Contacts of the strand formed by residues 829 - 837 (chain B) in PDB entry 1SER
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 ARG 829 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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606B TRP* 3.6 42.3 - - + +
620B ILE* 4.1 6.5 - - - +
795B PHE* 3.6 39.9 - - + -
817B GLU* 2.8 37.4 + - - +
823B MET* 4.6 2.5 - - - -
827B LYS* 4.5 3.0 - - - +
828B TRP* 1.3 96.5 - - + +
830B GLN* 1.3 63.2 + - - +
831B VAL* 3.6 11.3 - - - +
850B SER* 3.3 2.9 - - - -
851B ALA* 2.9 29.2 + - + +
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Residues in contact with GLN 830 (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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795B PHE* 4.2 0.2 - - - -
817B GLU* 4.2 3.8 + - - +
818B VAL* 3.2 38.6 + - + +
822B ASP 4.3 1.9 + - - +
823B MET* 3.3 35.7 - - + +
827B LYS* 3.3 22.8 + - + +
829B ARG* 1.3 77.5 - - - +
831B VAL* 1.3 62.7 + - - +
832B ASP* 2.9 28.3 + - - +
848B SER* 3.7 13.2 + - - -
849B CYS 3.1 16.4 - - - +
850B SER* 3.4 9.2 - - - +
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Residues in contact with VAL 831 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620B ILE* 4.0 11.7 - - + -
795B PHE* 3.6 22.2 - - + -
799B LEU* 4.0 21.2 - - + +
815B LEU* 3.8 24.0 - - + -
816B VAL 3.7 7.6 - - - +
817B GLU* 4.0 5.4 - - - +
829B ARG* 3.6 29.2 - - - +
830B GLN* 1.3 75.4 - - - +
832B ASP* 1.3 71.7 + - - +
833B ILE* 4.9 0.5 - - - +
849B CYS* 2.8 32.0 + - - +
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Residues in contact with ASP 832 (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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617B ASN* 5.2 3.3 - - - +
814B ARG 3.9 0.2 - - - +
815B LEU* 3.3 5.7 - - - -
816B VAL* 3.0 41.9 + - + +
818B VAL* 3.7 16.9 - - - +
822B ASP* 5.2 2.6 - - - +
830B GLN* 2.9 26.9 + - - -
831B VAL* 1.3 75.4 - - - +
833B ILE* 1.3 65.6 + - - +
834B GLU* 4.6 14.2 - - + +
845B GLU* 4.2 14.7 - - + +
847B HIS 3.6 7.0 - - - +
848B SER* 3.2 14.8 + - - -
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Residues in contact with ILE 833 (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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799B LEU* 4.0 28.9 - - + +
802B ALA* 3.6 33.7 - - + -
803B GLU* 4.7 4.9 - - + -
806B LEU* 3.5 28.5 - - + -
813B TYR* 3.7 21.8 - - + -
814B ARG 3.5 4.9 - - - +
815B LEU* 4.3 6.3 - - + -
831B VAL 4.9 0.7 - - - +
832B ASP* 1.3 79.3 - - - +
834B GLU* 1.3 63.7 + - - +
845B GLU* 3.9 1.4 - - - +
846B THR* 3.1 23.3 + - - +
847B HIS* 3.2 29.1 + - + +
879B ASN* 4.7 2.9 - - - +
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Residues in contact with GLU 834 (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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813B TYR* 3.1 6.6 - - - +
814B ARG* 2.9 74.5 + - - +
816B VAL* 3.8 16.7 - - + +
832B ASP* 4.6 13.5 - - + +
833B ILE* 1.3 81.6 - - - +
835B VAL* 1.3 63.2 + - - +
843B TYR* 3.7 17.4 - - + +
844B ARG 3.2 13.5 - - - +
845B GLU* 4.2 16.3 + - - +
846B THR 4.3 0.2 - - - +
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Residues in contact with VAL 835 (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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806B LEU* 3.8 29.2 - - + -
811B LEU* 4.1 30.7 - - + -
812B PRO* 3.4 12.3 - - + +
813B TYR* 3.9 4.9 - - + -
834B GLU* 1.3 78.4 - - - +
836B TYR* 1.3 66.6 + - - +
837B LEU 3.6 0.9 + - - -
843B TYR* 3.1 3.7 - - - -
844B ARG* 2.7 32.4 + - - +
846B THR* 3.8 30.5 - - + +
890B MET* 4.0 19.4 - - + +
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Residues in contact with TYR 836 (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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626B PRO* 3.8 42.3 - - + +
627B PRO* 4.1 4.3 - - + -
812B PRO* 3.3 22.0 + - + -
835B VAL* 1.3 76.7 - - - +
837B LEU* 1.3 58.3 + - - +
838B PRO* 3.0 32.8 + - + +
841B GLY* 3.5 22.6 - - - -
842B ARG* 3.5 29.4 - - - -
843B TYR* 3.8 29.4 - + + +
890B MET* 4.0 4.2 - - - +
894B ASN* 2.9 28.2 + - - -
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Residues in contact with LEU 837 (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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636B HIS* 4.6 4.0 - - + +
770B MET* 4.0 19.1 - - + -
835B VAL 3.6 1.2 + - - -
836B TYR* 1.3 75.1 - - - +
838B PRO* 1.4 69.6 - - - +
839B SER* 3.8 11.4 - - - +
840B GLU* 3.1 45.2 + - + +
841B GLY 3.3 7.3 + - - -
842B ARG 2.7 18.4 + - - +
844B ARG* 4.4 4.0 - - + -
889B ALA* 3.7 22.0 - - + +
890B MET* 3.8 26.9 - - + -
893B GLU* 3.5 26.2 - - + +
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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