Contacts of the helix formed by residues 821 - 837 (chain A) in PDB entry 1SIW
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 SER 821 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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789A ALA* 3.9 13.3 - - - +
793A GLU 5.4 0.4 - - - -
794A LYS* 4.0 28.0 - - - -
815A PRO* 4.8 3.1 - - - +
820A LYS* 1.3 76.9 - - - +
822A ASP* 1.3 66.3 + - - +
823A TRP* 3.9 8.1 + - - +
824A GLU* 3.1 32.1 + - - +
825A ILE* 2.9 20.6 + - - +
948A ALA* 5.7 1.4 - - - +
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Residues in contact with ASP 822 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A SER* 3.3 17.6 + - - +
201A SER* 3.5 22.0 + - - +
712A TRP* 4.2 9.7 - - + -
713A ARG* 4.1 0.5 - - - +
771A LEU* 3.6 11.5 - - + +
788A THR* 3.0 12.8 + - - -
794A LYS* 2.9 30.1 + - - +
821A SER* 1.3 71.2 - - - +
823A TRP* 1.3 63.2 + - - +
825A ILE* 3.2 6.6 + - - +
826A TYR* 3.1 23.6 + - - -
1247A GDP 2.8 38.9 + - - +
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Residues in contact with TRP 823 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A VAL* 3.6 27.6 - - + +
198A SER* 5.1 2.3 + - - +
200A ALA 4.9 0.9 - - - -
201A SER* 3.6 29.5 - - - -
204A ARG* 4.5 4.0 - - - -
592A LEU* 4.3 19.5 - - + -
821A SER* 3.2 7.5 - - - +
822A ASP* 1.3 78.7 - - - +
824A GLU* 1.3 74.4 + - + +
826A TYR* 3.6 1.6 + - - +
827A LYS* 3.0 33.6 + - + +
899A PHE* 3.7 38.3 - + - -
945A LEU* 3.4 29.2 - - + -
946A ASN 3.1 18.6 + - - -
947A THR 3.6 11.4 - - - -
948A ALA* 3.7 20.9 - - + -
951A ALA* 4.0 17.0 - - + -
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Residues in contact with GLU 824 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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820A LYS* 4.4 16.9 + - + +
821A SER* 3.1 28.0 + - - +
823A TRP* 1.3 83.2 - - + +
825A ILE* 1.3 64.2 + - - +
827A LYS* 2.9 32.9 + - - +
828A ALA* 3.1 24.8 + - - +
946A ASN 3.7 9.2 - - - +
947A THR* 4.6 5.9 - - - +
948A ALA 5.1 0.3 + - - -
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Residues in contact with ILE 825 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A TRP* 3.8 18.8 - - + -
166A ASN* 4.8 0.3 - - - +
771A LEU* 3.9 31.0 - - + -
786A LEU* 3.9 22.9 - - + -
787A PRO 3.8 15.3 - - - +
788A THR* 3.7 13.2 - - - +
820A LYS* 3.4 35.0 - - + +
821A SER 2.9 16.3 + - - +
822A ASP 3.2 4.7 + - - +
824A GLU* 1.3 79.0 - - - +
826A TYR* 1.3 59.5 + - + +
828A ALA* 3.5 4.3 + - - +
829A ILE* 3.0 36.9 + - + +
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Residues in contact with TYR 826 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A SER* 3.2 37.7 - - - +
202A GLY* 3.2 27.8 - - - -
205A TYR* 4.2 21.5 - + + -
206A LEU* 6.1 0.7 - - + -
710A PHE* 3.6 37.8 - + + +
712A TRP* 3.2 32.6 - + - -
771A LEU* 3.7 32.6 - - + +
822A ASP 3.1 17.8 + - - +
823A TRP 4.3 0.2 - - - +
825A ILE* 1.3 75.0 - - + +
827A LYS* 1.3 61.9 + - - +
829A ILE* 3.6 12.6 - - + +
830A ALA* 2.8 30.1 + - - +
899A PHE* 4.4 6.8 - - + -
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Residues in contact with LYS 827 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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823A TRP* 3.0 28.0 + - - +
824A GLU* 2.9 42.8 + - - +
825A ILE 3.3 0.2 - - - -
826A TYR* 1.3 77.5 - - - +
828A ALA* 1.3 57.1 + - - +
830A ALA* 3.3 5.8 + - - +
831A LYS* 2.9 27.3 + - - +
896A TYR* 3.6 20.7 - - + -
899A PHE* 4.0 15.8 - - + -
900A THR* 3.5 25.4 - - + -
945A LEU 4.5 0.4 - - - +
946A ASN* 3.0 34.4 + - - +
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Residues in contact with ALA 828 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A TRP* 6.2 0.9 - - + -
166A ASN* 4.2 20.1 + - - +
820A LYS* 4.8 13.0 - - + +
824A GLU 3.1 18.4 + - - +
825A ILE* 3.8 5.6 - - - +
827A LYS* 1.3 76.4 - - - +
829A ILE* 1.3 65.2 + - - +
831A LYS* 3.6 11.7 - - + +
832A LYS* 3.0 23.7 + - - +
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Residues in contact with ILE 829 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ASN* 3.0 39.5 - - - +
