Contacts of the helix formed by residues 301 - 309 (chain B) in PDB entry 1BK6
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 301 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B VAL* 3.5 19.5 - - + +
296B ILE* 4.1 19.7 - - + +
299B ARG* 4.5 2.0 - - - -
300B ILE* 1.3 95.8 - - + +
302B LYS* 1.3 63.2 + - - +
304B LEU* 3.4 11.8 + - + +
305B VAL* 3.0 31.2 + - + +
323B VAL* 5.4 1.1 - - + +
326B ILE* 4.4 13.7 - - + -
336B VAL* 4.3 18.6 - - + -
337B VAL* 4.6 14.8 - - + -
340B ALA* 4.5 4.9 - - + -
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Residues in contact with LYS 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B ARG 4.6 7.3 + - - +
300B ILE 2.9 3.0 + - - -
301B PRO* 1.3 78.0 - - - +
303B ARG* 1.3 62.7 + - - +
305B VAL* 3.4 5.1 + - - +
306B GLU* 3.3 37.2 + - - +
339B ASN 5.4 0.4 + - - -
340B ALA* 3.2 44.0 + - + +
341B GLY* 5.1 1.2 - - - -
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Residues in contact with ARG 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B ILE* 3.0 49.3 + - + +
267B TYR* 3.5 54.8 + - + +
268B SER 5.7 0.8 + - - -
274B LEU* 6.1 0.8 - - - +
299B ARG 4.9 3.0 + - - +
300B ILE* 2.8 10.4 + - - +
302B LYS* 1.3 74.0 - - - +
304B LEU* 1.3 60.5 + - - +
305B VAL 2.9 1.3 - - - -
306B GLU* 2.7 70.0 + - - +
307B LEU* 3.0 30.9 + - + +
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Residues in contact with LEU 304 (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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266B ILE* 4.3 15.3 - - + -
278B CYS* 5.1 7.4 - - + -
281B ILE* 4.3 17.0 - - + -
285B SER* 6.0 0.2 - - - +
295B VAL* 5.2 0.2 - - + -
300B ILE* 3.0 33.4 + - + +
301B PRO* 3.5 10.5 - - + +
303B ARG* 1.3 80.2 - - - +
305B VAL* 1.3 61.1 + - - +
307B LEU* 3.3 22.7 + - + +
308B LEU* 3.5 11.6 + - - +
319B ALA* 4.2 18.3 - - - +
322B ALA* 3.8 27.1 - - + -
323B VAL* 4.3 16.8 - - + +
326B ILE* 4.5 15.0 - - + -
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Residues in contact with VAL 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B PRO 3.0 20.2 + - - +
302B LYS* 3.5 9.9 - - - +
303B ARG 2.9 1.0 - - - -
304B LEU* 1.3 73.8 - - - +
306B GLU* 1.3 67.8 + - - +
307B LEU 3.0 1.6 - - - -
308B LEU* 2.9 24.2 + - + +
309B SER* 4.2 1.6 + - - -
323B VAL* 4.8 7.2 - - + -
337B VAL* 4.8 4.7 - - + -
340B ALA* 3.4 34.5 - - + +
341B GLY 3.8 15.9 - - - +
342B VAL* 4.0 24.9 - - + -
345B ALA* 4.2 10.8 - - + +
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Residues in contact with GLU 306 (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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267B TYR* 4.7 4.2 + - - -
302B LYS* 3.3 35.1 - - - +
303B ARG* 2.7 56.8 + - - +
305B VAL* 1.3 74.4 - - + +
307B LEU* 1.3 59.1 + - - +
309B SER* 2.9 27.0 + - - -
310B HIS* 5.2 0.2 - - - -
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Residues in contact with LEU 307 (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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266B ILE* 3.9 26.9 - - + +
274B LEU* 4.2 9.9 - - + -
278B CYS* 3.9 26.5 - - - -
303B ARG* 3.0 42.5 + - + +
304B LEU* 3.5 16.2 - - + +
305B VAL 3.0 0.4 - - - -
306B GLU* 1.3 73.6 - - - +
308B LEU* 1.3 62.5 + - - +
309B SER 3.1 3.2 + - - -
310B HIS* 3.3 30.8 + - + +
315B VAL* 3.9 22.3 - - + +
316B GLN* 4.4 2.8 - - - +
319B ALA* 4.3 9.2 - - + +
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Residues in contact with LEU 308 (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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304B LEU 3.5 6.9 + - - +
305B VAL* 2.9 17.6 + - - +
307B LEU* 1.3 78.4 - - - +
309B SER* 1.3 57.0 + - - +
310B HIS 3.3 0.2 - - - -
316B GLN* 3.3 30.2 - - + +
319B ALA* 4.0 10.1 - - + +
320B LEU* 3.8 44.9 - - + +
323B VAL* 4.3 7.6 - - + -
342B VAL* 4.1 21.1 - - + +
345B ALA* 3.7 30.5 - - + +
346B LEU* 5.0 1.1 - - + -
349B LEU* 4.1 29.4 - - + +
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Residues in contact with SER 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B VAL 4.2 1.5 + - - -
306B GLU* 2.9 19.5 + - - -
307B LEU 3.1 0.2 - - - -
308B LEU* 1.3 77.9 - - - +
310B HIS* 1.3 63.1 + - - +
311B GLU* 5.5 0.5 - - - +
316B GLN* 4.4 1.1 - - - -
345B ALA* 6.2 3.6 - - - -
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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