Contacts of the helix formed by residues 768 - 779 (chain I) 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 768 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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766I GLU* 3.9 3.4 + - - -
767I PRO* 1.3 73.2 - - - +
769I PRO* 1.3 64.8 - - - +
770I GLU* 3.7 13.5 + - - +
771I GLU* 2.8 32.5 + - - +
772I ARG* 2.5 34.3 + - - +
65J ARG* 5.6 0.2 - - - -
362L GLN* 5.0 10.4 - - - +
365L LEU* 5.4 1.0 - - - +
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Residues in contact with PRO 769 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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767I PRO 3.8 0.2 - - - -
768I SER* 1.3 87.6 - - - +
770I GLU* 1.3 65.9 + - - +
772I ARG* 3.3 4.7 + - + +
773I LEU* 2.9 24.1 + - - +
65J ARG* 3.1 37.7 - - - +
388L LYS* 3.4 17.4 - - - +
389L GLY 3.2 20.4 - - - +
390L LEU* 3.3 27.0 - - + +
393L GLY* 5.2 0.2 - - - -
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Residues in contact with GLU 770 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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768I SER* 3.7 15.0 + - - +
769I PRO* 1.3 89.7 - - - +
771I GLU* 1.3 58.1 + - - +
773I LEU* 3.4 1.7 + - - +
774I LEU* 2.9 24.3 + - - +
362L GLN* 3.5 22.4 + - + +
365L LEU* 4.3 9.4 - - + -
366L SER* 3.8 34.3 + - - +
369L LEU* 3.3 29.1 - - + +
390L LEU* 3.8 25.7 - - + +
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Residues in contact with GLU 771 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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767I PRO* 3.3 27.1 - - + +
768I SER* 2.8 24.6 + - - +
770I GLU* 1.3 78.6 - - - +
772I ARG* 1.3 58.0 + - - +
774I LEU* 3.3 6.1 + - + +
775I ARG* 2.9 40.6 + - + +
365L LEU* 4.1 17.6 - - + +
438L GLU* 4.1 21.4 - - - +
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Residues in contact with ARG 772 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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766I GLU* 4.3 9.9 - - - +
767I PRO* 3.6 42.4 + - + +
768I SER 2.5 19.0 + - - +
769I PRO* 3.6 7.2 - - + +
771I GLU* 1.3 71.0 - - - +
773I LEU* 1.3 59.4 + - - +
775I ARG* 3.0 14.2 + - + +
776I SER* 2.9 25.7 + - - +
388L LYS* 3.6 35.5 - - + +
395L GLU* 3.6 30.4 + - - -
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Residues in contact with LEU 773 (chain I).
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 2.9 17.3 + - - +
770I GLU* 3.8 4.7 - - - +
772I ARG* 1.3 75.0 - - - +
774I LEU* 1.3 58.2 + - - +
776I SER* 2.9 25.9 + - - -
777I ILE* 2.9 36.4 + - + +
369L LEU* 5.2 9.0 - - + -
373L LEU* 5.2 9.2 - - + -
384L LEU* 4.3 39.3 - - + +
385L LYS* 4.5 2.9 - - + +
388L LYS* 3.6 21.3 - - + +
390L LEU* 3.9 24.5 - - + -
420L LEU* 4.6 2.7 - - + -
423L LEU* 5.9 1.1 - - + -
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Residues in contact with LEU 774 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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770I GLU 2.9 18.6 + - - +
771I GLU* 3.4 10.8 - - + +
773I LEU* 1.3 76.5 - - - +
775I ARG* 1.3 62.3 + - + +
776I SER 3.4 0.2 + - - -
777I ILE* 3.5 15.0 + - + +
778I PHE* 3.7 32.3 + - + +
365L LEU* 4.0 20.0 - - + -
369L LEU* 3.7 25.2 - - + +
433L LEU* 4.4 19.7 - - + +
436L PHE* 3.5 32.8 - - + +
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Residues in contact with ARG 775 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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728I HIS* 4.9 3.4 + - - -
767I PRO* 3.4 33.3 - - - +
771I GLU* 2.9 29.2 + - - +
772I ARG* 3.2 13.7 - - + +
774I LEU* 1.3 78.2 - - + +
776I SER* 1.3 56.4 + - - +
778I PHE* 3.9 0.8 + - - -
779I GLY* 2.9 31.7 + - - -
780I GLU* 3.6 18.1 + - - +
781I LYS* 5.6 0.4 - - - +
782I ALA* 3.3 37.7 - - - +
786I LYS* 5.3 1.2 - - - +
438L GLU* 2.8 42.1 + - - +
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Residues in contact with SER 776 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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772I ARG* 2.9 10.3 + - - +
773I LEU* 2.9 19.1 + - - -
775I ARG* 1.3 76.7 - - - +
777I ILE* 1.3 65.1 + - - +
779I GLY* 3.3 11.1 + - - +
388L LYS* 3.2 30.7 + - - -
420L LEU* 3.2 28.5 - - - +
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Residues in contact with ILE 777 (chain I).
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* 2.9 41.4 + - + +
774I LEU* 3.5 13.4 + - + +
775I ARG 3.4 0.4 - - - -
776I SER* 1.3 78.6 - - - +
778I PHE* 1.3 85.7 + - + +
369L LEU* 5.3 7.9 - - + -
420L LEU* 3.4 26.4 - - + +
423L LEU* 3.7 31.0 - - + -
424L LYS* 3.3 38.4 + - + -
427L GLU* 5.0 9.6 - - + -
433L LEU* 6.5 0.2 - - + -
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Residues in contact with PHE 778 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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774I LEU* 3.7 31.4 + - + +
775I ARG* 4.8 0.4 - - - +
777I ILE* 1.3 94.5 - - + +
779I GLY* 1.3 57.9 + - - +
780I GLU* 3.0 25.7 + - + +
424L LYS* 5.1 8.2 + - - +
427L GLU* 4.5 4.3 - - + -
433L LEU* 3.3 28.5 - - + -
434L ARG* 3.4 47.8 - - + -
435L ASP 4.3 2.5 - - - -
437L LEU* 6.6 0.2 - - - -
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Residues in contact with GLY 779 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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775I ARG 2.9 14.0 + - - -
776I SER* 3.3 8.9 + - - -
777I ILE 3.3 3.4 - - - -
778I PHE* 1.3 76.7 - - - +
780I GLU* 1.3 64.2 + - - +
781I LYS* 3.2 5.9 + - - +
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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