Contacts of the strand formed by residues 551 - 555 (chain H) in PDB entry 1W1W
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 551 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1216D ILE* 3.9 16.4 - - + -
1217D THR 3.9 11.4 - - - +
1218D LEU* 5.0 2.9 - - + -
503H ILE* 3.5 6.1 - - - +
504H PHE* 3.0 57.2 + - + +
505H THR* 5.8 0.6 + - - -
528H PHE* 3.7 30.7 - - + -
531H ILE* 5.1 2.5 - - + -
542H LEU* 4.1 25.6 - - + -
543H SER 3.7 9.9 - - - +
544H GLN* 3.8 16.6 - - - +
549H GLY 4.1 2.7 - - - +
550H ASN* 1.3 76.6 - - - +
552H LYS* 1.3 61.6 + - - +
553H ILE* 3.5 2.4 + - + +
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Residues in contact with LYS 552 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501H GLU* 3.0 35.9 + - + +
502H VAL 3.7 4.5 - - - -
503H ILE* 5.0 10.1 - - + -
541H GLY 3.5 0.9 - - - +
542H LEU* 3.5 6.4 - - - -
543H SER* 2.9 50.2 + - - +
544H GLN* 6.4 0.2 - - - -
545H THR* 5.0 12.2 + - - +
550H ASN* 4.6 11.0 - - + +
551H ILE* 1.3 72.5 - - - +
553H ILE* 1.3 61.8 + - - +
554H ASP* 4.0 2.7 + - - +
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Residues in contact with ILE 553 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488H MET* 6.0 0.2 - - - -
492H LEU* 4.2 10.8 - - + -
496H LEU* 3.7 10.1 - - + +
501H GLU* 4.0 2.2 - - - -
502H VAL* 2.8 38.8 + - + +
504H PHE* 3.9 19.1 - - + +
507H VAL* 4.1 17.9 - - + -
531H ILE* 3.8 28.3 - - + -
540H ILE* 3.3 42.6 - - + -
541H GLY 3.4 2.5 - - - -
542H LEU* 3.9 12.3 - - + -
551H ILE* 4.0 6.7 - - + +
552H LYS* 1.3 74.1 - - - +
554H ASP* 1.3 62.4 + - - +
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Residues in contact with ASP 554 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496H LEU* 4.0 7.4 - - - -
500H LYS 4.0 12.1 - - - +
501H GLU* 4.5 9.9 - - - +
540H ILE* 3.6 3.5 - - - +
541H GLY* 2.7 46.2 + - - +
542H LEU 4.2 1.9 + - - -
543H SER* 5.4 2.1 + - - -
552H LYS 4.5 3.7 - - - +
553H ILE* 1.3 74.2 - - - +
555H ALA* 1.3 67.8 + - - +
556H LYS* 4.0 16.8 + - - -
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Residues in contact with ALA 555 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496H LEU* 3.2 41.1 - - + +
500H LYS 4.8 0.6 + - - -
539H CYS 4.2 4.3 - - - -
540H ILE* 4.4 0.2 - - - -
554H ASP* 1.3 84.8 - - - +
556H LYS* 1.3 63.9 - - - +
559H LEU* 3.5 16.2 - - + -
560H PHE* 4.4 11.7 - - + -
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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