Contacts of the strand formed by residues 287 - 291 (chain A) in PDB entry 5AM1
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 ARG 287 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254A GLU* 2.8 36.9 + - + +
255A LEU 3.8 2.7 - - - -
256A GLY 3.7 19.3 - - - +
257A SER* 3.7 2.5 + - - +
258A GLY 3.4 23.8 - - - +
259A PRO 2.9 9.7 + - - +
260A ALA* 3.3 11.1 - - - +
261A VAL 2.8 30.5 + - - +
286A TYR* 1.3 70.5 - - - +
288A VAL* 1.3 57.4 + - - +
289A LEU* 3.8 9.7 + - + +
324A LEU* 3.7 25.7 + - - +
326A LEU* 3.6 26.5 - - - +
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Residues in contact with VAL 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A VAL 3.5 0.3 - - - +
254A GLU* 3.2 11.1 - - - +
255A LEU 2.8 39.8 + - - +
261A VAL* 3.6 5.8 - - + +
263A LEU* 3.6 33.0 - - + -
278A ILE* 3.9 29.6 - - + +
281A LEU* 3.6 32.3 - - + -
282A ALA 3.7 11.9 - - - +
286A TYR* 4.1 4.3 - - + +
287A ARG* 1.3 74.6 - - - +
289A LEU* 1.3 62.6 + - - +
290A ALA 4.3 4.5 - - - +
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Residues in contact with LEU 289 (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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252A PHE* 3.4 28.0 - - + -
253A VAL 3.4 5.4 - - - -
254A GLU* 3.4 27.1 - - - +
260A ALA* 3.8 28.9 - - + -
261A VAL 2.9 14.9 + - - +
262A CYS* 3.4 14.6 - - + +
263A LEU 2.9 25.0 + - - +
287A ARG* 4.3 11.0 - - - +
288A VAL* 1.3 75.1 - - - +
290A ALA* 1.3 60.2 + - - +
291A MET* 3.6 3.1 + - - -
320A PHE* 4.7 9.9 - - + -
321A LEU* 5.8 0.4 - - + -
324A LEU* 4.1 13.9 - - + -
326A LEU* 3.9 14.1 - - + -
329A ALA* 5.2 1.3 - - + -
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Residues in contact with ALA 290 (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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252A PHE* 3.2 3.0 - - - -
253A VAL* 2.8 42.6 + - + +
263A LEU* 4.1 17.0 - - + -
271A TRP* 3.4 19.8 - - + +
274A TRP* 4.7 1.1 - - + -
278A ILE* 3.7 35.2 - - + -
288A VAL* 3.9 1.0 - - + -
289A LEU* 1.3 70.2 - - - +
291A MET* 1.3 62.4 + - - +
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Residues in contact with MET 291 (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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250A LEU* 4.0 18.6 - - + -
251A HIS 3.7 9.2 - - - +
252A PHE* 3.8 7.2 - - - -
262A CYS* 3.7 21.1 - - - -
263A LEU 3.2 21.7 + - - +
265A HIS* 3.2 12.0 + - - -
271A TRP* 3.2 21.2 - - - -
274A TRP* 5.2 0.5 - - - -
289A LEU 4.4 3.6 - - - +
290A ALA* 1.3 73.0 - - - +
292A ASP* 1.3 62.9 + - - +
293A MET* 3.6 22.7 - - - -
317A MET* 4.0 19.7 - - + -
320A PHE* 3.5 48.0 - - + -
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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