Contacts of the helix formed by residues 528 - 540 (chain A) in PDB entry 3RC3
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 THR 528 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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526A ASP 3.7 3.1 + - - +
527A ALA* 1.3 76.9 - - - +
529A LEU* 1.3 67.0 + - - +
530A SER* 3.8 6.4 + - - -
531A ASN* 3.3 24.9 + - + +
532A LEU* 2.9 19.8 + - - +
562A GLN* 5.0 12.6 - - + +
903A CL 3.8 15.7 - - + -
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Residues in contact with LEU 529 (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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517A ILE* 3.7 30.1 - - + -
527A ALA 3.9 0.4 + - - -
528A THR* 1.3 75.3 - - - +
530A SER* 1.3 65.4 + - - +
532A LEU* 3.1 11.6 + - + -
533A ILE* 3.0 22.8 + - + +
554A PHE* 3.7 37.0 - - + -
558A ALA* 4.0 6.7 - - + -
568A LEU* 4.6 9.4 - - + +
571A ARG* 3.7 36.6 - - + +
572A TYR* 4.6 3.1 - - + +
575A CYS* 3.9 13.2 - - + -
903A CL 3.2 19.0 - - + +
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Residues in contact with SER 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A THR* 3.3 7.5 + - - -
529A LEU* 1.3 79.8 - - - +
531A ASN* 1.3 61.2 + - - +
533A ILE* 3.4 5.4 + - - +
534A ASP* 3.2 26.7 + - - -
555A LYS* 3.5 26.7 + - - +
558A ALA* 4.1 12.0 - - - +
559A GLU* 2.5 43.2 + - - -
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Residues in contact with ASN 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU* 2.8 34.6 + - - +
65A VAL* 3.8 24.9 + - + +
527A ALA* 3.9 12.5 - - + +
528A THR* 3.3 24.2 + - - +
529A LEU 3.2 0.4 - - - -
530A SER* 1.3 77.5 - - - +
532A LEU* 1.3 64.3 + - - +
534A ASP* 3.2 9.9 + - - +
535A ILE* 3.0 40.7 + - - +
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Residues in contact with LEU 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A ILE* 4.3 15.4 - - + +
520A PHE* 4.0 22.8 - - + +
521A ALA* 3.7 29.6 - - + +
524A LEU* 3.8 30.1 - - + +
527A ALA* 3.7 25.8 - - + +
528A THR 2.9 18.1 + - - +
529A LEU* 3.5 14.1 - - + +
531A ASN* 1.3 77.2 + - - +
533A ILE* 1.3 59.2 + - - +
535A ILE* 3.4 5.3 + - + +
536A PHE* 2.8 30.0 + - - +
568A LEU* 4.2 12.8 - - + -
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Residues in contact with ILE 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A PRO* 4.8 2.0 - - + -
517A ILE* 3.7 30.3 - - + -
529A LEU* 3.0 24.1 + - + +
530A SER 3.6 7.2 - - - +
531A ASN 3.2 0.2 - - - -
532A LEU* 1.3 76.4 - - - +
534A ASP* 1.3 58.8 + - - +
536A PHE* 3.3 4.6 + - - +
537A VAL* 3.0 34.2 + - + +
551A MSE 3.8 45.8 - - + -
554A PHE* 3.6 34.5 - - + -
555A LYS* 4.1 14.1 - - + -
572A TYR* 5.2 0.2 - - + -
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Residues in contact with ASP 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU* 3.5 28.0 - - + +
530A SER* 3.2 14.4 + - - +
531A ASN* 3.2 13.4 + - - +
533A ILE* 1.3 80.5 - - - +
535A ILE* 1.3 59.5 + - - +
537A VAL* 3.4 6.2 + - - +
538A ASP* 3.0 27.9 + - - +
555A LYS* 2.6 36.2 + - - +
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Residues in contact with ILE 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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63A LEU* 3.9 24.7 - - + +
64A PHE* 4.5 8.7 - - + -
172A VAL* 4.4 14.1 - - + -
179A LEU* 4.5 0.7 - - + -
520A PHE* 3.8 14.8 - - + -
524A LEU* 4.3 23.6 - - + -
527A ALA* 5.1 3.1 - - + -
531A ASN* 3.0 47.9 + - - +
532A LEU* 3.8 5.8 - - - +
534A ASP* 1.3 73.4 - - - +
536A PHE* 1.3 68.1 + - - +
538A ASP* 3.3 1.5 + - - +
539A PHE* 3.0 47.2 + - + +
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Residues in contact with PHE 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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182A ILE 4.3 0.9 - - - -
183A SER* 3.5 33.8 - - - -
185A LEU* 4.3 12.1 - - + -
512A PRO* 3.6 29.4 - - + -
516A GLN* 3.6 42.4 - - + -
517A ILE* 3.7 21.3 - - + -
520A PHE* 3.5 27.0 - + + -
532A LEU 2.8 19.4 + - - +
533A ILE* 3.3 4.2 + - - +
535A ILE* 1.3 78.8 - - - +
537A VAL* 1.3 70.5 + - + +
539A PHE* 3.7 0.5 - - - -
540A SER* 2.8 33.5 + - - -
548A VAL* 5.5 1.8 - - + -
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Residues in contact with VAL 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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512A PRO* 5.0 1.8 - - + -
533A ILE* 3.0 32.8 + - + +
534A ASP* 3.9 6.7 - - - +
536A PHE* 1.3 85.8 - - + +
538A ASP* 1.3 62.2 + - - +
540A SER* 2.8 25.2 + - - +
548A VAL* 4.1 32.1 - - + -
549A CYS 5.5 0.7 - - - +
551A MSE 4.8 7.4 - - + -
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Residues in contact with ASP 538 (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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58A ILE* 4.8 7.8 - - - +
59A PRO* 3.4 13.2 - - - +
60A ASN* 2.8 46.9 + - - +
63A LEU* 3.6 13.7 - - + +
64A PHE* 5.7 0.3 - - - -
534A ASP 3.0 17.7 + - - +
535A ILE* 3.7 4.0 - - - +
536A PHE 3.1 0.2 - - - -
537A VAL* 1.3 79.9 - - - +
539A PHE* 1.3 67.3 + - + +
540A SER 4.4 2.8 - - - +
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Residues in contact with PHE 539 (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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59A PRO* 3.8 34.8 - - + -
64A PHE* 4.6 4.3 - + - -
172A VAL* 3.7 27.4 - - + -
176A LYS* 3.7 29.4 - - + -
179A LEU* 4.0 8.5 - - + +
180A ARG* 3.8 39.7 - - + +
183A SER* 3.4 17.3 + - - +
520A PHE* 4.4 6.1 - - + -
535A ILE* 3.0 41.4 + - + +
536A PHE 3.9 0.9 - - - +
538A ASP* 1.3 82.8 - - - +
540A SER* 1.3 68.0 + - - +
541A GLN* 3.7 8.8 + - - +
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Residues in contact with SER 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A SER* 3.1 22.9 + - - -
185A LEU* 4.3 9.9 - - - -
536A PHE* 2.8 32.2 + - - -
537A VAL* 2.8 21.4 + - - +
538A ASP 3.4 3.4 - - - +
539A PHE* 1.3 78.0 - - - +
541A GLN* 1.3 62.0 + - - +
542A VAL* 5.1 0.2 - - - +
548A VAL* 3.8 17.7 - - - +
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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