Contacts of the helix formed by residues 377 - 388 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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376F LEU* 1.3 74.5 - - - +
378F GLU* 1.3 68.8 + - - +
379F ARG* 3.0 12.3 + - - +
380F GLU* 3.4 24.9 + - - +
381F ALA* 2.9 23.2 + - - +
422F LYS* 6.1 1.7 - - - +
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Residues in contact with GLU 378 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376F LEU 3.5 2.7 + - - -
377F SER* 1.3 74.3 + - - +
379F ARG* 1.3 61.8 + - - +
381F ALA* 4.6 3.0 - - - +
382F MET* 3.6 17.5 + - - +
405F PHE* 5.5 0.2 - - - -
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Residues in contact with ARG 379 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377F SER* 3.0 8.4 + - - +
378F GLU* 1.3 77.1 - - - +
380F GLU* 1.3 61.8 + - - +
382F MET* 3.0 7.3 + - - +
383F VAL* 2.9 33.7 + - + +
405F PHE* 3.5 46.3 - - + -
407F VAL* 3.8 13.7 - - - +
411F ARG* 2.9 30.7 - - - +
415F ILE* 3.7 19.5 - - + +
1O C 2.9 27.1 + - - -
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Residues in contact with GLU 380 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376F LEU* 3.3 29.5 - - + +
377F SER* 3.4 30.7 + - - +
379F ARG* 1.3 78.5 - - - +
381F ALA* 1.3 59.0 + - - +
383F VAL* 3.2 1.8 + - - +
384F LEU* 2.9 36.2 + - - +
415F ILE* 3.6 31.4 - - + +
418F LYS* 5.1 3.5 - - - +
419F ALA* 3.5 28.3 + - + +
422F LYS* 4.1 17.7 + - - +
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Residues in contact with ALA 381 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373F LEU* 3.7 46.0 - - + +
374F SER* 5.7 0.4 - - - -
376F LEU* 3.7 13.7 - - + +
377F SER 2.9 17.8 + - - +
378F GLU* 4.6 3.6 - - - +
380F GLU* 1.3 79.5 - - - +
382F MET* 1.3 61.0 + - - +
384F LEU* 3.6 0.5 + - - +
385F LYS* 3.3 24.8 + - - +
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Residues in contact with MET 382 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378F GLU 3.6 13.3 + - - +
379F ARG* 3.0 10.1 + - - +
381F ALA* 1.3 76.6 - - - +
383F VAL* 1.3 61.8 + - + +
385F LYS* 3.3 29.9 - - - +
386F LEU* 2.9 54.8 + - + +
391F ILE* 3.8 31.2 - - + -
404F TYR* 3.9 12.1 - - + +
405F PHE* 5.2 2.0 - - + -
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Residues in contact with VAL 383 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379F ARG* 2.9 26.3 + - + +
380F GLU* 3.5 11.0 - - - +
382F MET* 1.3 78.2 - - - +
384F LEU* 1.3 57.1 + - - +
386F LEU* 3.3 8.3 + - - +
387F ARG* 2.9 34.3 + - + +
401F VAL* 3.7 19.7 - - + -
405F PHE* 3.6 28.3 - - + -
412F ILE* 4.0 22.4 - - + -
415F ILE* 4.3 12.3 - - + -
416F GLU* 4.5 8.5 - - + -
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Residues in contact with LEU 384 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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773C LEU* 4.3 26.0 - - + -
373F LEU* 4.4 5.4 - - + -
376F LEU* 3.7 16.8 - - + -
380F GLU 2.9 23.0 + - - +
381F ALA 3.7 6.3 - - - +
382F MET 3.2 0.2 - - - -
383F VAL* 1.3 77.4 - - + +
385F LYS* 1.3 57.0 + - - +
387F ARG* 3.0 8.2 + - - +
388F LYS* 2.9 31.6 + - + +
416F GLU* 3.7 36.8 - - + +
419F ALA* 3.7 12.1 - - + -
420F LEU* 4.6 7.9 - - + +
423F LEU* 3.6 31.0 - - + -
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Residues in contact with LYS 385 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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773C LEU* 4.7 2.0 - - + -
370F GLU* 4.2 16.2 + - - +
373F LEU* 3.6 25.9 - - + +
381F ALA* 3.3 18.6 - - - +
382F MET* 3.3 34.5 - - - +
384F LEU* 1.3 76.0 - - - +
386F LEU* 1.3 57.7 + - - +
389F GLY* 3.2 4.3 + - - -
390F LEU* 2.7 60.4 + - + -
391F ILE* 3.4 24.0 + - + +
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Residues in contact with LEU 386 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382F MET* 2.9 39.3 + - + +
383F VAL* 3.6 9.4 - - - +
385F LYS* 1.3 76.5 - - - +
387F ARG* 1.3 62.1 + - - +
389F GLY* 5.2 0.2 - - - -
391F ILE* 3.7 32.1 - - + -
394F ARG 3.7 5.9 - - - +
396F HIS* 3.0 52.4 + - + +
401F VAL* 4.6 9.6 - - + -
404F TYR* 3.3 40.2 - - + +
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Residues in contact with ARG 387 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383F VAL* 2.9 29.2 + - + +
384F LEU* 3.0 7.2 + - - +
386F LEU* 1.3 79.4 - - - +
388F LYS* 1.3 75.9 + - + +
389F GLY 3.7 0.2 + - - -
395F GLU* 2.8 26.4 - - - +
396F HIS 2.6 39.8 + - - +
397F THR* 3.4 4.2 - - - +
398F LEU* 3.1 37.9 - - - +
401F VAL* 3.7 13.2 - - + -
412F ILE* 4.5 0.2 - - - -
416F GLU* 3.1 38.4 + - + +
43P G 3.3 26.4 + - - -
44P T 5.9 0.4 + - - -
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Residues in contact with LYS 388 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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769C PRO* 3.4 25.6 - - - +
772C ARG* 3.6 33.5 - - + +
773C LEU* 3.6 28.0 - - + +
776C SER* 3.2 27.1 + - - +
65D ARG* 5.5 0.2 + - - -
384F LEU 2.9 11.4 + - - +
387F ARG* 1.3 93.8 + - - +
389F GLY* 1.3 62.7 + - - +
390F LEU* 3.5 19.3 - - + -
395F GLU* 3.5 12.6 + - - +
416F GLU* 5.1 6.7 + - - -
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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