Contacts of the strand formed by residues 497 - 508 (chain A) in PDB entry 2ADS
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 ALA 497 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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495A VAL* 3.0 15.7 - - - +
496A ASP* 1.3 79.0 - - - +
498A PHE* 1.3 67.7 + - - +
499A VAL 4.0 0.9 - - - -
521A ILE* 4.5 7.4 - - + -
522A PHE 3.4 13.0 - - - +
555A LEU* 4.5 1.3 - - + -
560A PHE* 4.1 27.1 - - + -
565A LYS 3.1 3.8 + - - -
566A ILE* 3.4 18.3 - - + -
567A VAL 3.0 15.3 + - - -
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Residues in contact with PHE 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A ILE* 4.9 18.6 - - + -
493A GLY* 5.7 0.2 - - - -
495A VAL* 3.4 31.4 - - + -
497A ALA* 1.3 74.4 - - - +
499A VAL* 1.3 62.0 + - - +
520A LYS 3.4 2.9 - - - +
521A ILE* 4.7 0.2 - - - -
522A PHE* 3.0 43.1 + - + +
523A ASN 3.4 21.1 - - - -
524A SER* 4.2 12.8 - - - -
526A GLY* 5.6 1.6 - - - -
567A VAL* 3.5 24.9 - - + +
569A HIS* 4.2 0.4 - + - -
658A GLN* 3.4 41.5 - - + -
662A LEU* 3.8 33.4 - - + -
678A THR* 3.7 3.2 - - + +
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Residues in contact with VAL 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A ALA* 4.0 1.6 - - - +
498A PHE* 1.3 73.5 - - - +
500A GLY* 1.3 57.3 + - - +
501A ILE* 3.7 13.8 + - + -
519A THR* 3.3 33.2 - - + -
520A LYS 3.5 3.6 - - - -
521A ILE* 4.2 13.9 - - + +
551A VAL* 3.8 13.2 - - + -
552A PHE* 6.2 1.6 - - + -
555A LEU* 4.8 4.9 - - + -
566A ILE* 3.7 22.6 - - + +
567A VAL 2.9 27.2 + - - +
568A VAL* 3.7 23.3 - - + -
569A HIS* 3.0 13.3 + - - +
678A THR* 4.0 1.1 - - - -
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Residues in contact with GLY 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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498A PHE 3.6 1.2 + - - -
499A VAL* 1.3 73.2 - - - +
501A ILE* 1.3 60.7 + - - -
518A PHE 3.5 2.9 - - - +
519A THR* 3.2 4.3 - - - -
520A LYS* 2.9 36.1 + - - +
569A HIS 3.4 9.9 - - - -
678A THR* 3.7 33.0 - - - +
682A SER* 6.1 0.2 - - - -
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Residues in contact with ILE 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A VAL* 3.7 28.2 + - + +
500A GLY* 1.3 77.5 - - - -
502A ASP* 1.3 64.3 + - - +
503A ILE* 3.8 25.1 - - + -
517A ALA* 4.6 5.4 - - + -
518A PHE 3.8 2.5 - - - -
519A THR* 3.8 16.8 - - - +
548A ILE* 5.5 1.8 - - + -
551A VAL* 4.3 15.9 - - + -
552A PHE* 5.2 2.9 - - + -
568A VAL* 4.2 13.7 - - + -
569A HIS 3.2 6.2 + - - +
570A ARG* 3.4 10.9 - - - -
571A ASP* 3.2 22.7 + - - +
582A PHE* 3.4 36.8 - - + -
678A THR 5.8 0.2 - - - -
679A VAL* 5.0 1.0 - - - +
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Residues in contact with ASP 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901 CA 3.8 3.3 - - - -
501A ILE* 1.3 78.8 - - - +
503A ILE* 1.3 59.3 + - - +
504A SER* 3.0 20.9 + - - -
516A VAL 2.9 17.5 - - - +
