Contacts of the strand formed by residues 323 - 325 (chain T) in PDB entry 3FKS
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 LEU 323 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164T GLY* 3.2 17.0 - - - -
253T ALA* 4.5 15.3 - - + +
256T GLY* 4.1 25.8 - - - +
257T GLU* 4.6 2.5 - - + +
260T ARG* 4.2 8.8 - - + +
266T ALA* 3.4 24.2 - - + +
268T ILE* 3.6 35.9 - - + -
270T TYR* 5.6 1.3 - - - +
310T ARG* 4.0 9.6 - - + +
311T ALA* 3.4 33.8 - - + +
312T ALA 3.1 17.0 + - - +
322T SER* 1.3 78.7 - - - +
324T THR* 1.3 63.1 + - - +
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Residues in contact with THR 324 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148T VAL* 3.8 6.5 - - + +
161T ILE* 3.9 17.9 - - + -
162T GLY 3.7 13.5 - - - +
163T ARG* 3.5 8.7 - - - +
164T GLY 3.0 17.3 + - - +
165T GLN 3.3 13.9 - - - +
201T LEU* 5.3 2.6 - - - +
266T ALA 2.9 10.8 + - - -
267T LEU* 3.6 27.0 - - + +
268T ILE* 2.9 32.5 + - - +
322T SER* 5.0 1.0 + - - -
323T LEU* 1.3 72.8 - - - +
325T ALA* 1.3 66.6 + - - +
326T LEU* 5.2 0.7 - - + -
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Residues in contact with ALA 325 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165T GLN 2.9 10.4 + - - +
166T ARG* 3.6 25.9 - - + -
167T GLU 3.1 25.5 + - - +
268T ILE* 3.6 4.7 - - + -
270T TYR* 4.4 7.4 - - + -
308T LEU* 4.2 21.3 - - + -
311T ALA* 3.9 12.8 - - + -
323T LEU 4.2 0.4 + - - -
324T THR* 1.3 75.3 - - - +
326T LEU* 1.3 64.2 + - - +
327T PRO* 3.4 2.6 - - + +
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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