Contacts of the strand formed by residues 241 - 245 (chain A) in PDB entry 1AKZ
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 VAL 241 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A LYS 3.0 9.3 + - - +
139A VAL* 3.2 5.8 - - + +
140A VAL* 2.8 26.0 + - - +
240A LEU* 1.3 76.9 - - - +
242A PHE* 1.3 62.5 + - - +
243A LEU* 4.0 13.7 - - + -
262A HIS* 3.4 17.9 - - + +
264A LEU* 4.3 12.1 - - + -
287A THR* 3.6 43.3 - - + +
290A LEU* 4.2 15.5 - - + -
291A LEU* 4.0 23.8 - - + +
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Residues in contact with PHE 242 (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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140A VAL* 3.5 35.2 - - + +
142A LEU* 5.1 2.7 - - + -
230A VAL* 4.3 16.8 - - + -
233A LEU* 4.7 11.2 - - + -
234A ASN* 4.9 4.9 - - - -
240A LEU* 3.9 24.5 - - + -
241A VAL* 1.3 76.7 - - - +
243A LEU* 1.3 62.5 + - - +
244A LEU* 3.8 11.7 + - + -
256A ILE* 3.3 55.4 - - + -
261A HIS* 3.8 27.8 - + + -
262A HIS 2.8 11.9 + - - +
263A VAL* 3.6 5.4 - - + +
264A LEU* 2.9 28.4 + - - +
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Residues in contact with LEU 243 (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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139A VAL* 4.1 18.8 - - + -
140A VAL 2.8 12.6 + - - +
141A ILE* 3.8 25.0 - - + +
142A LEU 3.7 22.0 + - - +
241A VAL* 4.0 3.8 - - + -
242A PHE* 1.3 72.6 - - - +
244A LEU* 1.3 63.5 + - - +
245A TRP* 3.8 36.1 + - + +
264A LEU* 3.6 29.4 - - + -
283A HIS* 3.9 14.6 - - + +
284A PHE* 4.8 2.7 - - + -
287A THR* 3.5 23.3 - - - +
301A TRP* 4.6 9.6 - - + -
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Residues in contact with LEU 244 (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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142A LEU* 3.7 25.1 - - + -
242A PHE* 4.3 15.0 - - + +
243A LEU* 1.3 77.3 - - - +
245A TRP* 1.3 62.0 + - - +
246A GLY 4.0 0.2 - - - -
249A ALA* 3.6 22.4 - - - +
250A GLN* 3.6 19.0 + - + +
253A GLY* 3.9 27.4 - - - +
256A ILE* 4.4 2.9 - - + -
258A ARG* 4.9 0.9 - - - +
263A VAL* 3.6 30.7 - - + -
264A LEU 2.9 11.6 + - - +
265A GLN* 3.3 15.2 - - + +
266A THR 3.1 24.9 + - - +
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Residues in contact with TRP 245 (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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141A ILE* 3.9 30.1 - - + -
142A LEU 4.9 4.7 + - - +
158A PHE* 3.9 21.0 - + + -
173A ILE* 3.7 26.9 - - + -
195A TRP* 5.9 0.9 - + - -
243A LEU* 3.8 29.9 + - + +
244A LEU* 1.3 79.7 - - - +
246A GLY* 1.3 62.3 + - - +
249A ALA* 3.6 16.2 + - - +
266A THR* 3.4 23.8 - - + +
267A ALA 3.8 10.8 - - - +
268A HIS* 3.6 16.6 - - + -
269A PRO* 3.9 19.1 - - + -
278A PHE* 3.8 12.5 - + - -
283A HIS* 3.0 26.7 + + + -
284A PHE* 3.8 31.4 - + - -
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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