Contacts of the helix formed by residues 995 - 1007 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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464D 666 4.5 13.0 - - + -
895D LEU* 4.7 9.2 - - + -
898D HIS* 3.6 37.6 - - + +
899D PHE* 5.0 7.4 - - + -
938D ILE* 3.6 19.1 - - + -
991D PHE* 2.9 45.8 + - + +
993D THR 3.7 0.8 - - - -
994D HIS* 1.3 99.6 - - + +
996D VAL* 1.3 70.5 + - - +
997D GLY 3.4 0.9 - - - -
998D PRO* 3.2 14.4 - - - +
999D LEU* 3.2 10.7 + - - +
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Residues in contact with VAL 996 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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935D LEU* 5.3 1.6 - - + -
938D ILE* 3.6 30.7 - - + +
941D PRO* 3.7 21.1 - - + -
942D ALA* 5.4 2.7 - - + -
991D PHE* 3.0 42.1 + - + +
992D ILE* 4.2 4.5 - - - -
995D ILE* 1.3 73.0 - - - +
997D GLY* 1.3 68.8 + - - +
999D LEU* 3.1 12.9 + - - +
1000D CYS* 3.1 19.7 + - - -
1065D LEU* 3.4 28.0 - - + -
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Residues in contact with GLY 997 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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992D ILE* 2.7 24.9 + - - +
996D VAL* 1.3 76.3 - - - +
998D PRO* 1.3 64.8 - - - +
1000D CYS* 3.2 3.1 + - - +
1001D ASN* 2.8 31.8 + - - -
1065D LEU* 3.9 16.9 - - - +
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Residues in contact with PRO 998 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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898D HIS* 5.2 0.4 - - - +
899D PHE* 6.1 0.7 - - + -
902D LEU* 3.9 20.8 - - + +
992D ILE 3.8 0.7 - - - +
993D THR* 3.2 22.9 - - - +
994D HIS 3.7 17.0 - - - +
995D ILE 3.2 14.8 - - - +
997D GLY* 1.3 84.7 - - - +
999D LEU* 1.3 65.2 + - - +
1001D ASN* 3.6 10.7 - - + +
1002D SER* 3.1 22.2 + - - -
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Residues in contact with LEU 999 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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898D HIS* 4.3 15.3 - - + -
902D LEU* 3.7 26.5 - - + +
931D VAL* 4.2 22.0 - - + +
934D LYS* 4.0 19.7 - - + -
935D LEU* 3.4 46.2 - - + +
938D ILE* 4.0 15.0 - - + -
995D ILE 3.2 12.0 + - - +
996D VAL 3.1 11.0 + - - +
998D PRO* 1.3 78.1 - - - +
1000D CYS* 1.3 59.1 + - - +
1002D SER* 3.1 3.1 + - - -
1003D TYR* 2.9 27.2 + - + +
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Residues in contact with CYS1000 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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935D LEU* 3.3 33.0 - - + -
942D ALA* 5.2 4.9 - - - -
996D VAL* 3.1 17.8 + - - -
997D GLY 3.7 6.5 - - - +
999D LEU* 1.3 75.5 - - - +
1001D ASN* 1.3 60.4 + - - +
1002D SER 3.0 2.0 - - - -
1003D TYR* 4.1 5.1 - - - +
1004D ASP* 2.8 33.4 + - - +
1009D LEU* 4.3 1.2 - - + +
1061D LEU* 4.7 8.1 - - - -
1062D MET* 3.7 23.6 - - + +
1065D LEU* 3.8 19.3 - - + -
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Residues in contact with ASN1001 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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997D GLY* 2.8 30.5 + - - +
998D PRO* 3.6 9.3 - - + +
1000D CYS* 1.3 76.2 - - - +
1002D SER* 1.3 52.9 + - - +
1004D ASP* 3.8 4.2 - - - +
1005D ALA* 2.8 36.4 + - - +
1062D MET* 4.3 13.6 - - - +
1065D LEU* 5.4 2.4 - - - +
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Residues in contact with SER1002 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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902D LEU* 3.7 13.5 - - - +
905D PHE* 3.2 15.5 - - - -
906D ASN* 2.3 37.2 + - - -
910D ASN* 3.7 2.0 - - - +
998D PRO 3.1 13.6 + - - -
999D LEU 3.2 9.4 - - - -
1000D CYS 3.0 0.4 - - - -
1001D ASN* 1.3 73.5 - - - +
1003D TYR* 1.3 65.8 + - - +
1004D ASP 3.0 1.3 + - - -
1005D ALA* 3.1 7.3 + - - +
1006D ALA* 2.9 24.3 + - - +
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Residues in contact with TYR1003 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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752D LEU* 4.5 9.3 - - + +
802D LEU* 3.5 24.4 - - - +
905D PHE* 4.0 15.7 - + - -
928D VAL* 4.2 7.7 + - + +
931D VAL* 3.4 31.6 - - + +
932D CYS* 3.8 30.8 - - + +
935D LEU* 4.1 21.1 - - + -
999D LEU 2.9 17.5 + - - +
1000D CYS* 4.1 2.9 - - - +
1002D SER* 1.3 73.1 + - - +
1004D ASP* 1.3 60.1 + - - +
1006D ALA* 3.7 5.5 - - - +
1008D LEU* 3.4 52.6 + - + -
1009D LEU* 3.7 24.6 + - + -
1010D PRO* 5.0 0.2 - - + -
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Residues in contact with ASP1004 (chain D).
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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1000D CYS 2.8 21.0 + - - +
1001D ASN* 3.8 3.8 - - - +
1003D TYR* 1.3 75.3 - - - +
1005D ALA* 1.3 60.0 + - - +
1006D ALA 3.0 1.8 - - - -
1007D GLY* 2.6 28.1 + - - -
1009D LEU* 3.2 36.3 + - + +
1059D CYS* 4.4 10.4 - - - +
1062D MET* 4.3 14.3 - - - +
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Residues in contact with ALA1005 (chain D).
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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910D ASN* 2.7 22.2 - - - +
1001D ASN 2.8 20.3 + - - +
1002D SER* 3.5 5.2 - - - +
1004D ASP* 1.3 78.6 + - - +
1006D ALA* 1.3 61.2 + - - +
1007D GLY* 3.2 1.2 + - - -
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Residues in contact with ALA1006 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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905D PHE* 3.4 34.5 - - + -
909D ALA* 3.8 11.2 - - + -
910D ASN* 2.6 15.7 + - - +
917D ILE* 5.2 5.4 - - + +
1002D SER 2.9 7.1 + - - +
1003D TYR 3.7 6.7 - - - +
1004D ASP 3.0 0.2 - - - -
1005D ALA* 1.3 76.5 - - - +
1007D GLY* 1.3 58.9 + - - +
1008D LEU* 3.5 18.0 - - + +
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Residues in contact with GLY1007 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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757D VAL* 3.1 20.7 - - - +
758D PRO 4.7 4.6 - - - +
759D GLY 5.7 0.3 - - - -
760D LEU* 4.5 8.3 - - - +
1004D ASP 2.6 21.6 + - - -
1005D ALA 3.1 1.5 - - - -
1006D ALA* 1.3 72.3 - - - +
1008D LEU* 1.3 64.7 + - - +
1009D LEU* 3.3 5.4 - - - -
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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