Contacts of the helix formed by residues 995 - 1006 (chain C) in PDB entry 1SO2
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 ILE 995 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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463C 666 5.0 7.4 - - + -
895C LEU* 4.8 5.8 - - + -
898C HIS* 3.7 32.5 + - + +
899C PHE* 3.8 24.2 - - + -
938C ILE* 3.9 9.2 - - + -
991C PHE* 2.6 57.5 + - + +
993C THR 3.7 0.8 - - - -
994C HIS* 1.3 104.1 - - + +
996C VAL* 1.3 69.8 + - - +
997C GLY 3.3 0.7 - - - -
998C PRO* 3.2 5.2 - - - +
999C LEU* 3.2 21.5 + - - +
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Residues in contact with VAL 996 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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938C ILE* 3.8 33.7 - - + +
939C ASN* 5.6 0.2 - - - -
941C PRO* 3.9 23.6 - - + -
942C ALA* 5.4 3.4 - - + -
991C PHE* 3.3 39.4 + - + +
992C ILE* 4.2 9.0 - - - -
995C ILE* 1.3 72.6 - - - +
997C GLY* 1.3 63.8 + - - +
999C LEU* 3.2 6.5 - - + +
1000C CYS* 3.0 31.0 + - - -
1065C LEU* 3.9 15.5 - - + -
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Residues in contact with GLY 997 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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992C ILE* 2.9 22.3 + - - +
993C THR* 5.6 0.2 - - - -
996C VAL* 1.3 69.8 - - - +
998C PRO* 1.3 70.7 - - - +
999C LEU 3.0 1.1 - - - -
1000C CYS* 2.9 3.6 + - - +
1001C ASN* 2.9 35.4 + - - +
1065C LEU* 4.2 17.7 - - - -
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Residues in contact with PRO 998 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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898C HIS* 5.2 0.4 - - - +
899C PHE* 6.3 0.2 - - + -
902C LEU* 4.1 18.7 - - + +
992C ILE 3.5 3.6 - - - +
993C THR 3.3 22.4 - - - +
994C HIS* 3.5 20.2 - - - +
995C ILE 3.2 15.0 - - - +
997C GLY* 1.3 86.7 - - - +
999C LEU* 1.3 57.9 + - - +
1001C ASN* 3.6 12.3 + - + +
1002C SER* 3.3 23.6 + - - -
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Residues in contact with LEU 999 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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898C HIS* 4.1 18.2 - - + -
902C LEU* 4.1 22.1 - - + +
931C VAL* 4.0 24.6 - - + +
934C LYS* 4.2 13.0 - - + -
935C LEU* 3.6 42.0 - - + +
938C ILE* 3.9 20.2 - - + -
995C ILE 3.2 12.7 + - - +
996C VAL 3.2 9.6 - - - +
997C GLY 3.0 0.2 - - - -
998C PRO* 1.3 78.8 - - - +
1000C CYS* 1.3 63.7 + - - +
1002C SER* 3.4 4.9 + - - -
1003C TYR* 3.1 19.9 + - - +
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Residues in contact with CYS1000 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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935C LEU* 4.3 23.8 - - + -
942C ALA* 5.3 3.1 - - - -
996C VAL* 3.0 26.8 + - - +
997C GLY 2.9 7.0 + - - +
999C LEU* 1.3 73.2 - - - +
1001C ASN* 1.3 57.3 + - - +
1002C SER 3.0 1.8 - - - -
1003C TYR* 2.9 8.2 + - - +
1004C ASP* 2.7 35.7 + - - +
1009C LEU* 4.4 2.3 - - + +
1061C LEU* 4.5 13.5 - - + -
1062C MET* 3.8 20.9 - - - -
1065C LEU* 3.8 19.3 - - + -
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Residues in contact with ASN1001 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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997C GLY* 2.9 27.5 + - - +
998C PRO* 3.6 10.2 - - + +
1000C CYS* 1.3 75.3 - - - +
1002C SER* 1.3 57.2 + - - +
1004C ASP* 3.8 2.0 - - - +
1005C ALA* 2.9 30.3 + - - +
1062C MET* 2.8 34.0 - - - +
1065C LEU* 5.3 1.0 - - - +
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Residues in contact with SER1002 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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902C LEU* 3.5 12.0 - - - +
905C PHE* 3.4 15.2 - - - -
906C ASN* 2.4 38.1 + - - -
910C ASN* 3.0 15.0 + - - +
998C PRO 3.3 16.6 + - - -
999C LEU 3.4 5.8 - - - -
1000C CYS 3.0 0.6 - - - -
1001C ASN* 1.3 77.7 - - - +
1003C TYR* 1.3 65.4 + - - +
1005C ALA* 3.2 1.7 + - - -
1006C ALA* 3.0 18.9 + - - +
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Residues in contact with TYR1003 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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752C LEU* 4.6 10.7 - - + +
802C LEU* 3.7 21.1 - - - +
905C PHE* 4.0 14.5 - + + -
928C VAL* 4.6 3.6 - - + +
931C VAL* 3.8 28.0 - - + -
932C CYS* 3.7 35.3 - - + +
935C LEU* 4.0 19.5 - - + -
999C LEU 3.1 10.5 + - - +
1000C CYS 2.9 7.9 + - - +
1002C SER* 1.3 79.2 - - - +
1004C ASP* 1.3 58.8 + - - +
1006C ALA* 3.2 8.5 + - - +
1008C LEU* 3.1 61.5 + - + +
1009C LEU* 3.5 29.2 - - + -
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Residues in contact with ASP1004 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1000C CYS 2.7 19.0 + - - +
1001C ASN* 3.9 3.8 - - - +
1003C TYR* 1.3 70.1 - - - +
1005C ALA* 1.3 61.9 + - - +
1006C ALA 3.0 1.8 - - - -
1007C GLY* 2.8 20.2 + - - +
1009C LEU* 3.3 37.5 + - + +
1057C ILE* 4.5 18.8 - - - +
1059C CYS* 4.6 2.2 - - - -
1062C MET* 4.1 23.8 - - + +
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Residues in contact with ALA1005 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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910C ASN* 3.5 23.1 - - - +
1001C ASN 2.9 21.0 + - - +
1002C SER* 3.2 5.1 + - - +
1004C ASP* 1.3 76.5 - - - +
1006C ALA* 1.3 57.2 + - - +
1007C GLY* 3.0 3.2 + - - -
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Residues in contact with ALA1006 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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760C LEU* 5.9 0.2 - - - +
905C PHE* 3.8 18.2 - - + -
909C ALA* 4.5 14.6 - - + -
910C ASN* 3.7 9.6 + - - +
917C ILE* 5.8 1.1 - - + +
1002C SER 3.0 12.1 + - - +
1003C TYR 3.3 10.8 - - - +
1004C ASP 3.0 0.6 - - - -
1005C ALA* 1.3 77.7 - - - +
1007C GLY* 1.3 62.3 + - - +
1008C LEU* 3.0 25.6 + - + +
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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