Contacts of the helix formed by residues 288 - 292 (chain A) in PDB entry 3L4U
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 SER 288 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A LEU 3.7 0.8 + - - -
287A PRO* 1.3 79.4 - - - +
289A TYR* 1.3 66.4 + - - +
290A TRP* 3.4 34.4 + - - -
291A ALA* 3.0 20.2 + - - +
292A LEU* 3.9 1.7 + - - +
520A ARG* 3.4 17.8 - - - +
521A SER 2.7 34.7 + - - -
773A GLY 3.5 9.8 + - - -
774A GLU* 4.7 4.7 - - - +
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Residues in contact with TYR 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A PRO 3.5 2.0 + - - -
288A SER* 1.3 71.6 - - - +
290A TRP* 1.3 62.4 + - - +
292A LEU* 3.1 25.8 + - + +
293A GLY 4.1 1.4 + - - -
631A TYR 5.3 0.2 + - - -
634A LEU* 3.4 30.5 - - + +
635A PRO* 3.6 14.9 - - - +
638A TYR* 3.5 51.1 - + + -
738A GLN* 3.9 11.3 + - - -
744A THR* 3.7 22.6 - - + +
747A SER* 4.6 4.0 + - - -
748A ARG* 3.4 56.1 - - + +
770A TRP* 4.1 9.2 - + - -
773A GLY* 2.9 20.6 + - - +
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Residues in contact with TRP 290 (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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288A SER* 3.4 21.0 + - - -
289A TYR* 1.3 79.2 - - - +
291A ALA* 1.3 74.3 + - - +
293A GLY* 3.0 20.3 + - - -
295A HIS* 4.8 0.4 - - - -
322A ASP* 3.8 15.5 - - - +
323A VAL* 3.6 33.5 - - + +
360A LYS* 3.6 48.9 - - + +
362A VAL* 4.4 6.5 - - + -
438A ASP* 3.8 32.1 - - + -
521A SER* 4.1 8.8 - - - +
522A PHE* 3.4 33.4 - + + -
744A THR* 3.3 21.7 + - - +
773A GLY 5.2 2.5 - - - -
774A GLU* 5.4 11.1 - - + +
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Residues in contact with ALA 291 (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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287A PRO* 4.5 4.0 - - + -
288A SER* 3.0 20.0 + - - +
290A TRP* 1.3 91.2 - - + +
292A LEU* 1.3 56.2 + - - +
293A GLY 3.2 2.1 - - - +
295A HIS* 2.9 26.5 - - - -
522A PHE* 3.6 33.0 - - + -
567A MET* 3.4 21.2 - - + +
595A PRO 5.1 0.3 - - - +
596A PHE* 4.7 1.2 - - - -
597A SER 5.6 0.2 + - - -
630A ARG* 5.3 0.2 + - - -
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Residues in contact with LEU 292 (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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287A PRO* 4.0 13.7 - - + -
288A SER 4.4 2.7 - - - +
289A TYR* 3.1 19.4 + - + +
290A TRP 3.1 1.0 - - - -
291A ALA* 1.3 74.2 - - - +
293A GLY* 1.3 62.3 + - - +
567A MET* 3.4 26.2 - - + -
630A ARG* 2.8 33.0 + - - +
634A LEU* 3.8 21.4 - - + +
637A LEU* 3.9 16.4 - - + -
638A TYR* 3.8 45.3 - - + +
641A PHE* 3.5 20.9 - - + -
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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
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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