Contacts of the strand formed by residues 401 - 406 (chain E) in PDB entry 1NBF
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 401 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235E THR* 5.0 6.5 - - + +
323E LEU* 2.9 31.1 + - + +
324E PHE* 3.6 35.0 - - + -
348E TYR 5.5 0.7 - - - +
399E PRO* 4.1 7.0 - - - +
400E PRO* 1.3 82.7 - - - +
402E LEU* 1.3 61.9 + - - +
403E HIS* 3.8 1.0 + - - +
517E VAL* 4.1 23.6 - - + -
518E TYR 3.6 2.9 - - - -
519E ILE* 3.8 13.5 - - + -
527E VAL* 3.3 38.6 - - + -
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Residues in contact with LEU 402 (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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347E TYR* 4.8 2.0 - - + -
349E ASP* 5.8 0.7 - - - -
350E ILE* 3.4 32.3 - - + +
398E LEU* 4.6 6.3 - - + -
399E PRO* 4.5 19.3 - - + -
400E PRO 4.0 1.8 - - - -
401E VAL* 1.3 73.5 - - - +
403E HIS* 1.3 71.7 + - - +
404E LEU* 3.8 21.8 - - + -
433E LEU* 3.5 32.8 - - + -
448E TYR* 3.6 29.9 - - + +
517E VAL* 3.4 7.1 - - - +
518E TYR* 2.6 41.7 + - + +
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Residues in contact with HIS 403 (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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228E LEU* 5.0 3.6 - - + -
231E THR* 4.4 5.7 - - - +
232E LEU* 4.9 8.0 - - + +
235E THR* 5.7 1.6 + - - -
300E CYS* 3.8 27.2 - - - -
304E LEU* 5.8 0.2 - - - +
324E PHE* 3.5 35.7 - + - -
348E TYR 4.2 17.0 + - - +
349E ASP* 3.7 3.6 - - + +
350E ILE* 3.1 24.9 + - - +
401E VAL* 3.8 1.9 + - + +
402E LEU* 1.3 86.7 - - - +
404E LEU* 1.3 64.4 + - - +
405E GLN* 3.9 9.5 + - - +
515E MET* 3.5 23.4 - - + +
516E LEU 3.8 2.2 - - - -
517E VAL* 3.7 30.3 - - + +
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Residues in contact with LEU 404 (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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350E ILE* 3.6 25.8 - - + -
352E LEU* 4.0 22.4 - - + -
360E ILE* 4.6 3.8 - - + -
364E PHE* 3.8 21.1 - - + -
402E LEU* 3.8 23.1 - - + -
403E HIS* 1.3 73.5 - - - +
405E GLN* 1.3 61.6 + - - +
406E LEU* 3.7 3.1 + - + +
431E LEU* 4.3 13.5 - - + -
515E MET* 3.3 3.1 - - - +
516E LEU* 2.7 48.7 + - + +
518E TYR* 3.5 37.5 - - + -
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Residues in contact with GLN 405 (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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296E VAL* 4.4 8.2 - - + -
297E GLN* 3.5 49.3 + - + +
300E CYS* 5.9 1.9 - - - +
349E ASP* 3.6 31.6 + - - +
350E ILE 3.0 23.4 + - - -
351E GLN* 3.6 6.6 - - - +
352E LEU 3.2 22.0 + - - -
403E HIS* 4.1 6.0 + - - +
404E LEU* 1.3 72.6 - - - +
406E LEU* 1.3 65.2 + - - +
407E MET* 3.4 4.3 + - - +
514E TYR 3.7 7.4 - - - +
515E MET* 3.8 32.4 - - + +
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Residues in contact with LEU 406 (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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352E LEU* 3.9 27.1 - - + -
354E ILE* 3.0 34.3 - - + -
360E ILE* 4.2 4.0 - - + -
404E LEU* 4.6 3.1 - - + +
405E GLN* 1.3 70.2 - - - +
407E MET* 1.3 54.1 + - - +
408E ARG* 2.7 25.1 + - + +
409E PHE* 4.7 1.7 + - - -
425E PHE* 3.8 22.7 - - + -
427E PHE* 5.1 2.5 - - + -
513E ALA* 3.9 24.9 - - + +
514E TYR* 3.1 25.5 + - - +
515E MET 4.5 1.6 - - - +
516E LEU* 4.1 27.1 - - + -
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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