Contacts of the helix formed by residues 397 - 404 (chain L) in PDB entry 4XLN
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 THR 397 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387L ARG* 3.4 2.2 - - - +
395L GLU* 4.1 2.0 + - - +
396L HIS* 1.3 73.4 - - - +
398L LEU* 1.3 56.3 + - - +
399L GLU* 3.5 15.6 + - + +
400L GLU* 2.7 57.7 + - + +
401L VAL* 3.0 10.2 + - - +
42S T 3.2 39.5 + - - +
43S G 2.6 25.4 + - - -
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Residues in contact with LEU 398 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387L ARG* 3.1 16.9 - - - +
397L THR* 1.3 73.9 + - - +
399L GLU* 1.3 57.8 + - + +
401L VAL* 3.9 5.8 - - - +
402L GLY* 2.9 27.7 + - - -
409L ARG* 3.6 30.5 - - + +
412L ILE* 3.8 11.0 - - + +
413L ARG* 4.1 14.4 - - + +
416L GLU* 3.2 28.3 - - - +
43S G 2.9 40.9 + - + +
44S T 3.6 33.4 - - + +
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Residues in contact with GLU 399 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397L THR* 3.0 14.3 - - + +
398L LEU* 1.3 78.3 - - + +
400L GLU* 1.3 57.7 + - + +
402L GLY* 3.7 0.7 - - - -
403L ALA* 2.9 28.8 + - - +
409L ARG* 3.3 43.6 + - + +
42S T 4.0 30.5 - - + +
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Residues in contact with GLU 400 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395L GLU 5.5 1.5 - - - +
396L HIS* 3.1 35.0 + - - +
397L THR* 2.7 36.6 + - + +
399L GLU* 1.3 72.7 - - + +
401L VAL* 1.3 63.3 + - - +
402L GLY 3.1 1.6 - - - -
403L ALA* 3.1 16.7 + - + +
404L TYR* 3.4 15.6 + - - +
42S T 5.2 1.9 + - - -
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Residues in contact with VAL 401 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383L VAL* 3.7 31.2 - - + +
386L LEU* 4.6 7.9 - - + -
387L ARG* 3.7 14.4 - - + -
396L HIS* 3.4 30.5 - - + +
397L THR 3.0 15.7 + - - +
398L LEU 4.0 0.2 - - - +
400L GLU* 1.3 75.9 - - - +
402L GLY* 1.3 60.1 + - - +
404L TYR* 3.4 27.0 - - + -
405L PHE* 3.5 12.1 - - - +
412L ILE* 3.6 27.2 - - + +
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Residues in contact with GLY 402 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398L LEU 2.9 16.9 + - - -
399L GLU 3.7 1.6 - - - -
401L VAL* 1.3 78.5 - - - +
403L ALA* 1.3 54.9 + - - +
404L TYR 3.4 0.4 - - - -
405L PHE 3.8 0.7 - - - -
406L GLY 2.7 29.1 + - - -
407L VAL* 2.8 39.6 + - - +
408L THR 4.7 0.7 - - - -
409L ARG 5.3 0.2 - - - -
412L ILE* 3.6 3.5 - - - +
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Residues in contact with ALA 403 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399L GLU 2.9 19.2 + - - +
400L GLU* 3.1 12.0 + - + +
402L GLY* 1.3 80.6 - - - +
404L TYR* 1.3 61.2 + - + +
406L GLY* 3.5 8.2 + - - -
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Residues in contact with TYR 404 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382L MET* 3.9 10.5 - - + +
386L LEU* 3.3 31.6 - - + +
400L GLU 3.4 10.9 + - - +
401L VAL* 3.4 20.0 - - + -
403L ALA* 1.3 79.2 - - + +
405L PHE* 1.3 107.3 + + - +
406L GLY 3.4 0.2 - - - -
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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