Contacts of the strand formed by residues 434 - 437 (chain F) in PDB entry 6O81
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 434 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401F VAL* 3.3 20.9 - - + +
403F LEU* 4.3 10.1 - - + -
424F ALA* 4.0 22.0 - - + +
427F ALA* 3.8 29.2 - - + -
428F ARG 5.4 0.2 - - - +
432F VAL 4.0 1.8 - - - +
433F PRO* 1.3 75.1 - - - +
435F LEU* 1.3 61.0 - - - +
436F VAL* 4.9 0.4 - - + -
496F LEU 3.9 6.7 + - - +
497F VAL* 3.7 42.6 - - + -
498F ASP* 3.9 5.2 + - - +
499F LEU* 3.5 24.8 + - - +
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Residues in contact with LEU 435 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323F ALA* 6.1 1.1 - - + -
326F LYS* 4.4 22.7 - - + -
327F ILE* 6.0 3.6 - - + -
400F LYS* 4.4 11.0 - - + -
401F VAL 2.6 29.0 + - - +
402F LEU* 3.3 20.5 - - + +
403F LEU 2.5 34.9 + - - +
433F PRO 3.6 11.2 - - - +
434F VAL* 1.3 82.1 - - - +
436F VAL* 1.3 58.8 + - - +
499F LEU* 3.7 21.3 - - + -
501F ILE* 3.8 25.8 - - + -
241H LEU* 3.9 19.1 - - + -
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Residues in contact with VAL 436 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403F LEU* 3.4 30.3 - - + +
404F GLY 5.7 0.2 - - - -
405F ALA* 4.1 19.5 - - + -
408F LEU* 4.9 2.9 - - + -
414F VAL* 4.1 22.4 - - + -
420F THR* 5.5 0.2 - - + -
434F VAL* 4.2 0.6 - - + -
435F LEU* 1.3 76.4 - - - +
437F CYS* 1.3 64.7 + - - +
438F CYS 5.2 0.2 - - - +
497F VAL* 3.8 23.8 - - + -
499F LEU 3.3 19.7 + - - +
500F VAL* 3.8 17.7 - - + -
501F ILE* 3.2 25.5 + - - +
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Residues in contact with CYS 437 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319F ILE* 4.1 7.0 - - + -
341F LEU* 3.6 28.3 - - + +
342F VAL* 5.0 3.1 - - + -
345F ILE* 3.7 25.1 - - + -
402F LEU* 3.8 22.0 - - - -
403F LEU 3.2 15.4 + - - +
404F GLY* 4.4 1.6 - - - -
405F ALA 3.4 19.3 + - - +
435F LEU 4.3 1.1 - - - -
436F VAL* 1.3 80.5 - - - +
438F CYS* 1.3 60.2 + - - +
442F LYS* 4.9 0.9 + - - -
501F ILE* 3.9 20.2 - - - -
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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