Contacts of the helix formed by residues 78 - 92 (chain 8) 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 8).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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688 LYS* 5.4 1.2 - - - +
708 PRO* 3.2 17.4 + - + +
768 ILE* 4.0 2.6 - - - +
778 THR* 1.3 80.8 - - + +
798 TRP* 1.3 62.7 + - - +
808 ASP* 3.3 17.2 + - - +
818 ASP* 3.0 45.3 + - + +
828 MET* 3.1 25.5 + - - +
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Residues in contact with TRP 79 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
768 ILE* 3.8 49.2 + - + -
778 THR 4.6 7.5 + - - -
788 ASN* 1.3 72.7 + - - +
808 ASP* 1.3 62.0 + - - +
828 MET* 3.8 4.1 - - + +
838 GLU* 3.3 25.8 + - - +
868 TRP* 4.6 5.6 - + - -
1158 ASN* 3.6 53.5 + - + -
1188 LYS* 3.8 31.3 - - + +
1198 MET* 3.8 22.7 - - + -
1228 ILE* 3.6 23.9 - - + +
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Residues in contact with ASP 80 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378 ARG* 3.3 13.6 + - - -
788 ASN* 3.3 15.0 + - - +
798 TRP* 1.3 77.1 - - - +
818 ASP* 1.3 85.9 + - - +
838 GLU* 3.6 8.1 + - - +
848 LYS* 3.3 37.2 + - - +
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Residues in contact with ASP 81 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358 VAL* 3.4 19.3 - - + +
378 ARG* 2.9 26.4 + - - -
688 LYS* 3.1 32.3 - - - +
708 PRO* 3.4 19.6 - - + +
788 ASN* 3.0 28.4 + - - +
808 ASP* 1.3 89.4 + - - +
828 MET* 1.3 60.8 + - - +
848 LYS* 3.5 10.5 - - - +
858 ILE* 3.3 17.0 + - - +
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Residues in contact with MET 82 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128 ASN* 3.5 26.0 - - + +
178 VAL* 5.8 0.7 - - + -
338 SER* 5.3 1.6 - - - +
708 PRO* 3.9 10.5 - - - -
718 ILE* 3.7 36.6 - - + -
768 ILE* 3.8 20.2 - - + -
788 ASN 3.1 16.6 + - - +
798 TRP* 4.0 6.3 - - + +
808 ASP 3.3 0.6 - - - -
818 ASP* 1.3 71.6 - - - +
838 GLU* 1.3 59.1 + - - +
848 LYS 3.0 1.3 - - - -
858 ILE* 2.7 44.7 + - + +
868 TRP* 2.9 46.3 + - + +
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Residues in contact with GLU 83 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798 TRP 3.3 16.4 + - - +
808 ASP* 3.8 7.3 - - - +
818 ASP 3.5 0.2 - - - -
828 MET* 1.3 76.2 - - - +
848 LYS* 1.3 57.1 + - - +
868 TRP* 3.9 13.3 - - + -
878 HIS* 2.9 31.7 + - + +
1228 ILE* 4.1 19.9 - - + +
1268 THR* 4.2 27.9 + - - +
1278 PHE* 3.7 16.8 - - + -
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Residues in contact with LYS 84 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358 VAL* 4.0 11.2 - - + -
378 ARG* 3.4 34.7 - - - +
518 ASP* 5.2 5.9 + - - +
528 SER* 3.5 25.6 - - - +
548 VAL* 4.4 10.6 - - + +
808 ASP* 3.3 26.3 + - - +
818 ASP* 3.5 24.9 - - - +
828 MET 3.0 0.2 - - - -
838 GLU* 1.3 78.7 - - - +
858 ILE* 1.4 61.4 + - - +
878 HIS* 3.2 7.8 + - - +
888 HIS* 3.1 22.5 + - - +
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Residues in contact with ILE 85 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178 VAL* 3.7 29.6 - - + -
318 PHE* 4.2 11.1 - - + -
338 SER* 3.9 26.9 - - - +
348 ILE 4.1 0.9 - - - +
358 VAL* 3.8 12.8 - - + -
548 VAL* 4.0 12.1 - - + -
708 PRO* 3.6 36.1 - - + -
818 ASP 3.3 7.6 + - - +
