Contacts of the strand formed by residues 874 - 884 (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 ALA 874 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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744B LEU* 5.9 0.2 - - + -
783B LEU* 3.2 30.5 - - + -
784B THR 3.8 6.7 - - - +
786B ALA* 4.9 0.4 - - - -
854B ASP* 3.4 5.7 - - - +
857B ALA* 3.2 20.1 - - + +
862B LEU 3.2 20.5 + - - +
863B ARG* 4.8 2.2 - - - -
864B TYR* 4.0 18.4 - - + -
872B ARG 3.6 0.4 + - - -
873B TYR* 1.3 77.2 - - - +
875B TYR* 1.3 71.4 + - - +
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Residues in contact with TYR 875 (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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783B LEU* 3.3 4.5 - - - +
784B THR* 2.8 53.9 + - + +
785B GLU 3.6 2.0 - - - -
786B ALA* 3.4 42.9 + - + -
787B SER 3.5 20.9 - - - -
788B LEU* 4.0 3.5 + - - +
791B SER* 4.3 8.1 - - - -
853B LEU* 3.0 57.0 - - + +
854B ASP* 3.7 18.5 + - + -
873B TYR 5.1 0.2 - - - -
874B ALA* 1.3 81.5 - - - +
876B THR* 1.3 62.5 + - - +
877B LEU* 5.1 2.5 - - + -
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Residues in contact with THR 876 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731B ASN* 4.2 8.1 - - - +
781B TYR* 3.6 23.6 - - + +
782B VAL 3.4 8.1 - - - +
783B LEU* 4.4 9.4 - - + -
852B LEU* 3.2 26.0 + - - +
853B LEU 3.1 9.8 + - - -
856B GLN* 2.9 36.5 + - + +
857B ALA* 4.5 9.1 + - + +
862B LEU* 4.3 12.3 - - + -
875B TYR* 1.3 78.3 - - - +
877B LEU* 1.3 69.0 + - - +
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Residues in contact with LEU 877 (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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781B TYR* 3.7 6.3 - - - -
782B VAL* 3.0 37.0 + - + +
784B THR* 4.0 27.6 - - + -
791B SER* 3.7 18.8 - - - +
794B ALA* 3.7 14.4 - - + -
795B PHE* 3.5 42.0 - - + +
798B LEU* 4.0 9.2 - - + -
850B SER 3.5 11.0 - - - +
851B ALA* 4.0 14.6 - - + -
852B LEU* 4.6 2.2 - - - -
856B GLN* 5.4 0.7 - - - -
875B TYR* 4.7 1.1 - - + -
876B THR* 1.3 82.5 - - - +
878B ASN* 1.3 64.0 + - - +
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Residues in contact with ASN 878 (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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727B GLU* 3.6 39.9 + - + +
779B GLU* 4.5 10.8 + - - +
780B GLN 3.2 13.2 - - - +
781B TYR* 4.5 6.3 - - + -
798B LEU* 3.8 8.0 - - - +
848B SER* 4.4 5.7 + - - -
849B CYS* 3.5 0.2 - - - -
850B SER* 3.0 40.7 + - - -
852B LEU* 3.9 17.2 - - - +
856B GLN* 4.3 1.4 + - - -
877B LEU* 1.3 75.7 - - - +
879B ASN* 1.3 66.3 + - - +
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Residues in contact with ASN 879 (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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779B GLU* 3.8 6.3 - - - +
780B GLN* 2.8 36.2 + - - +
798B LEU* 3.3 34.0 - - + +
799B LEU* 4.2 1.7 + - - -
802B ALA* 3.6 15.4 - - - +
833B ILE* 4.7 3.0 - - - +
847B HIS* 3.7 8.5 - - - +
848B SER* 2.9 41.7 + - - +
849B CYS* 3.3 20.2 - - - +
878B ASN* 1.3 78.3 - - - +
880B THR* 1.3 67.0 + - - +
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Residues in contact with THR 880 (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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777B LYS* 4.7 8.0 - - + -
778B VAL 4.0 7.2 - - - +
779B GLU* 3.9 15.6 + - - +
780B GLN* 3.1 12.9 - - - +
802B ALA* 4.2 1.0 - - - +
846B THR 4.1 12.1 + - - +
847B HIS* 3.1 31.8 - - + -
848B SER 3.9 12.0 + - - -
879B ASN* 1.3 78.6 - - - +
881B ALA* 1.3 62.9 + - - +
882B LEU* 3.6 23.6 - - - +
883B ALA* 4.3 10.5 - - + +
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Residues in contact with ALA 881 (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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676B ALA* 4.7 3.4 - - + -
680B MET* 4.1 26.2 - - + -
778B VAL* 2.9 34.3 + - + +
779B GLU* 4.4 0.9 - - - +
780B GLN* 4.1 9.4 - - + +
805B ILE* 3.7 22.1 - - + +
847B HIS* 2.9 21.5 + - - -
879B ASN 3.8 1.0 + - - -
880B THR* 1.3 73.8 - - - +
882B LEU* 1.3 65.0 + - - +
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Residues in contact with LEU 882 (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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672B LEU* 3.5 45.3 - - + +
673B LEU* 4.9 6.6 - - + +
675B PHE* 4.7 7.4 - - + -
676B ALA* 3.7 19.5 - - + -
777B LYS* 3.5 1.4 - - - -
778B VAL* 2.9 28.7 + - + +
805B ILE* 4.5 7.4 - - + -
806B LEU* 5.9 0.4 - - + -
809B LEU* 4.2 12.8 - - + -
847B HIS* 4.9 8.3 - - + -
880B THR* 3.6 5.9 - - - +
881B ALA* 1.3 84.6 - - - +
883B ALA* 1.3 61.6 + - - +
884B THR* 5.6 0.7 - - - +
887B ILE* 3.8 38.8 - - + -
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Residues in contact with ALA 883 (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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673B LEU* 5.6 0.4 - - - -
775B PHE* 4.7 7.9 - - + -
776B HIS 3.2 11.0 - - - +
777B LYS* 4.0 19.7 - - + -
846B THR 5.5 4.0 + - - +
880B THR* 4.3 9.7 - - + +
882B LEU* 1.3 77.3 - - - +
884B THR* 1.3 62.9 + - - +
886B ARG* 4.3 5.1 + - + +
887B ILE* 3.1 25.9 + - - +
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Residues in contact with THR 884 (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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659B TYR* 4.0 1.6 - - - +
669B GLU* 2.9 54.0 + - + +
672B LEU* 4.7 2.3 - - - +
673B LEU* 4.4 9.9 - - + +
775B PHE* 2.9 21.5 - - - +
776B HIS* 2.8 30.6 + - + +
882B LEU* 5.6 0.5 - - - +
883B ALA* 1.3 72.4 - - - +
885B PRO* 1.3 65.3 - - + +
886B ARG* 3.6 1.3 - - - -
887B ILE* 3.5 18.0 - - - +
888B LEU* 4.6 2.4 - - - +
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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