Contacts of the strand formed by residues 426 - 430 (chain D) 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 ALA 426 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424D ALA* 3.3 5.7 - - - +
425D ALA* 1.3 82.8 - - - +
427D LEU* 1.3 67.7 + - - +
428D ILE* 5.2 0.9 - - + -
447D ALA* 3.8 3.8 - - - -
448D PRO* 3.4 18.4 - - + +
450D ILE* 4.1 12.6 - - + -
502D PHE* 3.5 29.6 - - + -
508D VAL* 3.4 11.0 - - + +
509D ILE 3.0 22.3 + - - -
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Residues in contact with LEU 427 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415D SER* 3.9 33.9 - - - +
416D VAL* 4.3 2.9 - - - +
419D SER* 3.8 15.3 - - - +
426D ALA* 1.3 73.7 - - - +
428D ILE* 1.3 63.7 + - - +
429D VAL* 4.0 2.7 - - + -
440D VAL* 3.8 24.9 - - + -
445D PRO* 3.8 11.9 - - + -
447D ALA* 3.8 33.7 - - + +
448D PRO 2.9 8.9 + - - +
449D ILE* 3.3 14.7 - - + +
450D ILE 2.8 26.5 + - - +
509D ILE* 3.3 18.6 - - + +
511D LEU* 5.1 3.1 - - + -
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Residues in contact with ILE 428 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426D ALA* 5.2 0.2 - - + -
427D LEU* 1.3 74.2 - - - +
429D VAL* 1.3 59.3 + - - +
430D LEU* 4.0 20.6 - - + -
450D ILE* 3.3 18.8 - - + +
452D VAL* 4.6 0.7 - - + -
489D VAL* 4.4 10.3 - - + +
492D ALA* 3.7 36.3 - - + +
493D MET* 3.7 30.3 - - + -
502D PHE* 4.9 1.8 - - + -
508D VAL* 4.3 8.5 - - + -
509D ILE 2.7 15.4 + - - +
510D VAL* 4.2 22.9 - - + -
511D LEU* 2.6 36.3 + - - +
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Residues in contact with VAL 429 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427D LEU* 4.7 2.2 - - + +
428D ILE* 1.3 77.2 - - - +
430D LEU* 1.3 71.5 + - - +
431D THR* 3.4 8.4 + - - -
436D SER* 3.5 31.9 - - - +
437D ALA* 4.1 11.2 - - + +
440D VAL* 4.3 9.2 - - + -
449D ILE* 3.9 24.2 - - + -
450D ILE 3.1 6.9 + - - -
451D ALA* 3.3 4.3 - - - +
452D VAL 2.9 25.3 + - - -
511D LEU* 3.5 25.4 - - + -
521D THR* 4.3 9.9 - - + -
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Residues in contact with LEU 430 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428D ILE* 4.0 15.5 - - + -
429D VAL* 1.3 75.9 - - - +
431D THR* 1.3 58.6 + - - +
452D VAL* 3.9 11.2 - - + -
485D VAL* 3.6 29.6 - - + +
488D ARG* 3.7 52.4 + - + +
489D VAL* 4.0 17.5 - - + -
511D LEU 2.9 18.8 + - - +
512D THR* 3.8 23.6 - - + -
513D GLY 5.1 4.0 + - - +
521D THR* 4.6 6.9 - - - -
531D PO4 3.7 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