Contacts of the strand formed by residues 523 - 528 (chain D) in PDB entry 3SRF
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 523 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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411D MET* 3.7 2.5 - - - -
510D VAL 3.4 0.9 - - - +
511D LEU* 3.2 9.0 - - - +
512D THR* 3.0 45.4 + - - +
514D TRP* 3.4 28.6 + - + +
521D THR 3.4 0.8 - - - -
522D ASN* 1.3 93.3 + - - +
524D MET* 1.3 64.2 + - - +
525D ARG* 4.5 6.7 - - + -
514H TRP* 4.9 4.9 - - + -
523H THR* 3.7 27.6 - - + -
524H MET 3.3 3.6 - - - +
525H ARG* 4.0 7.0 - - + +
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Residues in contact with MET 524 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411D MET* 3.7 5.8 - - + +
414D GLY 4.1 7.9 - - - +
415D SER* 3.8 31.2 - - - +
418D ALA* 4.3 11.0 - - + -
509D ILE* 3.7 24.2 - - + -
510D VAL 3.2 4.0 - - - +
511D LEU* 4.1 4.7 - - + -
523D THR* 1.3 74.5 - - - +
525D ARG* 1.3 68.6 + - - +
411H MET* 3.6 40.8 - - + +
414H GLY* 5.1 2.7 - - - -
522H ASN 3.7 0.9 - - - +
523H THR* 3.3 5.5 - - - +
524H MET* 2.9 65.9 + - + -
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Residues in contact with ARG 525 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485D VAL* 4.4 5.3 - - - +
486D ASP* 4.1 11.5 + - - -
489D VAL* 3.9 20.0 - - - +
508D VAL 3.5 1.4 - - - +
509D ILE* 3.5 5.0 - - - +
510D VAL* 2.7 69.5 + - + +
512D THR* 3.7 22.0 + - - +
523D THR* 4.5 4.6 - - + +
524D MET* 1.3 80.5 - - - +
526D VAL* 1.3 62.8 + - - +
527D VAL* 3.7 21.9 + - + +
514H TRP* 3.4 62.7 - - - +
522H ASN* 3.4 5.6 - - - +
523H THR* 4.0 14.8 - - + +
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Residues in contact with VAL 526 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418D ALA* 5.1 5.4 - - + -
422D CYS* 4.8 5.6 - - - -
507D VAL* 3.7 26.0 - - + -
508D VAL 3.8 2.7 - - - -
509D ILE* 3.8 22.4 - - + -
524D MET* 5.3 1.8 - - - -
525D ARG* 1.3 71.6 - - - +
527D VAL* 1.3 63.4 + - - +
528D PRO* 4.3 3.6 - - - +
407H LEU* 3.7 31.2 - - + +
410H ALA* 5.5 0.4 - - + -
411H MET* 3.4 35.2 - - + +
520H PHE* 4.8 5.5 - - + -
522H ASN* 3.3 23.9 + - - +
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Residues in contact with VAL 527 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489D VAL* 5.6 2.7 - - + -
493D MET* 5.5 4.3 - - - -
507D VAL* 3.7 4.2 - - - -
508D VAL* 2.9 36.5 + - + +
510D VAL* 3.4 32.8 - - + -
525D ARG* 4.2 24.7 - - + +
526D VAL* 1.3 79.0 - - - +
528D PRO* 1.3 74.8 - - + +
514H TRP* 5.8 6.1 - - + -
522H ASN* 5.3 7.2 - - - +
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Residues in contact with PRO 528 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493D MET* 4.7 0.9 - - - +
505D GLY* 4.3 12.3 - - - +
506D ASP 3.3 11.0 - - - +
507D VAL* 4.3 9.9 - - + -
508D VAL* 5.2 0.4 - - - -
526D VAL 4.3 3.6 - - - +
527D VAL* 1.3 98.2 - - + +
529D VAL* 1.3 65.8 + - - +
530D PRO* 3.7 9.0 - - - +
407H LEU* 5.6 7.9 - - + -
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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