Contacts of the strand formed by residues 298 - 304 (chain B) in PDB entry 1B70
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 LEU 298 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206B ASP* 4.6 5.8 - - + +
209B GLY* 3.7 33.9 - - - +
210B ALA* 4.0 1.3 - - + +
274B VAL* 3.8 19.5 - - + -
275B ARG* 2.9 33.9 - - - +
276B ARG* 3.9 25.0 - - - +
296B GLU 3.2 4.8 + - - -
297B ASP* 1.3 71.2 - - - +
299B VAL* 1.3 74.2 + - - +
313B LEU* 3.1 26.0 - - - +
314B ALA* 3.4 13.3 - - + +
338B PHE* 4.1 13.9 - - + -
342B SER* 4.6 5.6 - - - +
343B ILE* 6.3 1.8 - - + -
346B THR* 4.2 5.3 + - - +
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Residues in contact with VAL 299 (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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273B ALA 3.6 0.7 - - - +
274B VAL* 3.4 5.2 - - - +
275B ARG* 2.8 80.7 + - + +
277B ALA* 4.1 14.1 - - + +
281B GLU* 5.4 0.2 - - - +
283B LEU* 5.1 2.5 - - + -
293B LEU* 5.4 5.6 - - + -
297B ASP* 4.4 2.5 - - + +
298B LEU* 1.3 78.5 - - - +
300B ILE* 1.3 74.8 + - - +
301B ALA* 4.7 2.7 - - + -
310B PRO* 3.9 23.1 - - + -
312B GLY 2.9 26.5 - - - +
313B LEU* 4.6 4.0 - - + -
314B ALA* 3.9 2.5 - - - +
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Residues in contact with ILE 300 (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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213B PHE* 4.3 20.0 - - + -
263B PHE* 3.7 30.1 - - + -
272B ILE* 4.1 21.3 - - + -
273B ALA 3.7 3.1 - - - -
274B VAL* 4.4 7.2 - - + -
299B VAL* 1.3 78.3 - - - +
301B ALA* 1.3 53.5 + - - +
311B LEU* 2.7 35.1 + - + +
312B GLY 3.0 13.1 + - - +
314B ALA* 3.2 40.8 - - + -
334B GLU* 4.4 11.9 - - + +
338B PHE* 4.0 17.7 - - + -
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Residues in contact with ALA 301 (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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272B ILE* 3.3 10.2 - - - +
273B ALA* 2.8 37.4 + - + +
275B ARG* 3.7 27.6 - - - +
299B VAL* 4.7 3.8 - - + -
300B ILE* 1.3 75.4 - - - +
302B GLY* 1.3 60.5 + - - +
308B SER* 4.3 0.9 - - - +
309B PHE 2.9 26.7 - - - +
310B PRO* 3.8 3.6 - - + -
311B LEU* 3.6 6.3 - - - +
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Residues in contact with GLY 302 (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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268B VAL 3.7 7.9 - - - -
271B GLY 3.0 15.0 - - - -
273B ALA* 5.4 0.2 - - - -
301B ALA* 1.3 75.4 - - - +
303B TRP* 1.3 68.0 + - - +
308B SER* 3.2 7.2 + - - -
309B PHE* 2.9 35.9 + - - -
311B LEU* 3.5 11.3 - - - +
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Residues in contact with TRP 303 (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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201B ALA* 4.1 19.7 - - + -
203B LYS* 4.3 18.4 - - + -
268B VAL 3.5 3.4 + - - -
269B GLY 3.7 0.2 - - - -
270B GLU* 2.7 68.3 + - + +
271B GLY* 3.4 46.9 + - - -
272B ILE 3.4 17.0 - - - -
273B ALA* 4.0 18.2 - - + -
302B GLY* 1.3 72.6 - - - +
304B ARG* 1.3 54.6 + - - +
305B GLY 3.7 13.2 + - - -
307B GLU 2.7 20.6 - - - +
308B SER* 4.1 7.2 - - - +
309B PHE* 3.5 5.6 - - - -
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Residues in contact with ARG 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 ARG 3.8 21.0 + - - -
267B PHE* 4.0 19.8 + - - +
269B GLY* 4.0 16.2 - - - +
270B GLU* 4.0 6.1 - - + -
303B TRP* 1.3 73.6 - - - +
305B GLY* 1.3 61.0 + - - +
306B GLU 3.0 1.4 + - - -
307B GLU* 2.9 34.3 + - + +
309B PHE* 3.6 24.9 - - + -
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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