Contacts of the helix formed by residues 691 - 698 (chain I) in PDB entry 4XLR
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 691 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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690I ILE* 1.3 80.3 - - - +
692I GLU* 1.3 62.5 + - - +
693I GLU* 3.2 15.2 + - - +
694I LEU* 3.5 18.5 + - - +
695I LEU* 4.0 2.4 + - - +
852I ILE* 3.3 8.6 - - - +
853I LEU 3.3 4.9 - - - -
855I VAL* 5.7 1.1 - - - -
858I MET* 3.4 24.0 - - - -
867I VAL 3.8 9.0 - - - -
868I ASP* 3.2 28.4 + - - -
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Residues in contact with GLU 692 (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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150G TYR* 3.5 40.0 - - + +
30H ARG* 3.8 29.3 + - - +
691I SER* 1.3 70.5 - - - +
693I GLU* 1.3 56.5 + - - +
695I LEU* 2.8 33.5 + - + +
696I LYS* 3.0 28.1 + - - +
852I ILE* 3.5 9.3 - - + +
853I LEU 2.9 16.5 + - - +
854I PRO* 4.2 2.7 - - + -
855I VAL* 3.8 20.9 + - - +
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Residues in contact with GLU 693 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691I SER* 3.1 12.7 + - - +
692I GLU* 1.3 76.7 - - - +
694I LEU* 1.3 65.0 + - + +
696I LYS* 3.2 21.9 - - + +
697I ARG* 3.1 27.7 + - + +
855I VAL* 4.2 21.7 - - + +
858I MET* 5.7 0.2 - - - +
865I THR* 5.3 4.0 - - - +
866I PRO* 3.6 34.4 - - - +
867I VAL 4.3 2.1 - - - +
868I ASP* 3.2 20.6 - - - +
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Residues in contact with LEU 694 (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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672I VAL* 4.2 16.8 - - + -
690I ILE* 4.0 23.1 - - + -
691I SER* 3.5 12.8 + - - +
692I GLU 3.2 0.4 - - - -
693I GLU* 1.3 75.7 - - + +
695I LEU* 1.3 54.8 - - - +
697I ARG* 2.9 2.8 + - - -
698I ASP 2.4 34.3 + - - -
699I PHE* 3.2 48.3 + - + -
700I TYR* 5.2 7.2 - - + +
868I ASP* 3.4 44.2 - - + +
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Residues in contact with LEU 695 (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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150G TYR* 3.1 34.1 + - + +
152G PRO* 4.8 7.2 - - + -
691I SER 4.0 1.7 + - - +
692I GLU* 2.8 24.8 + - + +
694I LEU* 1.3 77.1 - - - +
696I LYS* 1.3 61.5 + - - +
698I ASP* 3.4 18.3 + - - +
701I THR* 5.5 1.8 - - - +
832I LYS* 3.6 34.8 - - + -
833I LEU 4.9 10.5 - - - +
852I ILE* 4.5 22.4 - - + -
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Residues in contact with LYS 696 (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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45G LEU 4.8 0.6 + - - -
83G LYS* 3.8 12.1 + - - -
84G GLU* 5.5 0.5 - - - +
150G TYR* 3.9 35.4 + - + +
168G ASP* 4.3 0.7 - - - +
170G ILE* 3.6 43.8 - - + +
172G SER* 4.4 14.8 + - - -
692I GLU* 3.0 35.3 + - - +
693I GLU* 3.2 15.9 - - + +
695I LEU* 1.3 79.6 - - - +
697I ARG* 1.3 63.5 + - + +
698I ASP* 3.3 9.2 + - - +
855I VAL* 3.3 36.6 - - + +
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Residues in contact with ARG 697 (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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83G LYS* 5.8 0.4 - - - -
84G GLU* 3.8 26.5 + - - +
170G ILE* 6.0 0.9 - - + -
573I ARG* 3.0 56.6 + - - +
693I GLU* 3.1 17.7 + - + +
694I LEU* 2.9 2.9 + - - +
696I LYS* 1.3 80.6 - - + +
698I ASP* 1.3 70.8 + - - +
699I PHE* 3.1 41.7 + - + -
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Residues in contact with ASP 698 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83G LYS* 3.4 17.3 + - - +
168G ASP* 3.1 21.5 - - - +
572I ILE* 5.7 1.8 - - + +
573I ARG* 3.9 12.7 + - - +
694I LEU 2.4 17.8 + - - -
695I LEU* 3.5 10.8 - - - +
696I LYS 3.1 4.9 - - - +
697I ARG* 1.3 72.8 - - - +
699I PHE* 1.3 66.1 + - - +
700I TYR 3.6 1.1 - - - -
701I THR* 3.2 34.1 + - - +
832I LYS* 3.3 25.7 + - - +
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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