Contacts of the helix formed by residues 768 - 779 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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766C GLU* 3.9 3.9 + - - -
767C PRO* 1.3 72.9 - - - +
769C PRO* 1.3 65.7 - - - +
770C GLU* 3.7 13.5 + - - +
771C GLU* 2.8 31.3 + - - +
772C ARG* 2.5 34.8 + - - +
65D ARG* 5.7 0.2 - - - -
362F GLN* 5.0 10.2 - - - +
365F LEU* 5.4 1.2 - - - +
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Residues in contact with PRO 769 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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767C PRO 3.8 0.4 - - - +
768C SER* 1.3 88.5 - - - +
770C GLU* 1.3 66.6 + - - +
772C ARG* 3.3 5.3 + - + +
773C LEU* 2.9 24.1 + - - +
65D ARG* 3.2 29.8 - - - +
388F LYS* 3.4 18.0 - - - +
389F GLY 3.2 27.6 - - - +
390F LEU* 3.3 26.9 - - + +
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Residues in contact with GLU 770 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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768C SER* 3.7 15.0 + - - +
769C PRO* 1.3 89.7 - - - +
771C GLU* 1.3 57.1 + - - +
773C LEU* 3.4 1.5 + - - +
774C LEU* 2.9 24.9 + - - +
362F GLN* 3.5 21.2 + - + +
365F LEU* 4.3 9.2 - - + -
366F SER* 3.8 33.6 + - - +
369F LEU* 3.3 30.1 - - + +
390F LEU* 3.8 25.4 - - + +
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Residues in contact with GLU 771 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767C PRO* 3.3 16.0 - - + +
768C SER* 2.8 35.3 + - - +
770C GLU* 1.3 79.4 - - - +
772C ARG* 1.3 57.0 + - - +
774C LEU* 3.3 5.9 + - + +
775C ARG* 2.9 50.9 + - + +
365F LEU* 4.1 17.2 - - + +
438F GLU* 4.9 9.1 - - - +
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Residues in contact with ARG 772 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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766C GLU* 4.3 9.3 - - - +
767C PRO* 3.6 42.6 + - + +
768C SER 2.5 19.6 + - - +
769C PRO* 3.6 6.7 - - + +
771C GLU* 1.3 71.1 - - - +
773C LEU* 1.3 60.4 + - - +
775C ARG* 3.0 13.4 + - + +
776C SER* 2.9 25.7 + - - +
388F LYS* 3.6 35.8 - - + +
395F GLU* 3.6 30.6 + - - -
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Residues in contact with LEU 773 (chain C).
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 2.9 17.2 + - - +
770C GLU* 3.8 4.7 - - - +
772C ARG* 1.3 76.4 - - - +
774C LEU* 1.3 57.8 + - - +
776C SER* 2.9 25.3 + - - -
777C ILE* 2.9 37.5 + - + +
369F LEU* 5.1 9.4 - - + -
373F LEU* 5.2 9.6 - - + -
384F LEU* 4.3 39.5 - - + +
385F LYS* 4.5 2.7 - - + +
388F LYS* 3.6 20.6 - - + -
390F LEU* 3.9 25.1 - - + -
420F LEU* 4.6 2.5 - - + -
423F LEU* 5.9 0.7 - - + -
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Residues in contact with LEU 774 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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770C GLU 2.9 18.5 + - - +
771C GLU* 3.4 11.4 - - + +
772C ARG 3.2 0.2 - - - -
773C LEU* 1.3 76.6 - - - +
775C ARG* 1.3 61.6 + - + +
776C SER 3.4 0.2 + - - -
777C ILE* 3.5 15.2 + - + +
778C PHE* 3.7 34.3 + - + +
365F LEU* 4.0 20.0 - - + -
369F LEU* 3.7 26.6 - - + +
433F LEU* 4.2 19.3 - - + +
435F ASP 4.4 3.1 - - - +
436F PHE* 4.1 25.8 - - + +
437F LEU* 6.0 0.2 - - - -
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Residues in contact with ARG 775 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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728C HIS* 4.9 3.2 + - - -
767C PRO* 3.4 33.0 - - - +
771C GLU* 2.9 33.2 + - + +
772C ARG* 3.0 14.5 + - + +
774C LEU* 1.3 77.9 - - + +
776C SER* 1.3 56.5 + - - +
778C PHE* 5.8 0.4 - - - -
779C GLY* 2.9 31.5 + - - -
780C GLU* 3.6 19.3 + - - +
781C LYS* 5.6 0.7 - - - +
782C ALA* 3.3 34.0 - - - +
438F GLU* 2.6 38.3 + - - -
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Residues in contact with SER 776 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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772C ARG* 2.9 10.1 + - - +
773C LEU* 2.9 19.1 + - - -
775C ARG* 1.3 77.1 - - - +
777C ILE* 1.3 65.7 + - - +
779C GLY* 3.3 10.7 + - - -
388F LYS* 3.2 30.6 + - - -
420F LEU* 3.2 28.1 - - - +
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Residues in contact with ILE 777 (chain C).
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* 2.9 41.3 + - + +
774C LEU* 3.5 13.0 + - + +
775C ARG 3.4 0.4 - - - -
776C SER* 1.3 77.6 - - - +
778C PHE* 1.3 86.4 + - + +
369F LEU* 5.3 8.5 - - + -
420F LEU* 3.4 32.7 - - + +
423F LEU* 3.7 32.3 - - + -
424F LYS* 3.9 24.0 + - + +
427F GLU* 4.7 14.6 - - + -
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Residues in contact with PHE 778 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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774C LEU* 3.7 30.1 + - + +
775C ARG* 4.8 0.7 - - - +
777C ILE* 1.3 91.2 - - + +
779C GLY* 1.3 57.9 + - - +
780C GLU* 3.0 25.0 + - + +
424F LYS* 5.3 17.4 + - - +
427F GLU* 3.7 20.0 - - + -
433F LEU 3.8 14.1 - - - -
434F ARG* 3.7 39.7 - - + -
435F ASP 5.1 0.4 - - - -
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Residues in contact with GLY 779 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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775C ARG 2.9 14.0 + - - -
776C SER* 3.3 8.4 + - - -
777C ILE 3.3 3.4 - - - -
778C PHE* 1.3 77.9 - - - +
780C GLU* 1.3 63.9 + - - +
781C LYS* 3.2 5.7 + - - +
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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