Contacts of the strand formed by residues 261 - 265 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A LEU* 4.3 20.2 - - + -
172A HIS* 3.8 30.5 - - + +
174A ARG 3.7 2.4 + - - -
175A VAL* 3.5 7.9 - - + -
176A LEU 3.0 23.4 + - - -
259A PRO* 3.6 3.2 - - - +
260A SER* 1.3 80.6 + - - +
262A VAL* 1.3 67.7 - - - +
299A PRO* 3.5 14.4 - - + +
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Residues in contact with VAL 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LEU* 5.4 0.2 - - - +
168A LEU* 4.9 1.7 - - - +
176A LEU* 3.3 17.0 - - + +
178A ILE* 3.9 19.1 - - + -
254A MET* 3.9 15.0 - - + -
259A PRO* 4.7 0.2 - - + -
261A ALA* 1.3 81.3 - - - +
263A VAL* 1.3 71.8 + - - +
264A LEU* 5.0 0.4 - - + -
293A VAL* 3.8 24.7 - - + -
298A LEU* 3.8 31.4 - - + +
299A PRO 2.9 8.6 + - - +
300A LEU* 3.3 14.7 - - + -
301A LEU* 2.9 24.5 + - - +
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Residues in contact with VAL 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ILE* 3.9 7.0 - - + +
164A ALA* 5.5 0.2 - - + -
165A ILE* 3.8 17.9 - - + +
168A LEU* 3.5 31.4 - - + -
175A VAL* 4.4 3.1 - - + -
176A LEU 2.9 9.2 + - - +
177A TYR* 3.5 23.2 - - + -
178A ILE 3.0 26.3 + - - +
262A VAL* 1.3 75.4 - - - +
264A LEU* 1.3 62.9 + - - +
301A LEU* 3.3 19.7 - - + +
303A LEU* 3.7 29.8 - - + -
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Residues in contact with LEU 264 (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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178A ILE* 3.6 36.1 - - + +
180A ILE* 4.5 12.1 - - + -
246A PHE* 5.0 1.8 - - + -
262A VAL* 5.0 3.4 - - + -
263A VAL* 1.3 75.7 - - - +
265A GLN* 1.3 66.4 + - - +
266A CYS* 3.6 11.3 + - - -
289A CYS* 4.5 1.6 - - + -
290A VAL* 3.9 41.5 - - + +
293A VAL* 4.2 20.4 - - + -
300A LEU* 3.9 15.4 - - + +
301A LEU 2.7 10.3 + - - +
302A MET* 3.5 10.1 - - + -
303A LEU* 2.8 27.6 + - - +
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Residues in contact with GLN 265 (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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143A GLY* 2.9 34.0 + - - +
145A HIS* 3.5 14.3 + - - -
161A ILE* 3.8 2.2 - - + -
177A TYR* 3.4 29.8 - - + +
178A ILE 2.8 14.0 + - - +
179A ASP* 3.6 6.2 - - - +
180A ILE* 3.0 31.4 + - - +
181A ASP* 3.2 33.8 + - - +
263A VAL 4.0 1.0 + - - -
264A LEU* 1.3 73.1 - - - +
266A CYS* 1.4 57.1 + - - +
267A GLY 2.8 22.1 + - - -
303A LEU* 3.8 6.1 - - + -
304A GLY 3.2 15.5 - - - +
305A GLY* 3.5 6.7 - - - -
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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