169A ILE* 4.2 31.0 - - + -
170A ALA* 4.8 3.8 - - - +
205A TYR* 3.6 32.1 - - + +
710A PHE* 4.9 3.1 - - + -
786A LEU* 5.0 6.5 - - + -
825A ILE* 3.0 31.4 + - + +
826A TYR* 3.6 19.3 - - + +
827A LYS 3.3 0.2 - - - -
828A ALA* 1.3 75.8 - - - +
830A ALA* 1.3 59.3 + - - +
832A LYS* 3.1 5.9 + - - +
833A PHE* 2.8 28.4 + - + +
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Residues in contact with ALA 830 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A TYR* 3.9 24.7 - - + -
826A TYR 2.8 17.9 + - - +
827A LYS* 3.4 8.7 - - - +
829A ILE* 1.3 77.9 - - - +
831A LYS* 1.3 57.7 + - - +
833A PHE* 3.5 1.9 - - - +
834A SER* 2.9 34.1 + - - -
895A THR* 4.3 6.7 - - + +
896A TYR* 4.0 18.1 + - + -
899A PHE* 4.4 12.6 - - + -
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Residues in contact with LYS 831 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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827A LYS* 2.9 12.4 + - - +
828A ALA* 3.6 11.2 - - + +
829A ILE 3.2 0.2 - - - -
830A ALA* 1.3 77.9 - - - +
832A LYS* 1.3 62.0 + - - +
834A SER* 3.5 9.5 + - - -
835A GLU* 3.6 11.6 + - - +
896A TYR* 3.0 60.5 + - + -
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Residues in contact with LYS 832 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A GLN* 5.3 7.2 - - - +
166A ASN* 3.6 33.7 - - + +
167A GLU* 3.8 34.4 + - - +
170A ALA* 3.9 0.7 - - + -
828A ALA 3.0 17.1 + - - +
829A ILE 3.7 3.1 - - - +
831A LYS* 1.3 75.0 - - - +
833A PHE* 1.3 66.0 + - - +
835A GLU* 2.9 31.4 + - - +
836A VAL* 3.0 46.2 + - + +
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Residues in contact with PHE 833 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A ALA* 3.8 19.0 - - + +
173A ASN* 4.1 3.8 - - + -
174A VAL* 3.6 28.7 - - + -
177A ILE* 3.9 21.1 - - + -
205A TYR* 3.5 24.0 - + + +
209A ILE* 3.6 22.0 - - + -
829A ILE 2.8 17.3 + - - +
830A ALA 3.5 4.0 - - - +
832A LYS* 1.3 77.4 - - - +
834A SER* 1.3 63.8 + - - +
836A VAL* 4.0 0.6 - - - +
837A CYS* 3.0 29.9 + - + +
841A LEU* 4.2 7.2 - - + -
892A TYR* 3.6 31.2 - + - -
895A THR* 3.6 20.6 - - + -
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Residues in contact with SER 834 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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830A ALA 2.9 14.3 + - - -
831A LYS 3.7 6.7 - - - -
832A LYS 3.2 0.2 - - - -
833A PHE* 1.3 79.7 - - - +
835A GLU* 1.3 57.7 + - - +
837A CYS* 3.7 7.4 - - - -
838A VAL* 3.5 15.6 - - - +
892A TYR 4.2 4.3 - - - -
893A PRO* 3.4 24.8 + - - +
895A THR* 3.5 6.8 + - - -
896A TYR* 2.9 37.5 + - - -
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Residues in contact with GLU 835 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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831A LYS 3.6 7.2 + - - +
832A LYS* 2.9 43.8 + - + +
833A PHE 3.1 0.6 - - - -
834A SER* 1.3 76.2 - - - +
836A VAL* 1.3 74.5 + - + +
837A CYS 3.2 2.5 - - - -
838A VAL* 3.3 24.7 + - - +
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Residues in contact with VAL 836 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ASP* 5.1 1.2 - - - +
131A PRO* 3.9 23.8 - - + -
132A VAL* 3.7 22.8 - - + +
167A GLU* 5.0 2.2 - - + +
170A ALA* 4.0 9.0 - - + -
171A ALA* 4.0 15.5 - - - +
174A VAL* 4.2 4.0 - - + -
832A LYS* 3.0 46.8 + - + +
833A PHE* 4.0 2.5 - - - +
835A GLU* 1.3 80.7 - - + +
837A CYS* 1.3 60.8 + - - +
838A VAL 3.3 2.3 + - - +
840A HIS* 3.5 17.3 - - - -
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Residues in contact with CYS 837 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A VAL* 3.8 22.4 - - + +
833A PHE* 3.0 26.1 + - + +
834A SER 3.7 11.4 - - - -
836A VAL* 1.3 76.8 - - - +
838A VAL* 1.3 62.9 + - - +
839A GLY 3.1 0.2 + - - -
840A HIS 2.8 22.7 + - - -
841A LEU* 2.9 33.6 + - + +
892A TYR* 3.8 11.2 - - - -
893A PRO* 3.7 26.5 - - - -
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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