Contacts of the strand formed by residues 242 - 245 (chain B) in PDB entry 4LDQ
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 ALA 242 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B LEU* 3.9 39.0 - - + -
155B VAL* 4.4 4.7 - - + -
162B VAL* 5.6 0.7 - - + -
163B THR 3.2 5.5 + - - +
164B VAL* 3.3 9.4 - - + +
165B LEU 3.0 23.4 + - - -
240B VAL* 3.6 5.5 - - - +
241B SER* 1.3 82.8 - - - +
243B VAL* 1.3 63.8 + - - +
274B ILE* 3.9 3.3 - - - +
275B PRO* 3.8 13.2 - - + +
277B TYR* 4.9 0.7 - - + -
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Residues in contact with VAL 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B LEU* 3.4 17.3 - - + +
235B MET* 3.5 30.3 - - + -
240B VAL* 4.5 1.6 - - + -
242B ALA* 1.3 79.6 - - - +
244B VAL* 1.3 59.2 + - - +
245B VAL* 4.3 3.8 - - + -
265B LEU* 4.0 21.8 - - + -
269B ALA* 4.1 6.5 - - + -
274B ILE* 3.5 13.5 - - + -
275B PRO 3.1 8.9 + - - +
276B PHE* 3.6 31.6 - - + -
277B TYR* 2.7 35.3 + - - +
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Residues in contact with VAL 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B LEU* 3.7 25.4 - - + -
164B VAL* 3.6 23.3 - - + -
165B LEU 3.2 6.3 + - - -
166B THR* 2.8 34.4 + - - -
181B ALA* 3.7 30.4 - - + +
184B VAL* 4.2 11.4 - - + -
185B ILE* 5.6 0.4 - - + -
243B VAL* 1.3 78.0 - - - +
245B VAL* 1.3 59.5 + - - +
277B TYR* 3.4 17.9 - - + -
279B ALA* 4.0 13.5 - - + -
338B ILE* 4.3 5.8 - - + -
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Residues in contact with VAL 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B THR* 4.4 2.5 - - - -
167B HIS* 3.9 27.1 - - + +
181B ALA* 3.6 12.4 - - - +
243B VAL* 4.3 2.0 - - + -
244B VAL* 1.3 79.1 - - - +
246B GLY* 1.3 62.4 + - - +
256B THR* 6.0 0.2 - - + -
258B ASN* 4.1 3.6 - - - +
262B THR* 3.8 19.1 - - + -
265B LEU* 3.9 16.4 - - + -
276B PHE* 3.5 26.2 - - + -
277B TYR 2.9 20.2 + - - +
278B VAL* 3.8 8.7 - - + -
279B ALA* 2.7 31.0 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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