Contacts of the helix formed by residues 920 - 930 (chain E) in PDB entry 6C3P
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 920 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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917E GLN 4.6 1.1 + - - -
918E ARG 3.6 4.8 + - - -
919E SER* 1.3 71.9 - - - +
921E CYS* 1.3 64.3 + - - +
923E LEU* 4.9 0.4 - - - -
924E PHE* 2.9 33.1 + - - +
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Residues in contact with CYS 921 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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919E SER* 3.4 1.9 - - - +
920E GLU* 1.3 79.6 - - - +
922E GLN* 1.3 63.9 + - + +
924E PHE* 3.3 4.6 + - - +
925E GLU* 2.9 28.9 + - - +
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Residues in contact with GLN 922 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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901E ALA* 4.8 7.0 - - - +
908E GLN* 3.9 30.4 + - - +
909E ARG* 4.0 13.3 - - - +
918E ARG* 3.8 17.8 + - - +
919E SER* 3.8 16.8 - - - -
921E CYS* 1.3 79.0 - - + +
923E LEU* 1.3 65.2 + - + +
925E GLU* 3.2 6.8 - - - +
926E HIS* 2.9 43.5 + - + +
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Residues in contact with LEU 923 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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916E PHE* 3.0 49.8 - - + +
917E GLN* 4.6 3.4 - - - +
919E SER* 3.1 29.0 + - - +
920E GLU* 4.4 0.7 - - - +
921E CYS 3.1 0.4 - - - -
922E GLN* 1.3 82.8 - - + +
924E PHE* 1.3 61.3 + - - +
926E HIS* 3.6 23.3 + - + +
927E TRP* 2.9 26.7 + - - +
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Residues in contact with PHE 924 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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920E GLU 2.9 21.0 + - - +
921E CYS* 3.8 4.5 - - - +
923E LEU* 1.3 75.2 - - - +
925E GLU* 1.3 54.1 + - - +
927E TRP* 3.0 10.5 + - + +
928E LYS* 2.7 32.1 + - - +
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Residues in contact with GLU 925 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714E GLN* 5.8 2.0 - - - +
890E LEU* 5.3 1.6 - - + +
921E CYS 2.9 13.4 + - - +
922E GLN* 3.2 14.4 - - - +
923E LEU 3.3 0.2 - - - -
924E PHE* 1.3 75.6 - - - +
926E HIS* 1.3 65.5 + - + +
928E LYS* 3.0 32.4 + - - +
929E THR 4.3 1.2 + - - -
1513E MET* 5.0 6.2 - - - +
1514E ALA* 3.2 36.4 + - + +
1517E ASN* 5.3 1.2 - - - +
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Residues in contact with HIS 926 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712E VAL* 4.7 17.9 - - + +
890E LEU* 3.4 43.2 - - + +
893E LEU* 5.3 11.2 - - + +
899E ILE* 6.2 2.0 - - + -
922E GLN* 2.9 34.2 + - + +
923E LEU* 3.6 27.1 - - + +
925E GLU* 1.3 82.7 - - + +
927E TRP* 1.3 57.1 + - - +
928E LYS 3.8 0.3 + - - -
929E THR* 4.1 5.1 + - - -
930E LEU* 3.8 11.3 + - - -
1513E MET* 5.6 0.8 - - - +
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Residues in contact with TRP 927 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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923E LEU 2.9 18.2 + - - +
924E PHE* 3.0 12.5 + - - +
926E HIS* 1.3 74.2 - - - +
928E LYS* 1.3 65.6 + - - +
929E THR 3.1 3.5 + - - -
930E LEU* 3.2 24.1 + - + +
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Residues in contact with LYS 928 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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924E PHE 2.7 13.7 + - - +
925E GLU* 3.0 24.2 + - - +
927E TRP* 1.3 76.0 - - - +
929E THR* 1.3 58.1 + - - +
1513E MET* 6.6 0.2 - - + -
1517E ASN* 4.9 13.7 - - - +
1540E HIS* 4.2 12.2 + - - -
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Residues in contact with THR 929 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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891E GLN* 6.2 3.4 - - - -
925E GLU 4.3 1.0 + - - -
926E HIS 4.1 5.2 + - - -
927E TRP 3.1 0.4 - - - -
928E LYS* 1.3 79.8 - - - +
930E LEU* 1.3 70.9 + - - +
1513E MET* 3.9 35.6 - - - -
1540E HIS* 4.3 26.2 + - - -
1581E LYS 3.8 10.8 - - - +
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Residues in contact with LEU 930 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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891E GLN* 6.2 2.7 - - - -
926E HIS 3.8 5.8 + - - -
927E TRP* 3.2 26.4 + - + +
928E LYS 5.1 0.2 - - - +
929E THR* 1.3 86.8 - - - +
1581E LYS* 3.1 30.4 - - - +
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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