Contacts of the strand formed by residues 798 - 806 (chain B) in PDB entry 4QUN
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 GLU 798 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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733B TRP* 4.3 1.6 - - - -
736B LYS* 5.4 0.3 - - - -
789B LEU* 3.8 28.3 - - + +
790B VAL 3.4 2.2 - - - -
791B THR* 3.3 24.2 + - - +
796B GLY 3.6 9.9 + - - +
797B GLU* 1.3 87.2 - - - +
799B HIS* 1.3 62.6 - - - +
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Residues in contact with HIS 799 (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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732B VAL* 4.6 7.9 - - + -
733B TRP* 3.6 23.1 - + + -
736B LYS* 3.4 49.2 - - + +
737B LEU 2.7 24.7 + - - -
738B SER* 4.4 5.8 - - - -
788B MET 3.8 0.2 - - - +
789B LEU* 3.8 2.6 - - - -
790B VAL* 2.8 37.6 + - + +
798B GLU* 1.3 76.1 - - - +
800B THR* 1.3 73.4 + - - +
801B VAL* 3.5 21.4 + - + -
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Residues in contact with THR 800 (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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738B SER* 4.2 8.0 - - - -
787B GLU* 3.8 32.3 + - + +
788B MET 3.4 9.6 - - - +
789B LEU* 4.0 13.1 - - + +
799B HIS* 1.3 89.2 + - - +
801B VAL* 1.3 69.2 + - - +
802B THR* 5.1 2.2 - - - +
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Residues in contact with VAL 801 (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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729B TRP* 4.5 1.8 - - + -
732B VAL* 3.9 12.1 - - + -
737B LEU 3.6 8.5 - - - +
738B SER 3.7 14.1 - - - +
740B ILE* 3.8 30.7 - - + -
787B GLU* 3.7 2.3 - - - -
788B MET* 2.8 49.5 + - + +
790B VAL* 4.2 15.7 - - + -
799B HIS* 3.5 23.3 - - + -
800B THR* 1.3 82.0 - - - +
802B THR* 1.3 73.2 + - - +
803B HIS* 4.9 1.3 - - + +
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Residues in contact with THR 802 (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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738B SER 2.9 14.5 + - - -
739B LEU* 3.4 20.3 - - + +
740B ILE 2.9 25.8 + - - -
785B SER* 5.8 1.6 - - - -
786B ARG 3.7 7.2 - - - +
787B GLU* 4.9 2.7 - - - +
800B THR* 5.1 2.3 - - - +
801B VAL* 1.3 73.7 - - - +
803B HIS* 1.3 62.2 + - - +
804B LEU* 4.0 19.1 - - + -
827B TYR* 5.4 2.7 - - - +
831B LEU* 4.5 13.5 - - + +
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Residues in contact with HIS 803 (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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740B ILE* 3.5 23.6 - - + -
742B MET* 3.8 29.6 - - + +
757B TYR* 2.7 37.4 + + - -
758B TRP* 4.2 7.6 - + - -
784B VAL 3.6 0.9 - - - +
785B SER* 3.5 2.4 - - - -
786B ARG* 2.8 55.1 + - + +
788B MET* 3.4 42.9 - - + +
801B VAL* 3.8 0.6 + - + -
802B THR* 1.3 74.0 - - - +
804B LEU* 1.3 62.9 + - - +
805B GLN* 4.1 9.9 - - + -
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Residues in contact with LEU 804 (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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739B LEU* 4.1 15.9 - - + -
740B ILE 2.9 10.3 + - - +
741B VAL* 3.6 3.7 - - + +
742B MET* 2.8 28.9 + - - +
783B TYR* 4.7 2.2 - - + -
784B VAL 3.4 2.0 - - - +
785B SER* 3.2 30.3 - - - +
802B THR* 4.0 11.4 - - + -
803B HIS* 1.3 81.3 - - - +
805B GLN* 1.3 59.7 + - - +
806B TYR 4.0 0.6 + - - -
824B PHE* 3.9 24.5 - - + -
827B TYR* 3.9 24.7 - - + +
828B VAL* 4.3 14.6 - - + -
831B LEU* 3.9 23.1 - - + -
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Residues in contact with GLN 805 (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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742B MET* 3.3 25.1 - - + +
744B THR 2.9 28.1 + - - +
745B THR* 3.7 14.8 - - - +
746B LEU* 4.3 4.9 - - - +
758B TRP* 4.2 7.9 - - - -
783B TYR* 3.1 5.6 - - - +
784B VAL* 2.8 37.3 + - + +
786B ARG* 3.0 36.1 + - - +
803B HIS* 4.1 8.3 + - + -
804B LEU* 1.3 72.5 - - - +
806B TYR* 1.3 62.5 + - - +
807B VAL* 3.4 21.2 + - + +
824B PHE* 5.2 0.2 - - - -
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Residues in contact with TYR 806 (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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742B MET 2.8 9.1 + - - -
743B LEU* 3.8 25.9 - - + -
744B THR* 3.6 22.2 + - - +
782B ALA* 3.6 24.1 - - + +
783B TYR* 3.8 2.9 - + + -
804B LEU 4.0 1.6 + - - -
805B GLN* 1.3 70.7 - - - +
807B VAL* 1.3 57.7 + - - +
808B ALA* 3.5 33.1 + - - +
809B TRP* 3.7 26.8 - + + +
815B PRO* 4.1 4.9 - - + +
817B ASP 3.8 4.3 + - - -
820B ASP* 3.5 12.9 - - - +
821B PHE* 3.2 33.0 + + + +
824B PHE* 3.5 50.3 - + + -
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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