Contacts of the strand formed by residues 842 - 851 (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 842 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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764B LYS* 6.1 3.2 - - - +
836B TYR* 3.5 11.4 - - - -
837B LEU* 2.7 37.0 + - - +
840B GLU* 3.1 52.4 + - + +
841B GLY* 1.3 78.6 - - - +
843B TYR* 1.3 70.4 + - - +
844B ARG* 3.3 26.1 - - + +
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Residues in contact with TYR 843 (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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622B ARG* 3.7 46.0 + - - +
624B GLY 3.8 11.8 + - - -
626B PRO* 4.2 10.8 - - + +
812B PRO* 4.0 7.3 - - - +
813B TYR* 3.8 17.8 + - - -
814B ARG* 3.6 56.3 + - + +
834B GLU* 3.7 21.6 - - + +
835B VAL 3.1 12.6 - - - -
836B TYR* 3.8 24.9 - + + +
842B ARG* 1.3 87.3 + - - +
844B ARG* 1.3 62.4 + - - +
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Residues in contact with ARG 844 (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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764B LYS* 5.7 6.4 - - - +
765B ASP* 2.8 42.6 + - - -
770B MET* 3.7 19.7 - - + +
771B ARG* 4.5 6.5 - - - +
834B GLU* 3.8 5.2 - - - -
835B VAL* 2.7 28.3 + - - +
837B LEU* 4.4 10.3 - - + -
840B GLU* 2.9 31.3 + - - +
842B ARG* 3.3 22.4 - - + +
843B TYR* 1.3 79.8 - - - +
845B GLU* 1.3 64.6 + - - +
846B THR* 3.9 3.3 - - - +
886B ARG* 4.4 18.6 - - - +
890B MET* 3.6 22.3 - - + +
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Residues in contact with GLU 845 (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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832B ASP* 4.2 17.5 - - + +
833B ILE 3.9 7.0 - - - +
834B GLU* 4.2 12.0 + - + +
844B ARG* 1.3 75.5 - - - +
846B THR* 1.3 63.4 + - - +
847B HIS* 4.0 16.9 + - - +
848B SER* 3.6 21.5 + - - -
886B ARG* 2.8 43.8 + - - +
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Residues in contact with THR 846 (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* 4.3 1.3 - - - +
833B ILE 3.1 12.7 + - - -
835B VAL* 3.8 37.2 - - + +
844B ARG 3.9 2.2 - - - +
845B GLU* 1.3 83.6 - - - +
847B HIS* 1.3 92.4 + - - +
880B THR* 4.1 10.9 + - - +
883B ALA* 5.5 4.0 + - - +
886B ARG* 5.0 8.1 - - + +
887B ILE* 4.7 15.7 - - + +
890B MET* 4.0 13.9 - - - -
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Residues in contact with HIS 847 (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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802B ALA* 3.5 21.5 + - + +
805B ILE* 5.1 1.5 - - + +
806B LEU* 4.2 27.7 - - + +
832B ASP* 3.6 4.0 - - - +
833B ILE* 3.2 37.5 + - + +
845B GLU* 4.0 7.1 - - - +
846B THR* 1.3 108.5 + - - +
848B SER* 1.4 61.4 + - - +
879B ASN* 3.7 9.9 - - - +
880B THR* 3.1 37.5 - - + -
881B ALA 2.9 21.9 + - - -
882B LEU* 5.1 9.0 - - + -
887B ILE* 5.8 0.9 - - + -
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Residues in contact with SER 848 (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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827B LYS* 5.7 0.7 - - - -
830B GLN* 3.7 17.3 + - - -
831B VAL 3.7 5.4 - - - -
832B ASP* 3.2 18.9 + - - -
845B GLU* 3.6 14.9 + - - -
847B HIS* 1.4 74.0 + - - +
849B CYS* 1.3 60.2 + - - +
850B SER* 3.9 5.1 + - - -
878B ASN* 3.7 6.3 + - - +
879B ASN* 2.9 20.8 + - - +
880B THR* 3.9 7.4 + - - -
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Residues in contact with CYS 849 (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* 3.6 32.0 - - + -
798B LEU* 3.5 39.5 - - - -
799B LEU* 3.8 19.7 - - + -
830B GLN* 3.1 6.1 - - - +
831B VAL 2.8 34.6 + - - +
848B SER* 1.3 68.6 - - - +
850B SER* 1.3 61.8 + - - +
878B ASN 3.5 1.8 - - - -
879B ASN* 3.3 16.1 - - - +
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Residues in contact with SER 850 (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* 3.8 4.2 - - - -
798B LEU* 5.2 0.2 - - - +
827B LYS* 2.9 43.2 + - - -
829B ARG 3.3 6.1 - - - -
830B GLN* 3.4 6.8 - - - +
848B SER* 4.2 7.3 + - - -
849B CYS* 1.3 77.1 + - - +
851B ALA* 1.3 58.1 + - - +
852B LEU* 3.8 8.0 - - - +
877B LEU* 3.5 4.3 - - - +
878B ASN* 3.0 41.2 + - - -
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Residues in contact with ALA 851 (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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791B SER* 4.2 13.9 - - - +
792B ASP* 6.0 0.2 - - - +
795B PHE* 3.7 18.3 - - + -
827B LYS* 3.6 4.5 - - - -
828B TRP* 2.8 41.6 + - + -
829B ARG* 2.9 12.3 + - + +
850B SER* 1.3 73.5 - - - +
852B LEU* 1.3 58.0 + - - +
853B LEU* 3.6 2.5 - - + +
877B LEU* 4.0 18.8 - - + -
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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