Contacts of the strand formed by residues 401 - 407 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B THR* 4.1 17.3 - - + +
323B LEU* 2.9 28.5 + - + +
324B PHE* 3.6 33.4 - - + +
348B TYR 5.3 0.3 - - - +
399B PRO* 3.5 12.1 - - - +
400B PRO* 1.3 78.1 - - - +
402B LEU* 1.3 60.5 + - - +
403B HIS* 3.8 14.1 + - - +
517B VAL* 3.8 16.4 - - + -
518B TYR 3.6 3.4 - - - +
519B ILE* 4.6 5.4 - - + +
527B VAL* 3.7 33.7 - - + -
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Residues in contact with LEU 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B TYR* 4.7 2.2 - - + -
349B ASP* 5.6 0.9 - - - -
350B ILE* 3.8 27.8 - - + -
398B LEU* 4.6 6.1 - - + -
399B PRO* 4.3 20.6 - - + -
400B PRO 3.9 0.8 + - - -
401B VAL* 1.3 70.6 - - - +
403B HIS* 1.3 68.3 + - - +
404B LEU* 3.8 23.6 - - + +
431B LEU* 5.0 0.4 - - + -
433B LEU* 3.6 31.6 - - + -
448B TYR* 4.0 26.0 - - + -
516B LEU 3.5 1.6 - - - +
517B VAL* 3.2 6.1 - - - -
518B TYR* 2.7 49.3 + - + +
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Residues in contact with HIS 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B THR* 4.8 6.0 - - + +
232B LEU* 4.7 8.4 - - + +
235B THR* 5.6 1.0 + - - -
300B CYS* 3.8 30.3 - - - -
301B ARG* 4.8 2.4 + - - +
304B LEU* 4.6 1.7 - - + +
324B PHE* 3.4 36.0 - + - -
348B TYR 4.0 9.1 + - - +
349B ASP* 3.2 19.4 - - + -
350B ILE 3.0 23.9 + - - -
399B PRO* 5.6 0.2 - - - +
401B VAL* 3.8 11.7 + - + +
402B LEU* 1.3 78.8 - - - +
404B LEU* 1.3 65.3 + - - +
515B MET* 3.9 19.8 - - + +
516B LEU 3.4 3.4 - - - +
517B VAL* 3.7 28.8 - - + +
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Residues in contact with LEU 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B ILE* 3.6 25.4 - - + -
352B LEU* 3.9 25.4 - - + -
360B ILE* 4.1 9.9 - - + -
364B PHE* 4.2 12.1 - - + -
402B LEU* 3.8 23.8 - - + +
403B HIS* 1.3 79.0 - - - +
405B GLN* 1.3 60.9 + - - +
406B LEU* 3.9 1.9 + - + +
431B LEU* 4.4 10.5 - - + -
514B TYR 3.8 0.7 - - - +
515B MET* 3.1 9.5 - - - +
516B LEU* 2.7 49.2 + - + +
518B TYR* 3.9 31.2 - - + -
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Residues in contact with GLN 405 (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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297B GLN* 3.1 28.4 + - + -
349B ASP* 4.3 3.6 + - - +
350B ILE 2.7 13.2 + - - +
351B GLN* 2.9 33.5 + - - +
352B LEU* 2.8 27.0 + - - -
403B HIS 4.1 0.6 + - - -
404B LEU* 1.3 71.8 - - - +
406B LEU* 1.3 65.3 + - - +
407B MET* 3.5 2.5 + - - +
409B PHE* 4.1 4.9 - - - -
514B TYR* 3.0 39.3 + - + +
515B MET* 4.7 3.8 - - + +
342C ARG* 3.4 19.6 - - - +
370C VAL* 3.7 17.7 - - - +
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Residues in contact with LEU 406 (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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352B LEU* 3.7 24.7 - - + -
354B ILE* 3.6 13.5 - - + -
404B LEU 4.7 2.2 - - - +
405B GLN* 1.3 70.8 - - - +
407B MET* 1.3 52.2 + - - +
408B ARG* 2.6 27.3 + - + +
425B PHE* 3.6 36.1 - - + -
427B PHE* 5.3 0.9 - - + -
513B ALA* 3.3 37.9 - - + +
514B TYR* 2.8 42.0 + - - +
516B LEU* 4.2 23.6 - - + -
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Residues in contact with MET 407 (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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351B GLN* 3.9 17.5 - - + -
352B LEU 2.9 34.3 + - - +
353B SER* 4.1 12.1 - - - +
354B ILE* 3.5 14.8 + - - +
405B GLN* 3.5 4.0 + - - +
406B LEU* 1.3 66.6 - - - +
408B ARG* 1.3 56.5 + - - +
409B PHE* 2.9 46.4 + - + +
421B ILE* 3.9 5.5 - - - +
307C THR 4.5 3.1 - - - +
308C LEU* 3.9 29.8 - - + +
369C LEU 3.4 24.9 - - - +
370C VAL* 3.9 15.9 - - + -
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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