Contacts of the helix formed by residues 78 - 92 (chain 4) in PDB entry 1O1F
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 ASN 78 (chain 4).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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684 LYS* 5.5 0.8 - - - +
704 PRO* 3.2 16.6 + - + +
764 ILE* 4.1 2.2 - - - -
774 THR* 1.3 80.3 - - + +
794 TRP* 1.3 62.8 + - - +
804 ASP* 3.3 17.0 + - - +
814 ASP* 3.0 45.6 + - + +
824 MET* 3.1 25.5 + - - +
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Residues in contact with TRP 79 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
764 ILE* 3.8 48.5 + - + -
774 THR 4.6 7.3 + - - -
784 ASN* 1.3 74.0 + - - +
804 ASP* 1.3 62.3 + - - +
824 MET* 3.8 3.9 - - + +
834 GLU* 3.3 25.8 + - - +
864 TRP* 4.6 6.1 - + - -
1154 ASN* 3.6 53.1 + - + -
1184 LYS* 3.8 31.6 - - + +
1194 MET* 3.8 23.3 - - + -
1224 ILE* 3.6 23.4 - - + +
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Residues in contact with ASP 80 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374 ARG* 3.3 13.7 + - - -
784 ASN* 3.3 15.1 + - - +
794 TRP* 1.3 76.7 - - - +
814 ASP* 1.3 86.0 + - - +
834 GLU* 3.6 8.3 + - - +
844 LYS* 3.3 37.5 + - - +
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Residues in contact with ASP 81 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354 VAL* 3.4 19.2 - - + +
374 ARG* 2.9 26.8 + - - -
684 LYS* 3.1 32.4 - - - +
704 PRO* 3.4 19.2 - - + +
784 ASN* 3.0 28.2 + - - +
804 ASP* 1.3 89.2 + - - +
824 MET* 1.3 61.4 + - - +
844 LYS* 3.5 10.6 - - - +
854 ILE* 3.3 16.6 + - - +
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Residues in contact with MET 82 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124 ASN* 3.5 26.7 - - + +
174 VAL* 5.8 0.9 - - + -
334 SER* 5.3 1.6 - - - +
704 PRO* 3.9 11.2 - - - +
714 ILE* 3.7 36.6 - - + -
764 ILE* 3.8 20.2 - - + -
784 ASN 3.1 16.4 + - - +
794 TRP* 4.0 6.3 - - + +
804 ASP 3.3 0.6 - - - -
814 ASP* 1.3 71.2 - - - +
834 GLU* 1.3 59.2 + - - +
844 LYS 3.0 0.9 - - - -
854 ILE* 2.7 44.4 + - + +
864 TRP* 2.9 45.5 + - + +
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Residues in contact with GLU 83 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794 TRP 3.3 17.0 + - - +
804 ASP* 3.8 7.7 - - - +
814 ASP 3.5 0.2 - - - -
824 MET* 1.3 75.8 - - - +
844 LYS* 1.3 57.2 + - - +
864 TRP* 3.5 13.3 + - + -
874 HIS* 2.9 31.9 + - + +
1224 ILE* 4.1 20.3 - - + +
1264 THR* 4.2 28.1 + - - +
1274 PHE* 3.7 16.2 - - + -
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Residues in contact with LYS 84 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354 VAL* 4.0 10.8 - - + -
374 ARG* 3.4 34.0 - - - +
514 ASP* 5.2 5.5 + - - +
524 SER* 3.5 26.0 - - - +
544 VAL* 4.4 10.3 - - + +
804 ASP* 3.3 27.0 + - - +
814 ASP* 3.5 25.4 - - - +
824 MET 3.0 0.4 - - - -
834 GLU* 1.3 78.9 - - - +
854 ILE* 1.4 62.0 + - - +
874 HIS* 3.2 8.5 + - + +
884 HIS* 3.1 22.2 + - - +
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Residues in contact with ILE 85 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174 VAL* 3.7 29.6 - - + -
314 PHE* 4.2 11.1 - - + -
334 SER* 3.9 27.4 - - - +
344 ILE 4.1 0.9 - - - +
354 VAL* 3.8 12.1 - - + -
544 VAL* 4.0 13.0 - - + -
704 PRO* 3.6 36.8 - - + -
