Contacts of the strand formed by residues 871 - 882 (chain B) in PDB entry 2QEP
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 TYR 871 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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793B ASN* 5.0 4.5 + - - +
828B ALA 4.3 4.7 - - - -
831B TRP* 3.9 24.2 - - + -
832B GLN* 3.4 45.9 + - + +
835B TRP* 3.7 33.8 - + + +
836B GLU* 4.2 5.4 + - - -
866B ASN 3.8 0.2 - - - +
867B LEU* 3.6 5.4 - - - +
868B TYR* 2.9 43.1 + - + +
869B HIS* 3.4 7.6 - - + -
870B ILE* 1.3 108.5 - - + +
872B GLU* 1.3 61.6 + - - +
873B VAL* 3.6 2.6 + - + -
892B LEU* 4.0 18.8 - - + -
893B LYS 3.5 1.3 - - - -
894B ASN* 4.0 21.0 + - + -
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Residues in contact with GLU 872 (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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865B SER* 4.4 17.4 - - - -
866B ASN 3.7 4.7 - - - +
867B LEU* 3.8 17.9 - - + +
870B ILE 3.8 1.2 + - - -
871B TYR* 1.3 71.1 - - - +
873B VAL* 1.3 60.9 + - - +
874B ASN* 2.9 25.6 + - - +
891B TYR* 3.0 7.1 - - - +
892B LEU* 3.4 1.7 - - - -
893B LYS* 2.7 69.7 + - + +
895B LEU* 4.2 11.4 - - + +
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Residues in contact with VAL 873 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831B TRP* 3.4 52.9 - - + -
861B PRO* 3.2 28.6 - - + +
865B SER* 3.3 1.6 - - - -
866B ASN 3.0 31.1 + - - -
868B TYR* 3.5 25.8 - - + -
871B TYR 4.4 2.2 - - - +
872B GLU* 1.3 73.5 - - - +
874B ASN* 1.3 63.0 + - - +
890B PHE* 3.9 16.2 - - + -
891B TYR 3.5 3.1 - - - -
892B LEU* 4.0 10.5 - - + +
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Residues in contact with ASN 874 (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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864B GLY* 3.6 12.8 - - - +
865B SER* 3.2 20.8 - - - -
872B GLU* 2.9 26.9 + - - +
873B VAL* 1.3 73.6 - - - +
875B LEU* 1.3 69.0 + - - +
876B VAL* 3.2 1.7 + - - +
890B PHE* 3.0 9.5 - - - -
891B TYR* 2.8 61.5 + - + +
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Residues in contact with LEU 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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860B TRP* 5.7 0.2 - - + -
861B PRO* 3.8 18.6 - - - +
862B ASP 3.4 26.9 - - - +
863B GLU* 4.3 4.0 - - - -
864B GLY* 2.9 25.4 + - - +
874B ASN* 1.3 74.2 - - - +
876B VAL* 1.3 61.7 + - - +
877B SER* 4.0 23.3 - - - +
878B GLU* 5.0 13.0 - - + +
888B ARG* 4.1 18.2 - - + -
889B SER 4.2 1.1 - - - +
890B PHE* 3.3 31.2 - - + -
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Residues in contact with VAL 876 (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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874B ASN* 3.9 5.8 - - + +
875B LEU* 1.3 76.5 - - - +
877B SER* 1.3 63.6 + - - +
889B SER* 2.8 24.8 + - - +
890B PHE 4.3 0.9 - - - -
891B TYR* 3.3 57.7 - - + +
902B THR* 6.4 0.7 - - + -
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Residues in contact with SER 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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875B LEU* 3.7 7.5 - - - +
876B VAL* 1.3 86.9 - - - +
878B GLU* 1.3 64.2 + - - +
879B HIS* 5.2 1.6 + - - +
888B ARG* 3.3 4.3 - - - +
889B SER* 2.8 48.0 + - - +
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Residues in contact with GLU 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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875B LEU* 5.0 12.8 - - + +
877B SER* 1.3 77.6 - - - +
879B HIS* 1.3 64.5 + - - +
880B ILE* 4.3 14.5 - - + +
886B LEU* 4.2 13.5 - - + +
887B VAL 3.4 4.7 - - - +
888B ARG* 3.0 47.1 + - + +
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Residues in contact with HIS 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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883A GLU* 6.0 2.7 - - - -
877B SER* 5.2 1.7 + - - +
878B GLU* 1.3 74.6 - - - +
880B ILE* 1.3 79.7 + - - +
881B TRP* 3.4 52.5 + + + +
886B LEU* 3.4 2.2 - - - -
887B VAL* 2.8 39.9 + - + +
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Residues in contact with ILE 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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878A GLU* 6.0 0.7 - - - +
880A ILE* 3.9 39.1 - - + +
883A GLU* 5.9 0.3 - - - -
878B GLU* 4.9 13.7 - - + +
879B HIS* 1.3 87.2 + - - +
881B TRP* 1.3 61.2 + - - +
882B CYS 3.4 27.1 - - - +
883B GLU* 5.5 0.4 - - - -
885B PHE 4.0 3.1 - - - +
886B LEU* 3.8 25.8 - - + -
909B LEU* 5.3 2.2 - - + -
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Residues in contact with TRP 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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880A ILE* 4.1 1.1 - - - -
882A CYS* 3.1 28.8 - - - +
883A GLU* 3.1 27.7 + - + +
879B HIS* 3.4 40.6 + + + +
880B ILE* 1.3 74.0 - - - +
882B CYS* 1.3 62.0 + - - +
885B PHE* 3.3 39.6 + + + +
887B VAL* 3.6 28.0 - - + +
929B LYS* 3.3 36.0 - - + +
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Residues in contact with CYS 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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880A ILE* 3.3 14.8 - - - -
881A TRP 3.2 19.5 - - - +
882A CYS* 4.0 2.5 - - + -
880B ILE* 3.4 14.4 - - - +
881B TRP* 1.3 81.3 - - + +
883B GLU* 1.3 66.6 + - - +
884B ASP* 3.3 17.9 + - - -
885B PHE* 3.0 51.1 + - - +
909B LEU* 4.5 0.3 - - - +
922B SER* 4.8 3.6 - - - -
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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