Contacts of the strand formed by residues 254 - 259 (chain A) in PDB entry 4RM9
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 LYS 254 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A PHE* 3.1 5.8 - - - +
251A ASN* 3.0 46.0 + - - +
252A ASP 3.0 6.3 + - - +
253A LYS* 1.3 77.4 - - - +
255A PHE* 1.3 60.7 + - - +
256A VAL* 3.7 25.0 + - + +
268A VAL* 3.9 26.0 - - + -
269A PHE 3.7 2.2 - - - -
270A TYR* 4.2 20.9 - - + +
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Residues in contact with PHE 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ILE* 4.3 20.4 - - + -
249A SER 3.4 14.1 - - - -
250A PHE* 3.6 25.1 - + + -
253A LYS 4.8 1.3 - - - -
254A LYS* 1.3 72.6 - - - +
256A VAL* 1.3 65.8 + - - +
257A ILE* 4.2 0.9 - - + -
267A PHE 4.5 0.2 - - - -
268A VAL* 3.3 9.1 - - - +
269A PHE* 2.7 72.6 + + + +
271A ALA* 4.2 12.1 - - + -
277A ASN* 3.6 41.7 - - - -
280A ILE* 3.4 32.1 - - + -
281A LEU* 4.4 4.9 - - + -
284A CYS* 6.0 0.4 - - - -
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Residues in contact with VAL 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ASN* 3.7 5.7 - - - +
248A ILE* 3.9 0.3 - - - -
249A SER* 2.8 43.0 + - - +
250A PHE* 5.8 0.4 - - - -
254A LYS* 3.7 31.9 - - - +
255A PHE* 1.3 80.7 - - - +
257A ILE* 1.3 63.2 + - - +
258A LYS* 3.8 11.2 + - + +
266A ASP* 3.7 33.7 - - + +
267A PHE 3.6 2.9 - - - -
268A VAL* 4.2 9.2 - - + -
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Residues in contact with ILE 257 (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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225A LEU* 4.0 17.9 - - + -
240A PHE* 6.0 1.3 - - + -
244A GLU 5.7 0.4 - - - +
245A ILE* 3.7 37.5 - - + -
247A ASN 3.4 2.2 - - - -
248A ILE* 4.4 21.8 - - + -
255A PHE* 4.4 1.6 - - + -
256A VAL* 1.3 79.5 - - - +
258A LYS* 1.3 63.7 + - - +
259A PRO* 3.9 1.1 - - + +
266A ASP* 3.4 4.6 - - - -
267A PHE* 2.7 62.6 + - + +
269A PHE* 3.3 35.2 - - + -
284A CYS* 6.3 0.2 - - - -
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Residues in contact with LYS 258 (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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245A ILE* 3.7 4.3 - - - -
246A ARG* 2.7 42.5 + - + +
247A ASN* 2.9 42.7 + - + +
249A SER* 6.1 0.2 - - - +
256A VAL* 3.8 9.8 + - + +
257A ILE* 1.3 76.2 - - - +
259A PRO* 1.3 63.4 - - + +
266A ASP* 3.5 24.1 + - - +
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Residues in contact with PRO 259 (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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244A GLU 3.4 11.4 - - - +
246A ARG* 3.0 21.9 + - - +
257A ILE* 3.9 4.7 - - + +
258A LYS* 1.3 88.6 - - + +
260A ILE* 1.3 62.4 + - - +
261A ASP* 3.3 26.5 - - + +
262A LYS* 4.6 3.5 + - - -
264A ALA* 3.6 30.1 - - + +
265A PRO 3.9 8.3 - - - +
266A ASP* 3.3 17.0 - - - +
576A THR* 5.0 7.9 - - + +
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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