Contacts of the strand formed by residues 530 - 535 (chain A) in PDB entry 1S11
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 ILE 530 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460A PHE* 5.0 0.4 - - + -
528A PRO* 3.3 5.6 - - - +
529A PHE* 1.3 101.9 - - + +
531A GLU* 1.4 74.7 + - - +
532A THR* 5.5 0.2 - - - -
734B ALA* 6.0 2.2 - - + -
761B GLY* 3.7 1.2 - - - -
762B TYR* 3.0 35.0 + - + -
784B PHE* 6.0 3.1 - - + -
789B MET* 4.8 5.6 - - + -
790B GLU* 4.1 27.8 - - - +
793B GLU* 3.7 44.4 - - + +
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Residues in contact with GLU 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A PRO* 5.2 10.3 - - + -
530A ILE* 1.4 93.2 - - - +
532A THR* 1.3 64.4 + - - +
759B SER* 5.0 11.0 - - - -
760B THR 3.7 7.7 - - - +
761B GLY* 4.3 1.8 - - - -
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Residues in contact with THR 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A THR* 4.4 3.4 - - + -
530A ILE* 5.5 0.2 - - - -
531A GLU* 1.3 77.4 - - - +
533A GLY* 1.3 61.5 + - - -
732B ASP* 3.8 6.5 - - + +
733B ALA* 3.5 21.6 + - - -
734B ALA* 3.6 12.0 + - - -
756B VAL* 4.9 4.4 - - - +
759B SER* 3.4 8.3 - - - -
760B THR* 2.6 55.8 + - - +
761B GLY* 3.7 6.5 - - - +
762B TYR* 3.4 38.3 - - + -
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Residues in contact with GLY 533 (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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532A THR* 1.3 86.3 + - - -
534A ILE* 1.4 63.3 + - - -
732B ASP* 3.4 2.1 - - - -
733B ALA* 2.6 36.3 + - - +
756B VAL* 4.2 10.8 - - - -
758B ALA 3.0 14.8 - - - -
759B SER* 3.8 1.6 - - - -
760B THR* 3.3 11.3 + - - -
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Residues in contact with ILE 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533A GLY* 1.4 68.6 - - - -
535A SER* 1.4 60.5 + - - +
536A VAL* 5.5 0.2 - - - -
666B LEU* 5.4 0.9 - - + -
691B THR* 4.3 11.7 - - + +
694B ASN* 4.4 18.4 - - + +
695B ILE* 3.8 28.5 - - + -
699B TYR* 3.7 26.9 - - + +
730B ILE* 3.9 20.6 - - + -
731B TYR* 4.1 11.0 - - - +
732B ASP* 4.5 3.1 - - - +
756B VAL* 3.9 0.6 - - - +
757B PHE* 3.0 36.3 + - + +
758B ALA* 2.7 31.6 + - + +
760B THR* 4.3 8.7 + - + +
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Residues in contact with SER 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533A GLY 4.1 0.7 - - - -
534A ILE* 1.4 72.7 - - - +
536A VAL* 1.4 65.2 + - - +
730B ILE* 3.2 6.6 - - - +
731B TYR* 2.6 56.7 + - - -
733B ALA* 3.7 19.8 + - - -
736B LEU* 3.4 31.8 - - - +
751B ILE* 6.0 4.3 - - - -
756B VAL* 5.3 6.7 - - - +
757B PHE 4.9 2.2 - - - +
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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