Contacts of the helix formed by residues 874 - 888 (chain N) in PDB entry 6AH0
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 LEU 874 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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873N ASP* 1.3 73.3 - - - +
875N GLY* 1.3 60.7 + - - +
876N ASP 3.1 4.0 - - - +
877N ALA* 2.8 23.8 + - - +
878N TRP 3.6 3.5 + - - -
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Residues in contact with GLY 875 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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874N LEU* 1.3 71.4 - - - +
876N ASP* 1.3 63.3 + - - +
877N ALA 2.8 2.1 + - - -
878N TRP* 3.0 12.8 + - - -
879N ALA* 3.7 6.6 + - - -
906N PRO* 6.0 4.3 - - - -
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Residues in contact with ASP 876 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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874N LEU* 3.1 1.6 - - - +
875N GLY* 1.3 76.9 - - - +
877N ALA* 1.3 58.9 + - - +
879N ALA* 4.1 4.7 + - - -
880N PHE* 4.4 4.7 + - - -
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Residues in contact with ALA 877 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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845N LEU* 6.5 0.4 - - - +
864N PHE* 6.1 1.8 - - - +
873N ASP* 6.0 1.6 - - - +
874N LEU* 2.8 19.7 + - - +
876N ASP* 1.3 70.3 - - - +
878N TRP* 1.3 64.9 + - - +
879N ALA 3.1 3.9 + - - -
880N PHE* 3.2 11.4 + - - -
881N PHE* 3.3 9.5 + - - -
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Residues in contact with TRP 878 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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874N LEU 3.6 5.3 + - - -
875N GLY* 3.0 8.1 + - - -
877N ALA* 1.3 75.0 - - - +
879N ALA* 1.3 61.7 + - - +
881N PHE* 3.4 3.6 + - - +
882N TYR* 3.2 18.5 + - - -
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Residues in contact with ALA 879 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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875N GLY 3.7 8.0 + - - -
876N ASP 4.1 2.6 + - - -
877N ALA 3.1 1.6 - - - -
878N TRP* 1.3 78.7 - - - +
880N PHE* 1.3 62.4 + - - +
882N TYR* 3.5 1.4 + - - -
883N LYS* 3.2 17.8 + - - -
915N VAL 6.1 2.2 - - - -
916N SER* 5.6 10.3 - - - +
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Residues in contact with PHE 880 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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876N ASP 4.4 4.4 + - - -
877N ALA 3.2 7.2 + - - -
879N ALA* 1.3 76.3 - - - +
881N PHE* 1.3 62.6 + - - +
883N LYS* 3.2 2.1 + - - +
884N PHE* 2.9 21.0 + - - -
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Residues in contact with PHE 881 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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877N ALA 3.3 11.7 + - - -
878N TRP* 3.4 5.1 + - - +
879N ALA 3.2 1.0 - - - -
880N PHE* 1.3 74.1 - - - +
882N TYR* 1.3 63.5 + - - +
884N PHE* 2.9 12.8 + - - -
885N GLU* 3.3 9.4 + - - -
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Residues in contact with TYR 882 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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878N TRP 3.2 12.8 + - - -
879N ALA 4.0 2.0 - - - -
881N PHE* 1.3 73.6 - - - +
883N LYS* 1.3 62.1 + - - +
885N GLU* 3.7 1.8 + - - +
886N LEU* 3.2 18.2 + - - -
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Residues in contact with LYS 883 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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879N ALA 3.2 10.9 + - - -
880N PHE* 3.2 7.3 + - - +
881N PHE 3.1 1.0 - - - -
882N TYR* 1.3 76.5 - - - +
884N PHE* 1.3 63.0 + - - +
886N LEU* 3.2 10.3 + - - +
887N GLN* 3.3 9.4 + - - -
916N SER 6.1 1.1 - - - -
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Residues in contact with PHE 884 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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857N ILE* 5.4 12.7 - - - +
880N PHE 2.9 14.1 + - - -
881N PHE 2.9 3.9 + - - -
883N LYS* 1.3 77.5 - - - +
885N GLU* 1.3 57.1 + - - +
887N GLN* 2.9 18.4 + - - +
888N HIS* 3.1 10.9 + - - -
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Residues in contact with GLU 885 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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881N PHE 3.3 11.4 + - - -
882N TYR* 3.7 2.7 + - - +
884N PHE* 1.3 75.4 - - - +
886N LEU* 1.3 60.4 + - - +
887N GLN 3.4 0.2 + - - -
888N HIS* 3.6 17.8 + - - +
892N GLU 4.6 11.4 + - - +
893N GLN 6.1 2.5 - - - +
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Residues in contact with LEU 886 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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882N TYR 3.2 14.8 + - - -
883N LYS* 3.6 5.2 - - - +
884N PHE 3.1 1.2 - - - -
885N GLU* 1.3 76.9 - - - +
887N GLN* 1.3 62.5 + - - +
888N HIS 4.5 1.2 - - - -
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Residues in contact with GLN 887 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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883N LYS 3.3 7.7 + - - -
884N PHE* 2.9 9.1 + - - +
886N LEU* 1.3 77.5 - - - +
888N HIS* 1.3 63.1 + - - +
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Residues in contact with HIS 888 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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884N PHE 3.1 12.3 + - - -
885N GLU* 3.7 15.3 - - - +
886N LEU 4.5 1.3 - - - -
887N GLN* 1.3 79.0 - - - +
892N GLU 5.5 6.5 - - - -
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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