517A ALA* 3.6 5.5 - - - -
518A PHE 3.3 15.0 + - - +
570A ARG* 3.2 16.2 + - - +
571A ASP* 3.5 15.9 - - + +
678A THR 6.1 0.4 - - - +
679A VAL* 6.2 1.1 - - + -
682A SER* 3.6 11.3 - - - +
683A ASP* 3.3 32.7 - - - +
686A THR* 3.2 15.5 - - + +
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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
----------------------------------------------------------
501A ILE* 3.8 17.0 - - + -
502A ASP* 1.3 70.8 - - - +
504A SER* 1.3 63.0 + - - +
505A ARG* 3.7 21.9 + - + +
515A ALA* 5.2 5.8 - - + -
516A VAL 3.9 3.1 - - - -
517A ALA* 3.9 16.4 - - + +
543A LEU* 6.0 1.8 - - + +
544A THR* 4.9 8.5 - - + +
547A ALA* 5.4 1.1 - - + -
548A ILE* 4.4 13.9 - - + -
570A ARG* 3.0 28.4 + - - +
575A TYR* 5.0 3.1 - - - -
578A GLU* 3.2 41.4 - - + +
582A PHE* 4.0 23.1 - - + -
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Residues in contact with SER 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901 CA 3.7 13.9 - - - -
502A ASP* 3.0 21.7 + - - -
503A ILE* 1.3 71.0 - - - +
505A ARG* 1.3 71.4 + - - +
515A ALA* 3.3 19.3 - - - +
516A VAL 3.2 10.0 + - - -
683A ASP* 4.1 0.7 + - - -
686A THR* 2.9 35.6 + - - -
687A LYS 5.4 0.2 - - - -
690A LEU* 4.3 10.8 - - - -
12M G 5.0 3.2 + - - -
13M G 6.4 0.2 - - - -
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Residues in contact with ARG 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A ILE* 3.7 13.8 - - + +
504A SER* 1.3 84.5 - - - +
506A ILE* 1.3 71.3 + - - +
507A THR* 4.2 12.1 - - - +
512A THR* 5.8 3.2 - - + +
514A ASN 4.0 5.4 - - - -
515A ALA* 4.5 5.0 - - + +
543A LEU* 4.1 26.3 - - - +
544A THR* 2.9 28.5 + - - +
575A TYR* 3.9 23.8 - - + +
577A ASP* 4.8 8.5 - - - +
578A GLU* 3.1 36.1 + - - +
690A LEU* 4.9 1.1 - - - +
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Residues in contact with ILE 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A ARG* 1.3 81.1 - - - +
507A THR* 1.3 66.1 + - - +
508A ARG* 5.2 8.3 - - + +
512A THR* 3.6 4.0 - - - +
513A VAL* 2.9 47.2 + - + +
514A ASN 3.3 11.4 + - - +
687A LYS* 5.9 3.6 - - + -
690A LEU* 3.6 42.8 - - + -
691A ARG* 5.0 1.6 - - - +
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Residues in contact with THR 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A ARG* 4.2 10.0 - - - +
506A ILE* 1.3 80.2 + - - +
508A ARG* 1.3 64.0 + - - +
509A ASP 3.5 3.6 + - - +
510A GLY* 3.4 41.3 - - - +
511A LYS 3.9 4.3 - - - +
512A THR* 3.5 16.9 + - - +
12G C 4.1 10.9 - - - +
13G C 3.7 30.2 - - - +
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Residues in contact with ARG 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ARG* 4.8 25.2 - - - +
506A ILE* 5.2 8.0 - - + +
507A THR* 1.3 71.7 - - - +
509A ASP* 1.3 78.0 + - - +
510A GLY 3.6 0.7 - - - -
511A LYS* 3.0 28.4 + - + +
513A VAL* 3.5 38.1 - - + +
12G C 5.4 0.7 - - - -
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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