Contacts of the strand formed by residues 299 - 304 (chain A) in PDB entry 2B9E
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 299 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A HIS* 3.4 12.3 - - + +
231A ILE* 3.9 28.5 - - + +
255A PHE* 3.9 28.0 - - + -
296A TYR* 3.1 32.3 + - - +
297A HIS 3.4 0.6 - - - -
298A GLU* 1.3 74.8 - - - +
300A HIS* 1.3 59.4 + - - +
301A TYR 3.5 25.1 - - - +
302A ILE* 4.0 10.5 - - + -
348A PHE* 5.2 7.0 - - + +
350A SER* 3.4 23.2 + - - -
351A LEU* 3.7 3.7 + - + -
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Residues in contact with HIS 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A SER* 5.5 5.3 - - - -
229A HIS 3.1 6.2 + - - +
298A GLU* 3.2 21.9 + - + +
299A VAL* 1.3 74.6 - - - +
301A TYR* 1.3 82.1 + - + +
350A SER* 3.2 31.1 - - - -
351A LEU* 4.1 3.6 - - - -
352A GLN* 2.8 56.6 + - - +
353A ARG 3.2 9.2 + - - +
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Residues in contact with TYR 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A LEU* 3.8 45.8 - - + -
223A ASP 4.5 0.7 + - - -
224A PRO* 3.9 14.1 - - + -
225A PRO* 3.3 35.3 - - + +
228A SER* 3.9 15.0 - - - -
229A HIS 3.6 3.1 + - - -
230A VAL* 3.2 15.1 - - + -
231A ILE 2.9 22.7 + - - -
299A VAL* 3.5 2.3 - - - +
300A HIS* 1.3 102.1 - + + +
302A ILE* 1.3 66.1 + - - +
352A GLN* 4.0 14.2 + - + -
353A ARG* 3.3 30.5 + - + -
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Residues in contact with ILE 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A LEU* 3.7 7.5 - - - +
231A ILE* 3.3 31.4 - - + +
233A ALA* 4.7 3.4 - - + -
286A PHE* 5.1 0.9 - - + -
299A VAL* 4.0 4.7 - - + -
301A TYR* 1.3 80.8 - - - +
303A LEU* 1.3 72.6 + - - +
304A LEU* 4.3 3.8 - - + +
345A ALA* 3.6 37.0 - - + +
348A PHE* 4.0 21.5 - - + -
351A LEU* 3.7 16.6 - - + +
353A ARG 3.1 7.3 + - - -
354A LEU* 3.2 23.0 - - + +
355A VAL 2.9 25.6 + - - -
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Residues in contact with LEU 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A PRO* 4.1 12.3 - - + +
219A ALA* 3.9 25.4 - - - +
222A LEU* 4.0 10.0 - - + +
231A ILE 2.9 12.4 + - - +
232A ASP* 3.6 19.6 - - - +
233A ALA* 3.0 28.1 + - - +
240A LYS* 3.9 25.1 - - + -
244A LEU* 3.8 33.0 - - + -
302A ILE* 1.3 73.6 - - - +
304A LEU* 1.3 59.5 + - - +
305A ASP* 3.9 23.3 - - + -
355A VAL* 3.7 6.5 - - + +
357A SER* 5.2 0.4 - - - +
1201A SAM 4.8 0.7 - - - +
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Residues in contact with LEU 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A ALA* 3.8 22.9 - - + -
234A CYS* 3.8 17.0 - - - -
286A PHE* 4.8 1.1 - - + -
302A ILE* 4.0 8.3 - - + -
303A LEU* 1.3 73.0 - - - +
305A ASP* 1.3 62.2 + - - +
306A PRO* 3.4 13.1 - - + +
341A ALA* 3.7 19.1 - - + +
342A LEU* 3.5 42.2 - - + +
345A ALA* 4.6 4.7 - - + -
354A LEU* 4.7 4.0 - - + -
355A VAL 2.8 14.1 + - - +
356A TYR* 3.3 20.8 - - + -
357A SER* 2.9 25.2 + - - -
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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