828 MET* 2.7 27.8 + - + +
848 LYS* 1.4 70.6 - - - +
868 TRP* 1.3 55.4 + - + +
888 HIS* 3.3 4.0 + - - +
898 THR* 2.7 32.3 + - - +
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Residues in contact with TRP 86 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108 CYS* 4.0 16.3 - - - -
128 ASN* 2.9 37.6 + - - +
768 ILE* 4.2 10.1 - - + -
798 TRP* 4.6 2.2 - + - -
828 MET* 2.9 37.6 + - + +
838 GLU* 3.8 17.7 - - - +
858 ILE* 1.3 75.5 - - + +
878 HIS* 1.3 60.4 + - - +
898 THR* 2.8 23.2 + - - -
908 PHE* 3.0 27.2 + + + -
1058 LEU* 4.4 5.1 - - + +
1198 MET* 3.9 30.1 - - + -
1228 ILE* 4.1 24.9 - - + -
1238 MET* 3.3 29.1 - - + +
1278 PHE* 3.6 19.5 - + + -
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Residues in contact with HIS 87 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838 GLU* 2.9 19.7 + - + +
848 LYS* 3.2 8.7 + - + +
868 TRP* 1.3 76.4 - - - +
888 HIS* 1.3 59.5 + - - +
908 PHE* 4.5 0.2 - - - -
918 TYR* 2.9 65.7 + + + +
928 ASN* 4.6 6.2 + - - -
1278 PHE* 3.9 17.9 - - + -
567G LYS* 3.5 28.3 + - - -
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Residues in contact with HIS 88 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318 PHE* 3.6 21.3 - + - -
548 VAL* 3.9 37.9 + - + +
558 GLY* 5.2 0.6 - - - -
848 LYS 3.1 9.4 + - - +
858 ILE 3.4 8.3 - - - +
878 HIS* 1.3 80.4 - - - +
898 THR* 1.3 62.9 + - - +
928 ASN* 2.8 54.3 + - + -
938 GLU* 2.9 41.1 + - + -
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Residues in contact with THR 89 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108 CYS* 4.7 9.2 - - + -
178 VAL* 4.5 6.9 - - + +
198 ALA* 3.6 31.4 - - + -
318 PHE* 3.7 20.9 - - + -
858 ILE* 2.7 26.6 + - - +
868 TRP* 2.8 14.7 + - - -
888 HIS* 1.3 76.6 - - - +
908 PHE* 1.3 62.8 + - + -
938 GLU* 3.4 8.2 - - + +
948 LEU* 2.9 36.3 + - + +
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Residues in contact with PHE 90 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88 LEU* 4.0 27.8 - - + -
108 CYS* 5.8 6.1 - - + -
868 TRP* 3.0 29.0 + + + +
878 HIS* 4.1 2.0 - - - +
898 THR* 1.3 83.2 - - + +
918 TYR* 1.3 63.2 + + + +
948 LEU* 3.5 5.0 - - + -
958 ARG 2.8 26.3 + - - -
968 VAL* 3.1 23.6 + - + +
988 PRO* 3.9 27.1 - - + -
1038 THR* 4.4 16.6 - - + -
1058 LEU* 6.1 0.2 - - + -
1238 MET* 4.1 24.5 - - + -
1278 PHE* 3.6 44.6 - + - -
1298 VAL* 4.8 0.9 - - + -
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Residues in contact with TYR 91 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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878 HIS* 2.9 62.4 + + - +
908 PHE* 1.3 82.8 - - + +
928 ASN* 1.3 71.6 + - - +
958 ARG* 3.4 17.3 - - - +
968 VAL 3.8 12.8 - - - -
978 ALA* 4.6 5.2 - - + -
988 PRO* 3.7 34.6 - - + +
998 GLU* 4.1 10.6 + - - -
1278 PHE* 4.9 9.6 + + - -
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Residues in contact with ASN 92 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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878 HIS* 4.2 6.9 + - - +
888 HIS* 2.8 49.6 + - + +
918 TYR* 1.3 93.1 + - - +
938 GLU* 1.3 69.7 + - - +
958 ARG* 3.3 17.2 - - - +
567G LYS* 6.0 1.6 - - - +
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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