + - - +
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Residues in contact with ILE 502 (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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498A GLY 3.2 12.3 + - - +
499A LEU* 3.3 28.0 - - + +
501A GLU* 1.3 78.0 - - + +
503A ILE* 1.3 63.6 + - + +
505A GLU* 3.7 15.7 - - - +
506A ARG* 2.9 39.0 + - - +
530A PHE* 3.9 7.6 - - + -
533A ASP* 3.7 37.9 - - + +
534A VAL* 3.7 25.8 - - + +
536A LYS* 4.6 5.6 - - - +
537A VAL* 3.9 13.2 - - + -
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Residues in contact with ILE 503 (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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492A LEU* 4.5 15.3 - - + -
499A LEU* 3.1 40.3 + - + +
500A ALA 3.7 3.6 - - - +
502A ILE* 1.3 75.9 - - + +
504A ALA* 1.3 64.9 + - - +
506A ARG* 3.0 6.1 + - - +
507A ILE* 3.0 40.5 + - + +
511A TYR* 3.7 21.1 - - + +
518A LEU* 3.9 22.4 - - + -
521A LEU* 4.1 17.0 - - + -
530A PHE* 4.7 8.3 - - + -
805A ILE* 4.3 14.4 - - + -
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Residues in contact with ALA 504 (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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14A SER* 5.5 2.7 - - - +
15A VAL* 3.7 22.7 - - + -
500A ALA 3.0 18.3 + - - +
501A GLU* 3.2 7.4 + - - +
503A ILE* 1.3 75.9 - - - +
505A GLU* 1.3 60.2 + - - +
508A GLY* 2.8 47.9 + - - +
509A GLU* 4.2 6.3 - - + +
511A TYR* 4.2 3.1 - - + -
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Residues in contact with GLU 505 (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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501A GLU* 2.9 46.2 + - - +
502A ILE* 3.7 18.2 - - - +
503A ILE 3.2 0.2 - - - -
504A ALA* 1.3 75.6 - - - +
506A ARG* 1.3 82.8 + - - +
533A ASP* 4.7 3.3 - - - +
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Residues in contact with ARG 506 (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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502A ILE* 2.9 33.1 + - - +
503A ILE* 3.0 5.2 + - - +
505A GLU* 1.3 104.4 + - - +
507A ILE* 1.3 65.3 + - + +
508A GLY 3.7 0.9 - - - -
521A LEU* 4.7 2.2 - - + -
524A TYR* 3.9 45.6 + - + -
527A ASP* 5.5 1.8 + - - -
529A ALA* 4.0 7.1 - - - +
530A PHE* 3.6 50.2 - - + +
533A ASP* 2.8 26.5 + - - -
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Residues in contact with ILE 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A ILE* 3.0 39.0 + - + +
506A ARG* 1.3 89.0 - - + +
508A GLY* 1.3 64.1 + - - +
510A GLU* 5.1 1.4 + - - +
511A TYR* 4.3 13.5 + - + +
517A GLN* 3.7 40.3 - - + +
518A LEU* 4.4 6.5 - - + -
520A LYS* 3.8 33.4 + - + -
521A LEU* 4.3 13.0 - - + -
524A TYR* 4.3 9.6 - - + +
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Residues in contact with GLY 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A ALA* 2.8 32.5 + - - -
506A ARG 3.7 1.2 - - - -
507A ILE* 1.3 82.8 - - - +
509A GLU* 1.3 62.3 + - - -
510A GLU 3.6 0.9 - - - -
511A TYR* 3.3 14.1 - - - -
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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