Contacts of the strand formed by residues 421 - 427 (chain B) in PDB entry 3D8F
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 ASP 421 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420A LYS* 4.5 20.1 + - + +
372B VAL 3.7 3.5 - - - +
373B ARG* 3.0 54.4 + - - +
419B GLY 3.7 2.6 + - - +
420B LYS* 1.3 70.1 - - - +
422B LEU* 1.3 63.6 + - - +
436B PRO* 3.2 22.8 - - + +
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Residues in contact with LEU 422 (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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372B VAL* 2.8 55.6 + - + +
374B SER* 4.6 4.3 - - - -
415B GLY 4.2 7.0 - - - +
416B TRP* 3.5 38.8 - - + -
420B LYS* 3.9 13.2 - - + +
421B ASP* 1.3 74.3 - - - +
423B LEU* 1.3 65.2 + - - +
433B LEU* 4.0 36.1 - - + -
434B VAL 3.2 14.8 - - - +
435B GLU* 5.1 0.7 - - + -
436B PRO* 3.7 7.2 - - + -
442B LEU* 4.8 6.7 - - + -
482B PHE* 4.2 9.0 - - + -
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Residues in contact with LEU 423 (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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374A SER* 5.8 2.7 - - - +
376A GLY* 5.2 5.6 - - - +
377A TRP* 5.4 2.7 - - + +
369B CYS* 3.8 31.6 - - - -
370B PHE 3.8 1.3 - - - -
371B ALA* 4.1 24.5 - - + +
422B LEU* 1.3 73.3 - - - +
424B LEU* 1.3 59.7 + - - +
425B GLN* 3.8 2.3 + - + +
432B LYS 3.7 0.3 - - - +
433B LEU* 3.3 5.7 - - - -
434B VAL* 2.7 49.8 + - + +
436B PRO* 3.9 26.7 - - + +
439B GLN* 3.7 30.1 - - - +
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Residues in contact with LEU 424 (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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369B CYS* 3.7 0.7 - - - -
370B PHE* 2.9 51.0 + - + +
372B VAL* 4.0 11.9 - - + -
422B LEU 3.6 1.0 + - - -
423B LEU* 1.3 71.4 - - - +
425B GLN* 1.3 58.8 + - - +
426B LEU* 4.1 23.3 - - + -
431B LEU* 3.8 24.2 - - + -
432B LYS 3.5 3.6 - - - -
433B LEU* 3.9 11.4 - - + -
465B PHE* 4.3 23.8 - - + -
482B PHE* 4.3 19.1 - - + -
491B ILE* 4.1 22.4 - - + -
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Residues in contact with GLN 425 (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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377A TRP* 3.8 20.5 - - - +
367B ILE* 3.7 15.5 - - - +
368B LYS 3.4 3.8 - - - +
369B CYS* 3.4 34.0 - - + -
423B LEU* 3.8 2.9 + - + +
424B LEU* 1.3 74.5 - - - +
426B LEU* 1.3 62.7 + - - +
427B GLU* 4.0 15.7 - - + +
430B THR 3.6 0.7 - - - +
431B LEU* 3.5 3.1 - - - +
432B LYS* 2.6 54.0 + - + +
434B VAL* 4.0 18.0 - - + +
439B GLN* 3.9 20.0 + - - -
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Residues in contact with LEU 426 (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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366B GLY 4.4 1.6 - - - +
367B ILE* 3.4 25.9 - - - +
368B LYS* 3.1 16.3 + - + +
370B PHE* 4.0 16.2 - - + -
424B LEU* 4.1 11.0 - - + -
425B GLN* 1.3 75.2 - - - +
427B GLU* 1.3 59.4 + - - +
430B THR 3.4 4.5 - - - +
431B LEU* 3.8 34.1 - - + -
447B ILE* 4.6 1.3 - - + -
491B ILE* 4.4 8.7 - - + -
494B SER* 3.7 29.8 - - - -
495B LEU* 4.2 22.7 - - + +
498B ILE* 4.1 22.3 - - + +
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Residues in contact with GLU 427 (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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377A TRP* 5.9 0.5 - - - -
476A MET* 5.2 6.4 - - - +
367B ILE* 3.7 33.0 - - + +
425B GLN* 4.0 12.9 - - - +
426B LEU* 1.3 76.3 - - - +
428B ASP* 1.3 91.7 + - - +
429B GLU 3.4 1.8 - - - +
430B THR* 3.1 22.8 + - - +
432B LYS* 3.3 32.2 + - + +
447B ILE* 5.6 0.2 - - - +
498B ILE* 5.5 1.2 - - - +
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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