Contacts of the strand formed by residues 538 - 542 (chain B) in PDB entry 3I8E
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 VAL 538 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499B SER* 4.6 5.9 + - - -
500B VAL* 3.7 15.1 - - + +
511B ALA* 3.7 22.4 - - + -
513B GLY* 4.6 3.9 - - - -
514B ARG* 3.6 27.9 - - - +
515B ALA 3.8 18.2 - - - +
516B LEU* 4.5 1.6 - - + -
534B MET* 4.6 2.0 - - + -
537B GLU* 1.3 73.6 - - - +
539B ALA* 1.3 62.0 + - - +
540B CYS 3.9 9.4 - - - +
541B LEU* 4.2 7.6 - - + -
558B ILE* 3.5 33.4 - - + -
560B LEU* 3.8 9.0 - - + -
561B TRP* 3.6 8.8 + - - -
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Residues in contact with ALA 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500B VAL* 3.5 12.9 - - - +
537B GLU 3.4 1.6 + - - -
538B VAL* 1.3 74.1 - - - +
540B CYS* 1.3 65.7 + - - +
559B GLY 3.2 17.7 + - - +
560B LEU 3.6 13.7 - - - +
561B TRP* 3.6 20.0 - - + +
587B ILE* 4.5 5.2 - - + -
588B PRO* 3.7 21.8 - - + +
589B ARG* 4.7 3.3 - - - +
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Residues in contact with CYS 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500B VAL* 3.8 7.6 - - - -
538B VAL* 3.7 2.4 - - - +
539B ALA* 1.3 83.5 - - - +
541B LEU* 1.3 64.2 + - - +
558B ILE* 3.2 23.3 - - - +
559B GLY* 3.4 23.0 + - - -
588B PRO* 3.8 34.8 - - - -
589B ARG 4.0 15.5 - - - +
590B SER 4.5 0.4 - - - -
591B ILE* 3.7 27.8 - - + +
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Residues in contact with LEU 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500B VAL* 3.4 22.6 - - + +
501B ALA 3.9 11.4 - - - +
502B SER* 3.9 13.0 - - - +
509B VAL* 3.8 25.6 - - + +
510B VAL 3.6 33.7 - - - +
511B ALA* 3.9 7.9 - - + -
516B LEU* 4.0 11.4 - - + -
538B VAL* 4.2 4.5 - - + -
540B CYS* 1.3 76.0 - - - +
542B ASP* 1.3 65.2 + - - +
543B ILE* 6.2 0.4 - - + -
556B CYS* 5.3 6.7 - - - -
557B ALA 4.7 4.5 - - - +
558B ILE* 3.8 28.7 - - + -
591B ILE* 3.4 8.0 - - - +
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Residues in contact with ASP 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502B SER* 4.5 3.3 - - - -
541B LEU* 1.3 74.7 - - - +
543B ILE* 1.3 65.7 + - - +
544B THR* 3.3 19.4 + - - -
556B CYS* 3.4 13.7 - - - -
557B ALA 4.0 7.3 + - - +
591B ILE* 3.3 36.7 - - + +
592B LEU* 3.4 18.6 - - - +
593B MET* 3.0 47.1 + - + +
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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