Contacts of the helix formed by residues 1028 - 1038 (chain G) in PDB entry 1F66
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 PRO1028 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1020G SER* 4.6 4.9 - - - -
1026G GLN 3.7 0.8 - - - -
1027G PHE* 1.3 89.6 - - + +
1029G VAL* 1.3 55.8 + - - +
1030G GLY 3.3 2.5 - - - -
1031G ARG* 3.1 28.5 + - + +
1032G ILE* 2.7 40.1 + - + +
1434H TYR* 4.2 8.5 - - + -
1437H TYR* 3.5 52.9 - - + +
176J A 5.0 3.1 - - - +
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Residues in contact with VAL1029 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1019G ARG* 3.8 31.0 - - + +
1020G SER* 3.3 29.2 - - - +
1023G ALA* 4.8 0.2 - - + -
1025G LEU* 4.3 11.4 - - + -
1027G PHE 3.1 8.0 + - - +
1028G PRO* 1.3 70.6 - - - +
1030G GLY* 1.3 64.7 + - - +
1032G ILE* 3.3 5.9 + - - +
1033G HIS* 2.9 23.9 + - - +
1051G ALA* 3.7 13.5 - - + +
1052G VAL* 3.7 28.0 - - + +
1055G ALA* 4.1 14.1 - - + -
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Residues in contact with GLY1030 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1019G ARG* 4.5 9.4 - - - +
1020G SER* 5.3 0.4 - - - +
1028G PRO 3.3 0.8 - - - -
1029G VAL* 1.3 79.2 - - - +
1031G ARG* 1.3 62.2 + - - +
1033G HIS* 3.2 6.7 + - - +
1034G ARG* 3.1 19.6 + - - +
176J A 3.6 22.1 + - - -
177J G 4.5 17.3 + - - -
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Residues in contact with ARG1031 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1028G PRO* 3.1 23.0 + - + +
1030G GLY* 1.3 75.6 - - - +
1032G ILE* 1.3 64.9 + - - +
1033G HIS 3.2 0.2 + - - -
1034G ARG* 3.2 9.0 + - - +
1035G HIS* 3.0 42.6 + - + +
1432H GLU* 3.1 36.8 + - - +
1433H SER 2.7 32.7 + - - +
1434H TYR* 4.6 14.7 - - - +
1437H TYR* 3.6 24.4 + - - -
121I G 3.1 16.2 + - - -
122I G 2.7 22.2 + - - -
175J A 5.8 0.2 - - - +
176J A 3.5 25.7 + - - +
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Residues in contact with ILE1032 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1027G PHE* 5.2 1.6 - - + -
1028G PRO* 2.7 31.2 + - + +
1029G VAL* 3.7 6.1 - - - +
1031G ARG* 1.3 72.2 - - + +
1033G HIS* 1.3 63.5 + - - +
1035G HIS* 3.1 8.6 + - + +
1036G LEU* 3.0 22.6 + - + +
1051G ALA* 4.0 13.7 - - - +
1054G SER* 3.9 19.5 - - - -
1055G ALA* 4.3 15.5 - - + -
1058G LEU* 4.0 13.7 - - + -
1434H TYR* 3.0 41.1 - - + +
1467H PHE* 3.8 23.1 - - + -
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Residues in contact with HIS1033 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1019G ARG* 2.8 38.3 + - - +
1029G VAL 2.9 13.4 + - - +
1030G GLY 3.3 9.6 - - - +
1032G ILE* 1.3 72.9 - - - +
1034G ARG* 1.3 70.6 + - - +
1036G LEU* 3.0 16.8 + - - +
1037G LYS* 3.1 45.5 + - + +
1046G VAL* 4.0 26.8 + - + +
1047G GLY 4.2 6.5 + - - -
1048G ALA* 4.7 2.0 - - - -
1051G ALA* 3.6 17.7 - - + +
112I T 5.0 4.3 + - - -
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Residues in contact with ARG1034 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1030G GLY 3.1 8.5 + - - +
1031G ARG* 3.2 10.7 + - - +
1033G HIS* 1.3 83.2 + - - +
1035G HIS* 1.3 93.7 + - - +
1037G LYS* 2.9 24.9 + - - +
1038G SER* 3.6 17.9 + - - +
1432H GLU* 5.1 7.3 + - - -
175J A 3.7 39.2 + - - -
176J A 4.6 12.1 - - - +
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Residues in contact with HIS1035 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1031G ARG* 3.0 27.5 + - + +
1032G ILE* 3.5 8.5 - - - +
1034G ARG* 1.3 102.5 + - - +
1036G LEU* 1.3 61.8 + - - +
1038G SER* 3.2 10.1 + - - -
1039G ARG* 3.2 45.5 + - - +
1432H GLU* 3.5 27.3 + - - +
1434H TYR* 3.9 23.0 - + - -
1464H ASN* 6.1 0.7 - - - -
1467H PHE* 3.8 12.6 - + + -
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Residues in contact with LEU1036 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1032G ILE* 3.0 12.5 + - + +
1033G HIS 3.0 8.0 + - - +
1035G HIS* 1.3 71.4 - - - +
1037G LYS* 1.3 61.9 + - - +
1038G SER 3.0 6.5 + - - -
1039G ARG* 3.2 19.4 + - + +
1040G THR* 4.0 2.8 + - - -
1046G VAL* 3.9 32.8 - - + +
1050G ALA* 4.4 6.1 - - + -
1051G ALA* 4.3 18.4 - - + +
1054G SER* 4.0 18.6 - - - +
1467H PHE* 3.5 27.8 - - + -
1471H ALA* 3.6 24.9 - - + -
1486H ILE* 4.8 15.1 - - + +
1491H ILE* 4.6 9.2 - - + -
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Residues in contact with LYS1037 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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842C SER* 2.4 28.8 + - - -
1033G HIS* 3.1 36.7 + - + +
1034G ARG* 2.9 13.4 + - - +
1036G LEU* 1.3 76.0 - - - +
1038G SER* 1.3 51.7 + - - +
1039G ARG 3.5 0.2 - - - -
1040G THR* 3.3 11.6 - - - +
1044G GLY 4.4 11.3 + - - -
1046G VAL* 3.8 15.7 - - + +
112I T 2.6 44.4 + - - -
113I A 5.0 4.5 + - - -
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Residues in contact with SER1038 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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841C THR* 2.6 28.4 + - - +
842C SER* 3.6 8.5 + - - -
1034G ARG* 3.6 17.9 + - - +
1035G HIS* 3.2 11.6 + - - -
1036G LEU 3.0 0.6 - - - -
1037G LYS* 1.3 81.1 + - - +
1039G ARG* 1.3 60.3 + - - +
1040G THR 3.1 5.6 - - - -
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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