Contacts of the helix formed by residues 928 - 939 (chain U) 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 THR 928 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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909U LEU* 5.7 3.8 - - - -
926U SER 4.0 1.2 + - - -
927U TYR* 1.3 75.5 - - - +
929U CYS* 1.3 61.5 + - - +
930U GLU* 3.1 12.6 - - - -
931U THR* 3.9 12.4 - - - -
932U ALA* 2.9 29.4 + - - +
1015U GLU* 6.1 4.7 - - - -
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Residues in contact with CYS 929 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140M LEU* 3.8 8.7 - - - +
928U THR* 1.3 75.3 - - - +
930U GLU* 1.3 62.4 + - - +
932U ALA* 3.6 5.6 - - - +
933U GLY* 3.1 17.0 + - - -
1008U LEU* 3.3 34.3 - - + +
1009U GLU* 5.4 1.1 - - - -
1011U PHE* 4.6 2.5 - - + +
1012U ARG* 3.6 25.4 - - + +
1015U GLU* 5.5 6.6 - - + +
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Residues in contact with GLU 930 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139M ALA* 3.0 4.3 - - - +
140M LEU* 2.3 57.7 + - - +
141M PRO* 3.4 6.7 - - + -
928U THR* 3.1 7.7 - - - -
929U CYS* 1.3 80.0 - - - +
931U THR* 1.3 56.9 + - - +
934U TYR* 4.1 0.3 - - - +
1012U ARG* 5.3 1.5 - - - +
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Residues in contact with THR 931 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105M PHE* 3.4 4.0 - - - +
139M ALA* 3.0 3.4 - - - +
141M PRO* 6.1 0.7 - - - -
927U TYR* 4.7 8.5 - - - -
928U THR* 3.4 18.4 + - - -
930U GLU* 1.3 75.7 - - - +
932U ALA* 1.3 60.9 + - - +
934U TYR* 3.7 5.9 - - - +
935U PHE* 2.9 27.7 + - - +
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Residues in contact with ALA 932 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138M ARG 1.9 26.6 - - - +
139M ALA* 2.8 3.1 - - - -
909U LEU* 6.2 2.5 - - + -
912U VAL* 4.9 13.5 - - + -
927U TYR* 4.5 12.2 - - + +
928U THR 2.9 19.3 + - - +
929U CYS* 3.6 9.4 - - - +
931U THR* 1.3 74.8 - - - +
933U GLY* 1.3 48.0 - - - +
935U PHE* 3.2 8.1 + - - +
936U PHE* 2.9 11.8 + - - +
1005U PHE* 5.3 3.0 - - + +
1008U LEU* 4.7 14.4 - - + -
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Residues in contact with GLY 933 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137M LEU 3.9 2.5 - - - -
138M ARG* 1.5 35.0 + - - +
139M ALA* 0.5 267.2 + - - +
140M LEU* 2.6 4.2 - - - +
929U CYS 3.1 8.7 + - - -
932U ALA* 1.3 64.7 - - - +
934U TYR* 1.3 23.3 + - - -
937U LEU* 3.3 1.2 + - - +
1009U GLU* 6.5 0.9 - - - -
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Residues in contact with TYR 934 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105M PHE* 3.2 2.0 - - + -
106M MET 3.4 22.4 - - - +
110M PRO* 4.6 16.6 - - + -
136M ALA 5.2 0.4 - - - -
139M ALA* 0.5 120.2 - - + +
140M LEU 4.6 0.7 - - - +
141M PRO* 4.8 13.7 - - + -
930U GLU 4.1 3.8 - - - +
931U THR* 3.7 10.1 - - - +
933U GLY 1.3 16.8 - - - +
935U PHE* 1.3 55.7 + - - +
937U LEU* 3.4 2.4 + - - +
938U TYR* 3.0 32.4 + - - +
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Residues in contact with PHE 935 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104M VAL* 2.0 32.0 - - + +
105M PHE* 1.6 51.8 - - + +
138M ARG* 2.6 3.6 - - - -
139M ALA* 2.7 8.3 - - - +
912U VAL* 6.1 3.8 - - + -
931U THR 3.3 8.7 - - - +
932U ALA* 3.4 9.2 - - - +
934U TYR* 1.3 65.4 - - - +
936U PHE* 1.3 56.3 + - - +
939U GLN* 2.8 14.0 + - - +
940U VAL* 3.3 2.2 + - - -
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Residues in contact with PHE 936 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134M ASP 4.8 1.3 - - - +
137M LEU 3.6 3.6 - - - +
138M ARG* 1.2 170.4 - - + +
932U ALA 2.9 4.0 + - - +
935U PHE* 1.3 69.8 - - - +
937U LEU* 1.3 23.2 + - - -
940U VAL* 3.1 16.4 + - + +
941U MET* 2.7 34.5 + - - +
1005U PHE* 4.2 16.8 - - + -
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Residues in contact with LEU 937 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110M PRO* 4.7 7.0 - - + -
113M TRP* 4.6 4.7 - - + +
135M ARG* 1.2 102.0 - - - +
136M ALA* 2.3 47.6 - - - +
138M ARG* 1.3 62.7 - - + +
933U GLY 4.0 0.2 - - - +
934U TYR 4.0 4.9 - - - +
936U PHE 1.3 28.6 - - - +
938U TYR* 1.3 59.8 + - - +
941U MET* 3.7 2.4 - - - +
942U SER* 3.8 5.2 + - - -
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Residues in contact with TYR 938 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98M CYS 4.0 0.3 - - - +
99M HIS* 2.9 28.9 - - - +
102M ALA* 3.5 7.2 - - + +
106M MET 4.3 5.4 - - - +
109M MET* 1.7 57.5 - - + +
110M PRO 3.5 0.2 - - - -
113M TRP* 5.5 0.2 - - - -
934U TYR 3.0 18.8 + - - +
935U PHE 4.4 0.2 - - - +
937U LEU* 1.3 78.4 - - - +
939U GLN* 1.3 57.3 + - - +
942U SER* 3.6 0.2 - - - -
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Residues in contact with GLN 939 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99M HIS* 3.2 17.1 - - - +
100M GLU* 4.9 0.2 - - - -
102M ALA* 3.7 3.6 - - - +
103M PHE 1.8 37.2 - - - +
104M VAL* 1.8 42.8 + - - +
105M PHE 3.2 0.2 - - - +
935U PHE 2.8 9.1 + - - -
938U TYR* 1.3 74.1 - - - +
940U VAL* 1.3 59.9 + - - +
943U ARG* 3.5 15.8 + - - +
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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