Contacts of the helix formed by residues 995 - 1006 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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462B 666 3.9 15.0 - - + -
895B LEU* 4.1 11.7 - - + -
898B HIS* 3.4 37.2 + - + +
899B PHE* 5.2 4.9 - - + -
938B ILE* 3.9 14.6 - - + -
991B PHE* 3.0 52.6 + - + +
993B THR 3.7 0.6 - - - -
994B HIS* 1.3 95.9 - - + +
996B VAL* 1.3 68.9 + - - +
997B GLY 3.4 0.7 - - - -
998B PRO* 3.6 1.8 - - - +
999B LEU* 3.3 21.3 + - - +
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Residues in contact with VAL 996 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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935B LEU* 6.3 1.3 - - + -
938B ILE* 3.9 32.3 - - + +
939B ASN* 5.7 0.4 - - - -
941B PRO* 3.7 19.7 - - + -
942B ALA* 5.2 3.8 - - + -
991B PHE* 3.0 41.9 + - + +
992B ILE* 4.1 7.4 - - - -
995B ILE* 1.3 71.3 - - - +
997B GLY* 1.3 67.0 + - - +
999B LEU* 3.0 6.1 + - - +
1000B CYS* 3.0 31.5 + - - -
1065B LEU* 3.9 21.1 - - + -
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Residues in contact with GLY 997 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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992B ILE* 2.7 23.4 + - - +
996B VAL* 1.3 72.3 - - - +
998B PRO* 1.3 67.8 - - - +
1000B CYS* 3.0 4.5 + - - +
1001B ASN* 2.9 33.8 + - - -
1065B LEU* 4.3 15.7 - - - -
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Residues in contact with PRO 998 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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899B PHE* 5.7 1.1 - - + -
902B LEU* 3.8 18.0 - - + +
993B THR 3.2 24.5 - - - +
994B HIS* 3.2 27.8 - - - +
995B ILE 3.6 6.5 - - - +
997B GLY* 1.3 86.4 - - - +
999B LEU* 1.3 55.1 + - - +
1001B ASN* 3.9 11.8 - - + +
1002B SER* 2.9 30.2 + - - -
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Residues in contact with LEU 999 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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898B HIS* 3.9 16.6 - - + -
902B LEU* 3.9 19.7 - - + +
931B VAL* 3.6 30.5 - - + +
934B LYS* 3.8 17.7 - - + +
935B LEU* 3.8 34.3 - - + +
938B ILE* 3.8 23.3 - - + -
995B ILE 3.3 10.9 + - - +
996B VAL* 3.0 11.2 + - + +
998B PRO* 1.3 78.8 - - - +
1000B CYS* 1.3 58.6 + - - +
1002B SER* 3.6 0.9 - - - -
1003B TYR* 3.1 22.7 + - + +
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Residues in contact with CYS1000 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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935B LEU* 4.5 19.7 - - + -
942B ALA* 4.9 2.7 - - - -
996B VAL* 3.0 26.4 + - - -
997B GLY 3.0 6.4 + - - +
999B LEU* 1.3 74.6 - - - +
1001B ASN* 1.3 57.1 + - - +
1002B SER 2.9 1.3 - - - -
1003B TYR* 2.8 8.0 + - - +
1004B ASP* 2.6 38.0 + - - +
1009B LEU* 4.3 1.2 - - + +
1061B LEU* 3.9 17.0 - - + -
1062B MET* 3.8 19.5 - - + -
1065B LEU* 3.5 22.7 - - + -
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Residues in contact with ASN1001 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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997B GLY* 2.9 29.6 + - - +
998B PRO* 3.9 8.9 - - + +
1000B CYS* 1.3 74.6 - - - +
1002B SER* 1.3 58.3 + - - +
1004B ASP* 3.4 2.4 + - - +
1005B ALA* 3.0 30.8 + - - +
1062B MET* 3.2 26.7 - - - +
1065B LEU* 5.5 1.4 - - - +
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Residues in contact with SER1002 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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902B LEU* 3.4 22.6 - - - +
905B PHE* 3.5 9.6 - - - -
906B ASN* 2.6 33.8 + - - -
910B ASN* 2.9 25.4 + - - +
998B PRO 2.9 21.8 + - - -
999B LEU 3.6 1.6 - - - -
1000B CYS 2.9 0.4 - - - -
1001B ASN* 1.3 78.1 - - - +
1003B TYR* 1.3 61.4 + - - +
1005B ALA* 3.6 2.0 + - - -
1006B ALA* 3.3 8.0 + - - +
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Residues in contact with TYR1003 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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752B LEU* 4.3 13.1 + - + +
802B LEU* 4.2 16.6 - - - +
905B PHE* 4.2 13.0 - + - -
928B VAL* 4.6 4.0 + - + -
931B VAL* 3.4 29.2 - - + -
932B CYS* 3.9 36.6 - - + +
935B LEU* 3.9 20.0 - - + -
999B LEU 3.1 17.2 + - - +
1000B CYS* 2.8 7.5 + - - +
1002B SER* 1.3 70.4 - - - +
1004B ASP* 1.3 66.1 + - - +
1006B ALA* 3.4 13.4 - - - +
1007B GLY 3.5 3.1 + - - -
1008B LEU* 3.6 37.5 + - + -
1009B LEU* 3.3 39.0 + - + -
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Residues in contact with ASP1004 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1000B CYS 2.6 16.7 + - - +
1001B ASN* 3.7 7.2 - - - +
1003B TYR* 1.3 72.2 - - - +
1005B ALA* 1.3 58.1 + - - +
1006B ALA 2.9 1.8 - - - -
1007B GLY* 2.4 32.4 + - - -
1009B LEU* 3.4 34.3 + - + +
1059B CYS* 4.7 7.0 - - - +
1062B MET* 3.8 23.1 - - + +
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Residues in contact with ALA1005 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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909B ALA 5.0 0.2 - - - +
910B ASN* 3.0 23.9 - - + +
1001B ASN 3.0 17.2 + - - +
1002B SER* 3.9 2.2 - - - +
1004B ASP* 1.3 75.1 - - - +
1006B ALA* 1.3 62.2 + - - +
1007B GLY* 3.2 1.0 + - - -
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Residues in contact with ALA1006 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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905B PHE* 3.9 14.1 - - + -
909B ALA* 4.3 12.1 - - + +
910B ASN* 3.0 16.1 + - - +
917B ILE* 6.1 0.4 - - + -
1002B SER 3.3 10.3 + - - +
1003B TYR 3.4 12.1 - - - +
1004B ASP 2.9 0.6 - - - -
1005B ALA* 1.3 79.6 - - - +
1007B GLY* 1.3 58.4 + - - +
1008B LEU* 3.4 28.4 + - + +
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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