Contacts of the strand formed by residues 258 - 262 (chain B) in PDB entry 4LDD
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 ILE 258 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72B ALA* 3.6 22.0 - - + -
74B ILE* 4.3 10.5 - - + -
184B GLN* 3.6 35.4 - - + -
186B LEU* 4.6 7.0 - - + -
251B PRO* 4.0 0.5 - - - +
252B ILE* 2.7 46.6 + - + +
253B ASP* 2.9 28.8 + - + +
256B LYS* 3.4 17.0 - - + +
257B ASN* 1.3 74.5 - - - +
259B MET* 1.3 63.7 + - - +
286B PRO* 4.5 9.0 - - + -
287B VAL 4.0 14.8 - - - +
289B LEU 6.0 0.4 - - - +
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Residues in contact with MET 259 (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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249B ILE* 4.6 20.6 - - + -
250B VAL 3.4 9.4 - - - +
251B PRO* 3.8 29.4 - - + -
252B ILE* 4.1 4.5 - - - +
254B PRO* 5.9 7.4 - - + -
257B ASN* 4.0 8.0 + - - +
258B ILE* 1.3 82.3 - - - +
260B GLY* 1.3 59.8 + - - +
261B ILE* 6.0 0.7 - - + -
286B PRO* 3.5 3.6 - - - +
287B VAL* 3.1 40.7 + - + +
289B LEU* 3.7 22.9 - - + -
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Residues in contact with GLY 260 (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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248B LYS 3.4 1.2 - - - +
249B ILE* 3.5 1.9 - - - -
250B VAL* 2.6 46.7 + - - +
252B ILE* 4.3 0.9 - - - +
259B MET* 1.3 78.0 - - - +
261B ILE* 1.3 68.1 + - - +
284B ILE* 3.8 19.1 - - - -
285B ILE 3.7 9.0 - - - -
286B PRO* 4.0 2.7 - - - -
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Residues in contact with ILE 261 (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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207B ILE* 6.1 2.5 - - + -
209B PHE* 4.2 28.5 - - + -
216B ILE* 6.1 3.8 - - + -
247B PHE* 4.0 27.4 - - + -
248B LYS 3.2 3.8 - - - +
249B ILE* 3.7 31.4 - - + -
259B MET* 6.0 0.4 - - + -
260B GLY* 1.3 80.5 - - - +
262B GLU* 1.3 71.4 + - - +
263B VAL* 3.8 8.9 + - + +
284B ILE* 3.5 3.9 - - - +
285B ILE* 2.9 43.3 + - + +
287B VAL* 4.9 8.1 - - + -
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Residues in contact with GLU 262 (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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246B ASP 4.2 1.3 - - - +
247B PHE* 3.2 9.7 - - - -
248B LYS* 2.8 53.5 + - + +
250B VAL* 3.3 38.4 - - + +
261B ILE* 1.3 75.0 - - - +
263B VAL* 1.3 62.2 + - - +
282B GLN* 2.5 47.8 + - - +
283B PRO 3.7 6.1 - - - +
284B ILE* 4.2 12.1 - - + +
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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