Contacts of the strand formed by residues 577 - 581 (chain A) in PDB entry 3RTR
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 ARG 577 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513A VAL* 6.2 1.6 - - - +
517A LEU* 6.1 1.0 - - - +
570A TYR* 3.5 35.0 + - + -
571A ALA* 6.2 0.2 - - - -
574A HIS* 3.3 55.7 + - + +
575A SER 3.3 6.5 - - - +
576A GLY* 1.3 80.0 - - - +
578A LYS* 1.3 59.7 + - - +
33B TRP* 3.4 53.0 - - + +
34B ALA 3.9 4.5 - - - -
35B TRP* 3.8 24.2 - - + +
36B ASP* 4.4 2.9 - - - +
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Residues in contact with LYS 578 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570A TYR* 5.1 1.1 - - - -
577A ARG* 1.3 73.8 - - - +
579A LEU* 1.3 63.8 + - - +
580A THR* 4.2 17.0 - - - +
32B LEU 3.9 0.2 - - - +
33B TRP* 3.5 6.2 - - - +
34B ALA* 3.0 36.9 + - - +
35B TRP 4.1 12.2 + - - -
36B ASP* 3.5 42.9 + - + +
37B ILE 5.4 0.8 - - - +
38D VAL* 4.1 11.9 - - - +
39D VAL 4.4 6.5 + - - +
40D ASP* 2.8 36.1 + - - -
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Residues in contact with LEU 579 (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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537A ILE* 4.7 0.4 - - + -
539A VAL* 3.9 15.3 - - + -
563A TYR* 5.6 0.7 + - - -
566A PHE* 3.7 32.8 - - + -
567A THR* 5.4 10.8 - - + -
570A TYR* 3.9 32.9 - - + -
578A LYS* 1.3 76.1 - - - +
580A THR* 1.3 63.4 + - - +
581A TRP* 4.0 23.9 + - + +
31B ALA* 3.3 29.4 - - + -
32B LEU 3.6 17.7 - - - +
33B TRP* 4.0 6.1 - - + +
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Residues in contact with THR 580 (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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549A GLN* 3.1 31.7 + - - +
550A SER 5.9 0.2 - - - +
578A LYS* 4.2 19.8 - - - +
579A LEU* 1.3 75.0 + - - +
581A TRP* 1.3 65.1 + - - +
582A LEU* 3.6 13.6 + - + +
31B ALA* 3.0 5.6 - - - -
32B LEU* 2.7 48.9 + - + -
34B ALA* 6.1 0.3 - - - +
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Residues in contact with TRP 581 (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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535A PHE* 4.3 8.7 - + - -
537A ILE* 3.4 25.4 - - + -
550A SER* 3.8 14.4 + - - -
563A TYR* 3.1 61.8 + + - -
566A PHE* 4.1 13.2 - + - -
567A THR* 4.1 12.2 + - - +
579A LEU* 4.2 25.7 - - + +
580A THR* 1.3 79.3 - - - +
582A LEU* 1.3 63.6 + - - +
583A TYR* 3.5 37.7 + + + +
27B TRP* 4.0 14.6 - + - -
29B ALA* 3.6 31.0 - - + -
30B VAL 5.3 1.1 - - - -
31B ALA* 3.9 10.3 - - + -
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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
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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