Contacts of the strand formed by residues 427 - 430 (chain E) 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 LEU 427 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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415E SER* 3.8 35.7 - - - +
416E VAL* 4.4 3.1 - - + +
419E SER* 3.8 18.6 - - - +
426E ALA* 1.3 79.8 - - - +
428E ILE* 1.3 63.3 + - - +
429E VAL* 4.5 3.6 - - + -
440E VAL* 3.7 23.6 - - + -
445E PRO* 3.5 28.9 - - + -
447E ALA* 4.0 6.5 - - + +
448E PRO 2.9 16.4 + - - +
449E ILE* 3.3 15.9 - - + +
450E ILE 2.8 25.4 + - - +
509E ILE* 3.4 12.8 - - + +
511E LEU* 4.8 4.3 - - + -
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Residues in contact with ILE 428 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427E LEU* 1.3 72.3 - - - +
429E VAL* 1.3 58.8 + - - +
430E LEU* 4.1 17.3 - - + -
450E ILE* 3.3 18.4 - - + +
452E VAL* 4.7 0.2 - - + -
489E VAL* 4.7 5.8 - - + +
492E ALA* 3.6 31.4 - - + +
493E MET* 3.7 41.1 - - + +
502E PHE* 4.8 1.6 - - + -
508E VAL* 3.9 11.7 - - + -
509E ILE 2.8 9.2 + - - +
510E VAL* 3.4 31.8 - - + +
511E LEU* 2.6 35.2 + - - +
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Residues in contact with VAL 429 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427E LEU 4.2 2.9 - - - +
428E ILE* 1.3 75.9 - - - +
430E LEU* 1.3 64.2 + - - +
431E THR* 3.4 12.4 + - - -
436E SER* 4.3 8.7 - - - +
437E ALA* 3.9 33.7 - - + +
440E VAL* 4.1 9.2 - - + -
449E ILE* 3.7 24.5 - - + -
450E ILE 2.8 11.2 + - - +
451E ALA* 3.2 3.5 - - - -
452E VAL 2.9 27.7 + - - -
511E LEU* 3.6 25.6 - - + -
521E THR* 4.4 10.3 - - + -
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Residues in contact with LEU 430 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428E ILE* 4.1 12.1 - - + -
429E VAL* 1.3 76.7 - - - +
431E THR* 1.3 58.5 + - - +
432E GLU* 4.4 0.7 + - - +
452E VAL* 3.9 20.0 - - + -
485E VAL* 3.8 28.7 - - + +
488E ARG* 3.9 48.7 + - + +
489E VAL* 4.0 21.8 - - + -
511E LEU 3.0 17.0 + - - +
512E THR* 4.0 18.5 - - + -
513E GLY 5.3 1.6 - - - +
521E THR* 4.3 9.9 + - - -
531E PO4 3.5 8.5 + - - -
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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