Contacts of the helix formed by residues 777 - 786 (chain A) in PDB entry 5FLM
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 777 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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770A VAL* 3.7 17.5 - - - +
776A GLY* 1.3 74.2 - - - -
778A LYS* 1.3 65.6 + - - +
779A ILE* 3.2 19.8 - - - +
780A ASN* 3.0 32.5 + - - +
781A ILE 3.5 4.2 + - - -
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Residues in contact with LYS 778 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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757A GLN* 3.1 41.1 + - - +
770A VAL* 3.6 18.5 - - + +
771A VAL* 6.5 1.3 - - - -
777A SER* 1.3 74.3 - - - +
779A ILE* 1.3 62.3 + - - +
781A ILE* 3.1 11.2 + - + +
782A SER* 2.9 18.4 + - - -
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Residues in contact with ILE 779 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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749A ARG* 3.3 34.1 - - - +
750A ASP* 5.7 2.0 - - - +
757A GLN* 5.1 0.4 - - - +
777A SER* 3.2 18.1 + - - +
778A LYS* 1.3 78.9 - - - +
780A ASN* 1.3 68.8 + - - +
782A SER* 3.3 15.1 + - - +
783A GLN* 2.9 40.7 + - + +
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Residues in contact with ASN 780 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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770A VAL* 6.1 0.4 - - + -
776A GLY* 3.9 7.3 - - - -
777A SER* 3.0 34.6 + - - +
779A ILE* 1.3 84.9 - - - +
781A ILE* 1.3 59.6 + - + +
783A GLN* 3.2 5.6 + - - +
784A VAL* 2.9 36.3 + - + +
973B PRO* 3.6 24.0 - - + +
974B SER* 4.0 9.2 + - - -
976B MET* 3.3 33.7 - - + +
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Residues in contact with ILE 781 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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756A ALA 4.7 1.8 - - - +
757A GLN* 4.6 11.7 - - + -
760A LEU* 3.8 31.2 - - + -
766A PHE* 3.9 28.7 - - + +
767A LYS* 4.4 1.3 - - - +
770A VAL* 3.6 37.7 - - + -
777A SER 3.5 1.8 + - - +
778A LYS* 3.1 11.8 + - + +
780A ASN* 1.3 76.7 - - + +
782A SER* 1.3 58.5 + - - +
784A VAL* 4.5 4.7 - - - -
785A ILE* 2.9 54.2 + - + +
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Residues in contact with SER 782 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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749A ARG* 4.0 7.6 + - - +
753A GLY* 3.3 33.4 + - - -
756A ALA* 4.9 3.6 - - - -
757A GLN* 4.6 4.7 - - - +
778A LYS 2.9 12.2 + - - -
779A ILE* 3.4 23.8 - - - +
780A ASN 3.2 0.2 - - - -
781A ILE* 1.3 77.6 - - - +
783A GLN* 1.3 57.7 + - - +
786A ALA* 2.9 29.3 + - - +
787A VAL* 3.1 16.4 + - - +
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Residues in contact with GLN 783 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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749A ARG* 4.9 4.2 - - - +
779A ILE* 2.9 36.3 + - + +
780A ASN* 3.8 6.9 + - - +
782A SER* 1.3 75.9 - - - +
784A VAL* 1.3 61.6 + - - +
787A VAL 3.3 9.5 - - - +
788A VAL* 3.6 37.1 + - - +
791A GLN* 5.6 1.8 + - - -
826A SER* 3.3 19.2 - - - -
827A TYR* 3.5 30.4 + - + -
976B MET* 3.2 30.7 - - - +
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Residues in contact with VAL 784 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692A SER* 3.8 27.6 - - - +
766A PHE* 3.9 18.6 - - + -
780A ASN* 2.9 22.6 + - + +
781A ILE* 3.8 5.6 - - - +
782A SER 3.2 0.2 - - - -
783A GLN* 1.3 78.8 - - - +
785A ILE* 1.3 60.4 + - + +
826A SER* 3.1 20.6 + - - -
827A TYR* 4.6 10.1 - - + +
828A LEU* 3.6 12.9 + - + +
973B PRO* 5.5 2.0 - - + +
976B MET* 4.7 11.7 - - + -
978B ILE* 3.5 34.1 - - + -
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Residues in contact with ILE 785 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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691A ASP 5.0 3.6 - - - +
692A SER* 3.6 27.1 - - - +
693A ILE 5.5 0.9 - - - +
694A ALA* 3.7 31.0 - - + +
699A TYR* 4.4 13.3 - - + -
702A ILE* 4.4 8.2 - - + +
756A ALA* 3.6 25.1 - - + +
760A LEU* 3.6 31.4 - - + -
764A ASN* 5.1 0.4 - - - +
766A PHE* 5.1 2.7 - - + -
781A ILE* 2.9 27.6 + - + +
784A VAL* 1.3 81.6 - - + +
786A ALA* 1.3 61.2 + - - +
826A SER* 3.5 10.6 + - - -
828A LEU* 5.5 2.3 - - - +
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Residues in contact with ALA 786 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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702A ILE* 3.6 29.2 - - + +
706A ILE* 5.1 0.3 - - - +
752A THR* 3.7 32.3 - - - +
753A GLY 4.5 0.9 - - - +
756A ALA* 4.0 5.8 - - + -
782A SER* 2.9 12.0 + - - +
784A VAL 3.6 0.2 - - - -
785A ILE* 1.3 79.3 - - - +
787A VAL* 1.3 67.4 + - - +
824A GLU 3.9 6.6 - - - +
826A SER* 3.4 15.7 + - - -
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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