Contacts of the helix formed by residues 537 - 551 (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 PRO 537 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243B TYR 3.3 28.9 - - - +
244B MET* 3.8 22.4 - - + -
535B ASP 3.4 9.4 - - - +
536B ILE* 1.3 89.0 - - + +
538B GLN* 1.3 67.3 + - - +
539B GLN* 4.2 21.1 - - + +
540B LEU* 3.0 17.3 + - + +
541B VAL* 3.2 10.2 + - - +
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Residues in contact with GLN 538 (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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536B ILE 3.3 4.8 + - - -
537B PRO* 1.3 70.8 - - - +
539B GLN* 1.3 63.1 + - - +
541B VAL* 3.1 10.8 + - + +
542B GLU* 2.9 51.0 + - + +
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Residues in contact with GLN 539 (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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245B MET 5.3 2.9 - - - +
246B PRO* 5.8 0.7 - - - +
247B THR* 4.2 11.5 + - - -
248B GLU* 3.9 55.9 + - + +
537B PRO* 4.2 11.8 - - + +
538B GLN* 1.3 79.8 + - - +
540B LEU* 1.3 74.1 + - - +
542B GLU* 3.6 9.8 + - - +
543B ARG* 3.1 34.1 + - - +
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Residues in contact with LEU 540 (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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243B TYR* 3.9 23.1 - - + +
247B THR* 4.8 0.7 - - - +
258B LEU* 4.5 7.4 - - + -
261B GLN* 3.9 44.4 - - + +
536B ILE* 3.9 20.2 - - + -
537B PRO* 3.0 12.9 + - + +
539B GLN* 1.3 95.3 + - - +
541B VAL* 1.3 66.8 + - - +
543B ARG* 3.0 4.7 + - + +
544B LEU* 2.9 52.3 + - + +
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Residues in contact with VAL 541 (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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265B TYR* 3.8 29.1 + - + +
533B ASP* 5.2 6.1 - - + +
536B ILE* 3.8 26.5 - - + +
537B PRO 3.4 14.8 - - - +
538B GLN* 3.1 10.1 + - + +
540B LEU* 1.3 76.5 - - - +
542B GLU* 1.3 58.6 + - + +
544B LEU* 3.5 4.1 + - - +
545B GLN* 3.0 55.7 + - - +
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Residues in contact with GLU 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538B GLN* 2.9 46.2 + - + +
539B GLN* 3.8 8.9 - - - +
541B VAL* 1.3 76.5 - - + +
543B ARG* 1.3 65.9 + - - +
545B GLN* 3.4 15.2 + - - +
546B GLU* 2.9 23.9 + - - +
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Residues in contact with ARG 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A GLU* 4.3 8.9 + - - -
247B THR 2.7 30.9 + - - -
248B GLU* 3.7 10.2 + - - +
250B ASP 2.7 26.8 + - - -
252B SER* 3.5 24.7 - - - +
258B LEU* 3.7 31.7 - - + +
539B GLN* 3.1 24.2 + - - +
540B LEU* 3.0 11.2 + - + +
542B GLU* 1.3 74.6 - - - +
544B LEU* 1.3 64.9 + - + +
546B GLU* 3.1 16.5 + - + +
547B GLU* 3.1 24.4 + - + +
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Residues in contact with LEU 544 (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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258B LEU* 5.2 6.7 - - + -
261B GLN 4.7 0.2 - - - +
262B ARG* 3.7 32.5 - - + +
265B TYR* 3.3 54.5 - - + -
266B GLU* 6.0 0.4 - - - +
540B LEU* 2.9 40.4 + - + +
541B VAL* 3.8 3.8 - - - +
543B ARG* 1.3 77.6 - - + +
545B GLN* 1.3 62.1 + - + +
546B GLU 3.2 0.5 + - - -
547B GLU* 3.3 24.7 - - - +
548B LYS* 3.3 27.2 + - + +
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Residues in contact with GLN 545 (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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265B TYR* 4.5 8.9 + - + +
541B VAL* 3.0 40.9 + - + +
542B GLU* 3.8 16.2 - - - +
544B LEU* 1.3 76.3 - - + +
546B GLU* 1.3 58.0 + - - +
548B LYS* 3.5 11.7 - - + +
549B ARG* 3.1 32.3 + - + +
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Residues in contact with GLU 546 (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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542B GLU 2.9 13.2 + - - +
543B ARG* 3.2 14.4 - - + +
544B LEU 3.1 0.2 - - - -
545B GLN* 1.3 73.6 - - - +
547B GLU* 1.3 61.2 + - + +
548B LYS 2.9 3.8 - - - -
549B ARG* 2.8 30.1 + - - +
550B ILE* 2.8 42.4 + - + +
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Residues in contact with GLU 547 (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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252B SER* 4.2 5.7 + - - -
258B LEU* 4.7 2.9 - - - +
262B ARG* 3.4 28.3 + - - -
278B LYS* 3.3 29.5 + - - -
543B ARG* 3.1 16.1 + - + +
544B LEU* 3.3 32.3 - - - +
546B GLU* 1.3 82.2 - - + +
548B LYS* 1.3 61.5 + - + +
550B ILE* 4.0 9.9 - - - -
551B GLU* 3.3 37.9 + - - +
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Residues in contact with LYS 548 (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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265B TYR* 5.3 7.1 - - - -
266B GLU* 3.4 35.7 + - - -
270B SER* 6.2 0.6 - - - -
544B LEU* 3.3 18.3 + - - +
545B GLN* 3.5 15.5 - - + +
546B GLU 2.8 1.4 + - - -
547B GLU* 1.3 78.2 - - + +
549B ARG* 1.3 66.1 + - - +
551B GLU* 3.3 10.7 + - - +
552B ALA* 3.5 13.9 + - - +
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Residues in contact with ARG 549 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545B GLN* 3.1 15.2 + - - +
546B GLU* 2.8 21.0 + - - +
548B LYS* 1.3 77.1 - - + +
550B ILE* 1.3 64.2 + - - +
551B GLU 3.1 1.0 + - - -
552B ALA* 3.3 13.1 + - - +
553B GLN* 3.8 13.8 - - - +
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Residues in contact with ILE 550 (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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546B GLU* 2.8 61.7 + - + +
547B GLU* 4.0 9.0 - - - +
549B ARG* 1.3 74.8 - - - +
551B GLU* 1.3 62.4 + - + +
552B ALA 3.8 0.2 + - - -
553B GLN* 3.1 24.4 - - - +
554B LYS* 3.3 25.8 + - - +
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Residues in contact with GLU 551 (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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278B LYS* 4.0 24.2 + - - -
547B GLU* 3.3 26.5 + - - +
548B LYS* 3.3 3.9 + - - +
549B ARG 3.1 1.6 + - - -
550B ILE* 1.3 82.6 - - + +
552B ALA* 1.3 60.5 + - - +
553B GLN 3.3 1.6 - - - -
554B LYS* 3.9 34.3 - - + +
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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