Contacts of the strand formed by residues 261 - 265 (chain B) in PDB entry 4LXZ
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 261 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B LEU* 4.4 18.4 - - + -
172B HIS* 3.7 32.3 - - + +
174B ARG 3.8 1.6 + - - -
175B VAL* 3.7 6.9 - - + -
176B LEU 3.0 23.5 + - - -
259B PRO* 3.6 4.4 - - - +
260B SER* 1.4 79.0 + - - +
262B VAL* 1.3 66.9 + - - +
298B LEU* 4.7 0.8 - - - +
299B PRO* 3.5 16.2 - - + +
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Residues in contact with VAL 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B LEU* 5.4 0.2 - - - +
168B LEU* 5.0 1.6 - - - +
176B LEU* 3.2 16.6 - - + +
178B ILE* 3.8 20.0 - - + -
254B MET* 3.9 13.7 - - + -
261B ALA* 1.3 80.5 - - - +
263B VAL* 1.3 72.5 + - - +
264B LEU* 4.9 0.4 - - + -
293B VAL* 3.8 24.5 - - + +
298B LEU* 3.7 31.4 - - + +
299B PRO 2.9 9.3 + - - +
300B LEU* 3.4 15.9 - - + +
301B LEU* 2.9 24.8 + - - +
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Residues in contact with VAL 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B ILE* 4.1 7.0 - - + +
165B ILE* 3.8 17.9 - - + -
168B LEU* 3.5 31.4 - - + -
175B VAL* 4.4 3.1 - - + -
176B LEU 2.8 8.8 + - - +
177B TYR* 3.4 22.5 - - + -
178B ILE 2.9 26.5 + - - +
262B VAL* 1.3 77.2 - - - +
264B LEU* 1.3 62.2 + - - +
301B LEU* 3.4 18.2 - - + +
303B LEU* 3.6 30.5 - - + -
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Residues in contact with LEU 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B ILE* 3.4 35.7 - - + +
180B ILE* 4.4 12.3 - - + -
246B PHE* 4.9 1.8 - - + -
262B VAL* 4.2 3.6 - - + -
263B VAL* 1.3 74.3 - - - +
265B GLN* 1.3 67.3 + - - +
266B CYS* 3.6 13.1 + - - -
289B CYS* 4.5 1.8 - - + +
290B VAL* 3.7 42.2 - - + +
293B VAL* 4.3 19.7 - - + -
300B LEU* 3.9 15.5 - - + +
301B LEU 2.8 10.2 + - - +
302B MET* 3.5 9.3 - - + -
303B LEU 2.9 25.4 + - - -
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Residues in contact with GLN 265 (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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143B GLY* 2.9 32.9 + - - +
145B HIS* 3.5 14.9 + - - -
161B ILE* 3.8 2.5 - - + -
177B TYR* 3.3 30.6 - - + +
178B ILE 2.8 13.2 + - - +
179B ASP* 3.6 5.6 - - - +
180B ILE* 3.1 24.6 + - - +
181B ASP* 3.2 34.2 + - - +
263B VAL 4.1 0.8 - - - -
264B LEU* 1.3 73.1 - - - +
266B CYS* 1.3 55.5 + - - +
267B GLY 2.8 21.9 + - - -
303B LEU* 3.8 6.3 - - + -
304B GLY 3.2 16.6 - - - +
305B GLY* 3.4 6.9 - - - -
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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
------------------------------------------------------------
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