Contacts of the helix formed by residues 377 - 388 (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 SER 377 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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376L LEU* 1.3 74.5 - - - +
378L GLU* 1.3 68.3 + - - +
379L ARG* 3.0 11.5 + - - +
380L GLU* 3.5 24.3 + - - +
381L ALA* 2.9 23.2 + - - +
422L LYS* 6.1 1.5 - - - +
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Residues in contact with GLU 378 (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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376L LEU 3.5 2.4 + - - +
377L SER* 1.3 75.0 + - - +
379L ARG* 1.3 61.1 + - - +
381L ALA* 4.6 2.8 - - - +
382L MET* 3.6 17.7 + - - +
405L PHE* 5.5 0.3 - - - -
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Residues in contact with ARG 379 (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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377L SER* 3.0 8.8 + - - +
378L GLU* 1.3 78.0 - - - +
380L GLU* 1.3 62.6 + - - +
382L MET* 3.0 7.4 + - - +
383L VAL* 2.9 34.2 + - + +
405L PHE* 3.5 47.4 + - + -
407L VAL* 3.8 11.1 - - - +
411L ARG* 2.9 33.1 - - - +
412L ILE* 5.7 0.2 - - - -
415L ILE* 3.6 18.8 - - + +
1R C 2.8 28.7 + - - -
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Residues in contact with GLU 380 (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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376L LEU* 3.3 30.0 - - + +
377L SER* 3.5 30.8 + - - +
379L ARG* 1.3 78.2 - - - +
381L ALA* 1.3 59.2 + - - +
383L VAL* 3.5 1.5 - - - +
384L LEU* 2.9 36.4 + - - +
415L ILE* 3.6 31.1 - - + +
418L LYS* 5.2 3.6 - - - +
419L ALA* 3.5 26.5 + - + +
422L LYS* 4.0 18.1 + - - +
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Residues in contact with ALA 381 (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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373L LEU* 3.7 45.7 - - + +
374L SER* 5.7 0.4 - - - -
376L LEU* 3.7 14.8 - - + +
377L SER 2.9 18.0 + - - +
378L GLU* 4.6 3.1 - - - +
380L GLU* 1.3 78.8 - - - +
382L MET* 1.3 61.1 + - - +
384L LEU* 3.6 0.5 + - - +
385L LYS* 3.3 25.2 + - - +
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Residues in contact with MET 382 (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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378L GLU 3.6 13.2 + - - +
379L ARG* 3.0 9.9 + - - +
381L ALA* 1.3 76.2 - - - +
383L VAL* 1.3 60.1 + - - +
385L LYS* 3.3 29.0 - - - +
386L LEU* 2.9 56.0 + - + +
391L ILE* 3.8 31.0 - - + -
404L TYR* 3.9 11.9 - - + +
405L PHE* 5.2 2.7 - - + -
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Residues in contact with VAL 383 (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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379L ARG* 2.9 25.2 + - + +
380L GLU* 3.2 11.2 + - - +
382L MET* 1.3 76.8 - - - +
384L LEU* 1.3 56.8 + - - +
386L LEU* 3.3 9.0 + - - +
387L ARG* 2.9 34.2 + - + +
401L VAL* 3.7 21.5 - - + -
405L PHE* 3.6 27.6 - - + -
412L ILE* 4.0 22.9 - - + -
415L ILE* 4.3 11.7 - - + -
416L GLU* 4.5 8.7 - - + -
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Residues in contact with LEU 384 (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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773I LEU* 4.3 26.0 - - + -
373L LEU* 4.4 4.9 - - + -
376L LEU* 3.7 16.6 - - + -
380L GLU 2.9 23.2 + - - +
381L ALA 3.7 6.3 - - - +
382L MET 3.2 0.2 - - - -
383L VAL* 1.3 78.1 - - + +
385L LYS* 1.3 57.8 + - - +
387L ARG* 3.0 7.6 + - - +
388L LYS* 2.9 31.8 + - - +
416L GLU* 3.7 37.2 - - + +
419L ALA* 3.7 11.0 - - + -
420L LEU* 4.6 7.0 - - + +
423L LEU* 3.6 30.7 - - + -
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Residues in contact with LYS 385 (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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773I LEU* 4.5 2.2 - - + +
370L GLU* 4.2 15.5 + - - +
373L LEU* 3.6 24.6 - - + +
381L ALA* 3.3 18.4 - - - +
382L MET* 3.3 34.4 - - - +
384L LEU* 1.3 76.8 - - - +
386L LEU* 1.3 56.2 + - - +
389L GLY 3.2 4.8 + - - -
390L LEU* 2.7 60.7 + - + -
391L ILE* 3.4 25.1 + - + +
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Residues in contact with LEU 386 (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* 2.9 39.1 + - + +
383L VAL* 3.6 9.9 - - - +
385L LYS* 1.3 78.4 - - - +
387L ARG* 1.3 63.5 + - - +
389L GLY* 3.9 0.4 + - - -
391L ILE* 3.7 31.2 - - + -
394L ARG 3.7 5.4 - - - +
396L HIS* 3.0 51.8 + - + +
401L VAL* 4.6 9.0 - - + -
404L TYR* 3.3 39.9 - - + +
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Residues in contact with ARG 387 (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* 2.9 30.0 + - + +
384L LEU* 3.4 7.0 - - - +
386L LEU* 1.3 80.4 - - - +
388L LYS* 1.3 76.4 + - + +
389L GLY 3.7 0.2 + - - -
395L GLU* 2.8 27.0 - - - +
396L HIS 2.6 38.6 + - - +
397L THR* 3.4 4.8 - - - +
398L LEU* 3.1 38.0 - - - +
401L VAL* 3.7 13.0 - - + -
412L ILE* 4.5 0.2 - - - -
416L GLU* 3.1 37.9 + - + +
43S G 3.3 25.4 + - - -
44S T 5.6 1.0 + - - -
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Residues in contact with LYS 388 (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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769I PRO* 3.4 25.2 - - - +
772I ARG* 3.6 33.4 - - + +
773I LEU* 3.6 26.5 - - + +
776I SER* 3.2 26.7 + - - +
65J ARG* 5.1 1.4 + - - -
384L LEU* 2.9 11.5 + - + +
387L ARG* 1.3 94.7 + - - +
389L GLY* 1.3 61.0 + - - +
390L LEU* 3.5 19.7 - - + -
395L GLU* 3.5 12.0 + - - +
416L GLU* 5.1 6.6 + - - -
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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
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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