Contacts of the helix formed by residues 692 - 697 (chain M) in PDB entry 5D4C
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 GLU 692 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150K TYR* 3.6 29.7 - - + +
30L ARG* 3.4 37.8 + - - -
691M SER* 1.3 71.8 + - - +
693M GLU* 1.3 56.2 + - - +
694M LEU 3.1 0.4 - - - -
695M LEU* 3.0 16.0 + - + +
696M LYS* 3.0 45.3 + - - +
852M ILE* 3.8 19.0 - - + +
853M LEU 2.8 19.5 + - - +
854M PRO* 3.8 10.2 - - + +
855M VAL 4.8 1.1 - - - +
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Residues in contact with GLU 693 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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691M SER* 3.0 17.1 + - - +
692M GLU* 1.3 79.8 - - - +
694M LEU* 1.3 60.4 + - - +
696M LYS* 2.7 43.0 + - - +
697M ARG* 3.0 49.5 + - - +
855M VAL* 3.4 31.5 - - + +
866M PRO* 5.1 5.4 - - + -
868M ASP* 5.1 2.7 - - - +
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Residues in contact with LEU 694 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672M VAL* 3.9 12.8 - - + -
690M ILE* 3.8 38.1 - - + -
691M SER* 3.0 12.2 + - - +
693M GLU* 1.3 79.1 - - - +
695M LEU* 1.3 64.2 + - + +
697M ARG* 3.4 26.0 - - - +
698M ASP 3.0 6.6 + - - -
699M PHE* 2.8 59.0 + - + +
700M TYR* 4.3 15.9 - - + -
833M LEU* 4.7 0.7 - - + -
868M ASP* 4.1 16.2 - - + +
869M VAL* 4.2 7.6 - - + -
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Residues in contact with LEU 695 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83K LYS* 4.8 0.3 + - - -
150K TYR* 3.6 21.3 + - + +
690M ILE* 4.8 2.7 - - + -
691M SER 4.9 0.4 - - - +
692M GLU* 3.0 20.6 + - + +
694M LEU* 1.3 81.5 - - + +
696M LYS* 1.3 66.4 + - - +
698M ASP* 3.3 7.3 + - - +
699M PHE 4.8 3.1 - - - +
832M LYS* 3.6 35.0 + - + -
833M LEU* 3.2 50.7 - - + +
852M ILE* 3.7 27.6 - - + -
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Residues in contact with LYS 696 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45K LEU 5.1 4.2 + - - -
83K LYS* 3.0 29.8 + - - -
150K TYR* 3.6 42.8 - - + +
170K VAL* 4.1 24.0 - - + +
30L ARG* 6.0 0.6 - - - +
692M GLU* 3.0 39.2 + - - +
693M GLU* 2.7 44.8 + - - +
695M LEU* 1.3 78.3 - - - +
697M ARG* 1.3 58.0 + - - +
855M VAL* 4.1 15.8 - - - +
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Residues in contact with ARG 697 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80K LEU* 5.6 0.4 - - - +
573M ARG* 3.0 30.2 + - - +
693M GLU* 3.0 56.8 + - - +
694M LEU* 3.4 18.2 - - - +
696M LYS* 1.3 75.7 - - + +
698M ASP* 1.3 67.4 + - - +
699M PHE* 3.5 36.1 - - + -
868M ASP* 2.8 37.8 + - - -
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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