Contacts of the helix formed by residues 855 - 865 (chain C) in PDB entry 5LPI
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 GLY 855 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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843C ASN* 2.9 25.1 + - - +
854C PRO* 1.3 76.3 - - - +
856C GLU* 1.3 60.9 + - - -
857C GLU 3.6 2.0 - - - -
858C ALA 3.6 2.6 + - - -
859C TRP* 3.2 17.3 + - - -
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Residues in contact with GLU 856 (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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756C PHE 4.4 3.3 - - - +
779C MET* 4.0 9.5 - - - +
791C GLU* 5.5 2.8 - - - +
793C SER* 4.9 5.9 + - - -
855C GLY* 1.3 70.2 - - - -
857C GLU* 1.3 66.9 - - - +
858C ALA 3.1 1.3 - - - -
859C TRP* 3.0 25.5 + - - +
860C LYS* 3.0 49.3 + - - +
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Residues in contact with GLU 857 (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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856C GLU* 1.3 79.0 - - - +
858C ALA* 1.3 62.2 + - - +
860C LYS* 3.4 11.0 + - + +
861C ALA* 3.0 23.8 + - + +
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Residues in contact with ALA 858 (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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843C ASN* 3.9 0.9 - - - +
852C PHE* 3.7 8.7 - - + -
853C SER* 3.0 38.8 - - - +
854C PRO 3.9 6.3 + - - +
855C GLY 3.6 9.2 + - - +
856C GLU 3.1 0.4 - - - -
857C GLU* 1.3 75.7 - - - +
859C TRP* 1.3 55.1 + - - +
861C ALA* 3.1 6.0 + - - +
862C HIS* 2.7 37.2 + - - +
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Residues in contact with TRP 859 (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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779C MET* 3.9 13.4 - - + +
792C ILE* 4.3 7.2 - - + -
793C SER* 3.3 43.8 + - - -
843C ASN* 3.2 39.1 + - + -
844C ARG 3.2 32.8 - - - -
845C CYS* 3.8 12.1 - - + -
846C PRO* 3.9 5.2 - - + -
852C PHE* 3.7 17.0 - + - -
855C GLY 3.2 14.1 + - - -
856C GLU* 3.0 19.5 + - - +
858C ALA* 1.3 77.3 - - - +
860C LYS* 1.3 58.8 + - - +
862C HIS* 3.4 0.6 + + - +
863C LEU* 3.0 65.1 + - + +
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Residues in contact with LYS 860 (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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755C ILE 5.1 4.9 + - - -
756C PHE 3.6 19.6 + - - -
757C CYS 4.3 13.0 - - - +
758C GLY* 4.8 3.1 - - - +
779C MET* 3.8 15.5 - - + -
856C GLU* 3.0 51.2 + - - +
857C GLU* 3.8 11.2 - - + +
859C TRP* 1.3 73.0 - - - +
861C ALA* 1.3 60.8 + - - +
864C MET* 2.9 52.0 + - + +
865C GLY 3.5 0.2 + - - -
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Residues in contact with ALA 861 (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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857C GLU* 3.0 19.2 + - + +
858C ALA* 3.7 5.8 - - - +
860C LYS* 1.3 76.9 - - - +
862C HIS* 1.3 59.8 + - - +
865C GLY* 2.9 32.6 + - - +
866C PRO* 5.0 1.4 - - + +
868C GLY* 4.5 3.3 - - - -
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Residues in contact with HIS 862 (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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845C CYS* 3.4 10.8 - - + +
848C CYS* 3.6 4.9 - - - -
850C GLU* 3.3 33.8 + - + -
852C PHE* 3.6 31.8 - + + +
858C ALA 2.7 20.9 + - - +
859C TRP* 3.8 2.7 - + - +
861C ALA* 1.3 76.6 - - - +
863C LEU* 1.3 73.0 + - + +
868C GLY* 3.5 7.8 - - - -
869C CYS* 2.8 42.3 + - + +
901C ZN 2.1 36.7 - - - -
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Residues in contact with LEU 863 (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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778C LEU* 4.0 2.7 - - - +
779C MET* 4.0 28.3 - - + +
792C ILE* 3.8 42.4 - - + -
793C SER 5.1 1.3 - - - +
845C CYS* 4.4 2.2 - - - -
847C LEU* 4.4 3.1 - - + -
859C TRP* 3.0 39.7 + - + +
862C HIS* 1.3 94.9 - - + +
864C MET* 1.3 61.5 + - - +
869C CYS* 4.1 14.6 - - + -
872C ASN* 3.2 26.8 + - - +
875C LYS* 3.0 23.5 - - - +
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Residues in contact with MET 864 (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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757C CYS* 3.6 42.0 - - - +
759C GLU* 5.6 4.0 - - - +
778C LEU* 3.8 38.1 - - + +
779C MET* 3.8 13.9 - - - +
860C LYS* 2.9 44.5 + - + +
863C LEU* 1.3 83.7 - - - +
865C GLY* 1.3 66.8 + - - +
875C LYS* 4.4 6.4 - - - +
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Residues in contact with GLY 865 (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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860C LYS 3.5 1.8 + - - -
861C ALA* 2.9 25.1 + - - -
862C HIS 4.6 0.2 - - - -
864C MET* 1.3 84.5 - - - +
866C PRO* 1.3 78.6 - - - +
867C ALA 3.4 1.7 + - - -
868C GLY* 3.6 8.5 + - - -
875C LYS* 5.0 5.5 + - - -
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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