Contacts of the strand formed by residues 871 - 882 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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793A ASN* 4.9 4.7 + - - +
828A ALA 4.0 4.7 - - - -
831A TRP* 3.9 18.8 - - + -
832A GLN* 3.4 53.4 - - + +
835A TRP* 3.7 28.3 - + + +
836A GLU* 4.1 7.3 + - - -
867A LEU* 4.1 1.5 - - - +
868A TYR* 2.9 44.8 + - + +
869A HIS* 3.4 8.6 - + + -
870A ILE* 1.3 100.0 - - + +
872A GLU* 1.3 62.4 + - - +
873A VAL* 3.5 2.6 + - - +
892A LEU* 4.1 14.6 - - + -
893A LYS 3.6 2.5 - - - -
894A ASN* 3.8 32.6 + - + -
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Residues in contact with GLU 872 (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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865A SER* 3.1 23.3 + - - +
866A ASN 3.5 8.3 - - - +
867A LEU* 4.0 10.5 - - + +
870A ILE 3.9 2.2 + - - -
871A TYR* 1.3 70.7 - - - +
873A VAL* 1.3 58.8 + - - +
874A ASN* 2.7 24.3 + - - +
891A TYR 3.5 4.0 - - - +
892A LEU* 3.5 2.4 - - - +
893A LYS* 2.9 50.1 + - + +
895A LEU* 3.7 27.5 - - + +
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Residues in contact with VAL 873 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831A TRP* 3.7 29.4 - - + -
861A PRO* 3.3 17.0 - - + +
865A SER* 3.4 0.2 - - - -
866A ASN 2.9 32.8 + - - -
868A TYR* 3.6 31.2 - - + -
871A TYR 4.1 1.8 - - - +
872A GLU* 1.3 72.6 - - - +
874A ASN* 1.3 63.0 + - - +
890A PHE* 3.4 39.7 - - + -
891A TYR 3.5 3.4 - - - +
892A LEU* 3.8 16.2 - - + -
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Residues in contact with ASN 874 (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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864A GLY* 3.5 6.4 - - - +
865A SER* 2.8 22.2 + - - +
872A GLU* 2.7 31.8 + - - +
873A VAL* 1.3 74.5 - - - +
875A LEU* 1.3 63.6 + - - +
876A VAL* 3.4 2.8 + - + +
890A PHE* 3.3 10.2 - - - -
891A TYR* 2.9 49.4 + - + +
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Residues in contact with LEU 875 (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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860A TRP* 5.3 2.2 - - + +
861A PRO* 3.5 21.0 - - - +
862A ASP* 3.3 28.9 - - - +
863A GLU* 4.2 2.2 - - - +
864A GLY* 3.1 23.3 + - - +
873A VAL 4.2 0.2 + - - -
874A ASN* 1.3 71.0 - - - +
876A VAL* 1.3 61.9 + - - +
877A SER* 3.1 29.6 - - - +
878A GLU* 4.2 16.8 - - + +
888A ARG* 4.2 14.1 - - + -
889A SER 3.7 7.2 - - - +
890A PHE* 3.9 19.4 - - + -
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Residues in contact with VAL 876 (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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874A ASN* 4.0 3.8 - - + +
875A LEU* 1.3 75.8 - - - +
877A SER* 1.3 65.1 + - - +
889A SER* 2.8 26.3 + - - +
890A PHE 4.0 0.7 - - - -
891A TYR* 3.0 63.0 - - + +
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Residues in contact with SER 877 (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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875A LEU* 3.1 23.0 - - - +
876A VAL* 1.3 83.9 - - - +
878A GLU* 1.3 64.1 + - - +
879A HIS* 5.2 1.7 + - - +
888A ARG* 3.7 0.2 - - - -
889A SER* 3.1 29.6 + - - -
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Residues in contact with GLU 878 (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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860A TRP* 5.6 0.2 + - - -
862A ASP* 5.1 2.1 - - - +
875A LEU* 4.2 15.9 - - + +
877A SER* 1.3 82.9 + - - +
879A HIS* 1.3 62.7 + - - +
880A ILE* 4.0 18.4 + - + +
886A LEU* 4.0 18.8 - - + +
887A VAL 3.3 11.0 - - - +
888A ARG* 3.7 30.4 + - + -
880B ILE* 6.0 0.7 - - - +
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Residues in contact with HIS 879 (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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877A SER* 5.2 1.5 + - - +
878A GLU* 1.3 73.2 - - - +
880A ILE* 1.3 64.1 + - - +
881A TRP* 3.5 52.3 + + - +
886A LEU* 3.3 1.8 - - - -
887A VAL* 2.6 48.5 + - + +
883B GLU* 3.6 30.0 - - + +
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Residues in contact with ILE 880 (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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878A GLU* 4.0 17.6 + - + +
879A HIS* 1.3 76.2 - - - +
881A TRP* 1.3 58.2 + - - +
882A CYS 3.9 10.5 - - - +
885A PHE 4.4 1.8 - - - +
886A LEU* 3.8 29.2 - - + -
909A LEU* 6.1 1.8 - - + -
880B ILE* 3.9 43.1 - - + +
881B TRP 3.9 10.5 - - - +
882B CYS* 3.7 19.3 - - - +
883B GLU* 2.7 37.3 + - - +
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Residues in contact with TRP 881 (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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879A HIS* 3.5 33.7 + + - -
880A ILE* 1.3 72.5 - - - +
882A CYS* 1.3 63.6 + - + +
885A PHE* 3.3 42.5 + + + +
887A VAL* 3.5 34.3 - - + +
906A PHE* 5.6 0.2 - - - -
925A ASP* 6.0 1.8 - - - -
929A LYS* 4.8 19.4 - - + +
882B CYS* 3.2 15.8 - - - +
883B GLU* 4.3 2.8 + - + +
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Residues in contact with CYS 882 (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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880A ILE* 3.5 7.8 - - - +
881A TRP* 1.3 82.7 - - - +
883A GLU* 1.3 67.3 + - - +
884A ASP* 3.0 12.0 + - - -
885A PHE* 3.1 62.0 + - - +
909A LEU* 4.8 2.6 - - - +
922A SER* 4.6 5.6 - - - -
881B TRP 3.1 15.0 - - - +
882B CYS* 4.0 2.5 - - + -
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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