Contacts of the helix formed by residues 875 - 884 (chain D) 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 GLU 875 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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872D SER 2.9 9.9 + - - -
874D GLY* 1.3 74.9 - - - +
876D LEU* 1.3 62.7 + - - +
877D GLN 3.2 3.1 - - - -
878D TYR* 2.9 16.6 + - - +
879D TYR 3.3 10.2 + - - -
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Residues in contact with LEU 876 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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691D GLY* 5.5 6.1 - - - +
872D SER 3.2 6.2 + - - -
873D HIS* 3.0 17.0 + - - +
875D GLU* 1.3 79.6 - - - +
877D GLN* 1.3 61.8 + - - +
879D TYR* 3.8 2.4 + - - +
880D LEU* 3.6 12.5 + - - -
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Residues in contact with GLN 877 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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873D HIS 4.3 2.8 + - - -
874D GLY 4.4 3.8 + - - -
875D GLU 3.2 0.6 - - - -
876D LEU* 1.3 75.7 - - - +
878D TYR* 1.3 64.7 + - - +
880D LEU* 3.0 12.5 + - - -
881D SER* 3.2 9.7 + - - -
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Residues in contact with TYR 878 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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874D GLY 5.2 0.4 + - - -
875D GLU* 2.9 11.3 + - - +
877D GLN* 1.3 74.3 - - - +
879D TYR* 1.3 57.4 + - - +
881D SER* 2.9 20.9 + - - +
882D LEU* 3.4 7.6 + - - -
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Residues in contact with TYR 879 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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875D GLU 3.3 11.2 + - - -
876D LEU* 3.8 2.8 + - - +
878D TYR* 1.3 73.1 - - - +
880D LEU* 1.3 59.5 + - - +
882D LEU* 4.1 2.6 - - - +
883D LEU* 3.7 15.6 + - - -
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Residues in contact with LEU 880 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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876D LEU 3.6 8.0 + - - -
877D GLN 3.0 9.7 + - - -
879D TYR* 1.3 75.6 - - - +
881D SER* 1.3 56.8 + - - +
882D LEU 3.0 10.1 + - - -
883D LEU* 5.7 0.2 - - - +
884D ASN* 3.3 21.0 + - - +
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Residues in contact with SER 881 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428D CYS* 6.0 6.1 - - - +
877D GLN 3.2 7.9 + - - -
878D TYR* 2.9 10.3 + - - +
880D LEU* 1.3 74.1 - - - +
882D LEU* 1.3 56.6 + - - +
884D ASN 2.8 14.3 - - - +
885D GLN* 4.3 0.2 - - - -
886D GLN* 4.4 9.9 - - - +
887D LEU* 2.9 29.2 + - - +
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Residues in contact with LEU 882 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654D THR 4.4 8.1 - - - +
878D TYR 3.4 8.1 + - - -
879D TYR* 3.9 3.1 + - - +
880D LEU 3.0 1.0 - - - -
881D SER* 1.3 77.0 - - - +
883D LEU* 1.3 59.4 + - - +
884D ASN 2.9 17.5 + - - +
885D GLN* 4.3 2.9 - - - -
887D LEU* 5.6 0.9 - - - +
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Residues in contact with LEU 883 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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678D ASN* 6.1 0.7 - - - -
879D TYR 3.7 11.3 + - - -
880D LEU 3.7 2.6 + - - -
882D LEU* 1.3 73.0 - - - +
884D ASN* 1.3 54.8 + - - +
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Residues in contact with ASN 884 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654D THR 5.2 0.4 - - - -
880D LEU 3.3 11.7 + - - +
881D SER 2.8 17.2 - - - +
882D LEU 2.9 4.2 - - - +
883D LEU* 1.3 76.0 - - - +
885D GLN* 1.3 61.2 + - - +
886D GLN 2.7 10.2 + - - -
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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