Contacts of the helix formed by residues 86 - 97 (chain 1) in PDB entry 6FF7
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 ASP 86 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361 ALA* 4.5 5.6 - - - +
841 TYR* 4.1 6.5 - - - +
851 GLU* 1.3 82.6 - - + +
871 GLN* 1.3 64.0 + - - +
881 ARG* 3.3 9.9 - - + +
891 SER* 3.3 25.2 + - - +
901 THR* 3.7 2.9 + - - -
5013 LEU* 5.4 2.7 - - + -
5023 ALA* 4.7 17.0 - - + +
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Residues in contact with GLN 87 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321 TYR 5.4 3.8 - - - +
331 LYS* 5.5 2.7 - - - -
341 ASP 5.2 6.3 - - - +
351 SER 4.2 22.4 - - - +
361 ALA* 5.0 2.4 - - - +
861 ASP* 1.3 72.2 - - - +
881 ARG* 1.3 61.5 + - - +
901 THR* 3.1 11.7 + - - +
911 ILE* 3.0 24.5 + - - +
5023 ALA* 5.3 3.4 - - - +
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Residues in contact with ARG 88 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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861 ASP* 3.3 6.3 - - + +
871 GLN* 1.3 75.7 - - - +
891 SER* 1.3 59.0 + - - +
911 ILE* 3.2 10.3 + - + +
921 LEU* 2.9 28.4 + - - +
5763 PHE* 4.7 20.8 - - + +
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Residues in contact with SER 89 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591 TYR* 3.4 32.1 - - - +
601 GLY* 5.1 2.0 - - - -
841 TYR* 4.2 15.7 - - - -
861 ASP* 3.3 21.3 + - - +
871 GLN 3.2 0.4 - - - -
881 ARG* 1.3 79.3 - - - +
901 THR* 1.3 55.1 + - - +
921 LEU* 3.4 6.3 + - - +
931 ALA* 2.9 29.9 + - - +
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Residues in contact with THR 90 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351 SER 4.9 4.3 - - - -
361 ALA 4.7 18.8 - - - -
371 TRP 5.3 1.8 - - - -
381 ILE* 5.2 12.3 - - - -
841 TYR* 5.2 3.3 - - - +
861 ASP 3.7 2.8 + - - -
871 GLN* 3.1 17.2 + - - -
891 SER* 1.3 76.2 - - - +
911 ILE* 1.3 59.6 + - - +
931 ALA* 3.8 6.1 - - - +
941 VAL* 2.9 31.9 + - - +
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Residues in contact with ILE 91 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291 HIS* 5.0 16.8 - - + -
871 GLN 3.0 12.5 + - - +
881 ARG* 3.4 14.8 - - + +
901 THR* 1.3 77.3 - - - +
921 LEU* 1.3 58.1 + - - +
941 VAL* 3.8 2.7 - - - +
951 ASP* 3.0 31.7 + - - +
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Residues in contact with LEU 92 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591 TYR* 4.6 13.9 - - + -
881 ARG 2.9 16.3 + - - +
891 SER* 3.9 4.5 - - - +
911 ILE* 1.3 77.0 - - - +
931 ALA* 1.3 57.4 + - - +
951 ASP* 3.8 4.4 - - - -
961 ASN* 2.9 36.7 + - + +
5743 ASN* 5.0 19.5 - - + +
5763 PHE* 6.1 3.4 - - + -
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Residues in contact with ALA 93 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381 ILE* 5.9 6.5 - - + -
561 PHE* 6.4 2.0 - - + -
591 TYR* 5.2 6.0 - - + +
891 SER 2.9 18.8 + - - +
901 THR* 3.8 7.0 - - - +
911 ILE 3.2 0.4 - - - -
921 LEU* 1.3 77.7 - - - +
941 VAL* 1.3 58.1 + - - +
971 PHE* 3.1 39.1 + - + +
1091 VAL* 4.1 6.7 - - + +
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Residues in contact with VAL 94 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101 ILE* 6.0 1.9 - - - +
901 THR 2.9 17.0 + - - +
911 ILE* 4.2 4.0 - - - +
931 ALA* 1.3 78.1 - - - +
951 ASP* 1.3 59.7 + - - +
981 ASN* 3.8 17.3 - - - +
1091 VAL* 4.2 26.3 - - + +
1101 ASP* 5.3 6.1 - - - +
1111 HIS* 5.9 0.4 - - + +
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Residues in contact with ASP 95 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141 ASN* 6.2 6.2 - - + +
911 ILE 3.0 18.5 + - - +
921 LEU* 4.1 4.9 - - - +
941 VAL* 1.3 79.7 - - - +
961 ASN* 1.3 58.7 + - + +
981 ASN* 4.9 4.4 + - - +
5913 ASN* 5.7 1.2 - - - +
5933 PHE* 3.4 24.2 - - + +
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Residues in contact with ASN 96 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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921 LEU* 2.9 18.7 + - + +
931 ALA* 5.1 0.2 - - - -
951 ASP* 1.3 79.1 - - + +
971 PHE* 1.3 59.1 + - - +
981 ASN 3.2 8.6 + - - -
1001 ILE* 5.6 0.2 - - - +
5903 SER* 3.8 16.9 - - - -
5913 ASN* 3.2 30.4 + - - +
5933 PHE* 4.7 9.4 - - + +
5943 GLU* 5.8 5.6 - - + +
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Residues in contact with PHE 97 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561 PHE* 6.6 0.4 - - + -
931 ALA* 3.1 25.6 + - + +
961 ASN* 1.3 76.5 - - - +
981 ASN* 1.3 59.0 + - - +
991 GLY 3.9 1.0 + - - -
1001 ILE* 4.3 13.9 + - - +
1071 ILE* 5.0 6.9 - - - +
1081 ARG 5.5 0.5 - - - -
1091 VAL* 4.9 9.1 + - + +
5893 ARG 5.9 1.3 - - - +
5903 SER* 5.4 2.5 - - - +
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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