814 ASP 3.3 7.6 + - - +
824 MET* 2.7 26.8 + - + +
844 LYS* 1.4 70.4 - - - +
864 TRP* 1.3 55.4 + - + +
884 HIS* 3.3 4.0 + - - +
894 THR* 2.7 32.5 + - - +
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Residues in contact with TRP 86 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104 CYS* 4.0 16.1 - - - -
124 ASN* 2.9 37.0 + - - +
764 ILE* 4.2 10.5 - - + -
794 TRP* 4.6 2.5 - + - -
824 MET* 2.9 39.5 + - + +
834 GLU* 3.8 18.2 - - - +
854 ILE* 1.3 75.3 - - + +
874 HIS* 1.3 60.5 + - - +
894 THR* 2.8 22.7 + - - -
904 PHE* 3.0 27.3 + + + -
1054 LEU* 4.4 4.7 - - + +
1194 MET* 3.9 30.1 - - + -
1224 ILE* 4.1 24.5 - - + -
1234 MET* 3.3 29.7 - - + +
1274 PHE* 3.6 19.7 - + + -
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Residues in contact with HIS 87 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834 GLU* 2.9 19.7 + - + +
844 LYS* 3.2 9.2 + - + +
864 TRP* 1.3 77.0 - - - +
884 HIS* 1.3 59.8 + - - +
904 PHE* 4.5 0.2 - - - -
914 TYR* 2.9 65.9 + + + +
924 ASN* 4.6 6.6 + - - -
1274 PHE* 3.9 17.2 - - + -
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Residues in contact with HIS 88 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314 PHE* 3.6 21.4 - + - -
544 VAL* 3.9 39.0 + - + +
554 GLY* 5.2 0.6 - - - -
564 ASP 5.9 0.2 + - - -
844 LYS 3.1 10.0 + - - +
854 ILE 3.4 8.5 - - - +
874 HIS* 1.3 80.0 - - - +
894 THR* 1.3 63.6 + - - +
924 ASN* 2.8 54.6 + - + -
934 GLU* 2.9 42.0 + - + -
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Residues in contact with THR 89 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104 CYS* 4.7 9.6 - - + -
174 VAL* 4.5 7.3 - - + +
194 ALA* 3.6 31.0 - - + -
314 PHE* 3.7 20.7 - - + -
854 ILE* 2.7 26.4 + - - +
864 TRP* 2.8 14.5 + - - -
884 HIS* 1.3 76.5 - - - +
904 PHE* 1.3 62.5 + - + -
934 GLU* 3.4 8.2 - - + +
944 LEU* 2.9 36.4 + - + +
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Residues in contact with PHE 90 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84 LEU* 4.0 28.5 - - + -
104 CYS* 5.8 6.1 - - + -
864 TRP* 3.0 27.7 + + + -
874 HIS* 4.1 2.2 - - - +
894 THR* 1.3 83.3 - - + +
914 TYR* 1.3 62.2 + + + +
944 LEU* 3.5 4.9 - - + -
954 ARG 2.8 26.3 + - - -
964 VAL* 3.1 24.1 + - + +
984 PRO* 3.9 26.9 - - + -
1034 THR* 4.4 15.9 - - + -
1054 LEU* 6.1 0.2 - - + -
1234 MET* 4.1 24.5 - - + -
1274 PHE* 3.6 44.9 - + - -
1294 VAL* 4.8 0.9 - - + -
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Residues in contact with TYR 91 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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874 HIS* 2.9 60.8 + + - +
904 PHE* 1.3 82.2 - - + +
924 ASN* 1.3 72.1 + - - +
954 ARG* 3.4 16.9 - - - +
964 VAL 3.8 12.6 - - - -
974 ALA* 4.6 4.9 - - + -
984 PRO* 3.7 35.2 - - + +
994 GLU* 4.2 10.6 + - - -
1274 PHE* 4.9 9.3 + + - -
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Residues in contact with ASN 92 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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874 HIS* 4.2 7.4 + - - +
884 HIS* 2.8 50.3 + - + +
914 TYR* 1.3 93.5 + - - +
934 GLU* 1.3 68.9 + - - +
954 ARG* 3.3 17.6 + - - +
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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