Contacts of the helix formed by residues 876 - 891 (chain N) in PDB entry 5X22
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 SER 876 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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792N ILE 4.3 2.6 + - - -
794N GLN 4.6 1.2 + - - -
795N VAL* 3.9 21.1 - - - +
860N LEU 3.2 20.7 + - - -
861N GLN* 4.2 1.8 - - - -
862N ASP 3.2 14.1 - - - -
863N VAL* 4.4 0.4 - - - +
864N VAL* 4.9 0.7 - - - -
875N THR* 1.3 82.3 + - - +
877N PRO* 1.3 66.7 - - - +
878N GLY* 3.2 0.7 + - - -
879N ARG* 3.2 35.6 + - - +
880N ILE* 3.3 14.5 + - - +
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Residues in contact with PRO 877 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
849N ALA* 4.8 10.1 - - + -
850N LEU* 3.5 16.8 - - + +
853N VAL* 3.7 25.8 - - + -
858N VAL* 4.5 8.1 - - + -
859N ASP 3.7 14.1 - - - +
860N LEU* 3.7 12.3 - - + +
862N ASP 3.1 15.5 - - - +
864N VAL* 4.1 18.6 - - + -
866N VAL* 5.8 0.2 - - + -
876N SER* 1.3 86.0 - - - +
878N GLY* 1.3 54.6 + - - +
879N ARG 3.4 0.2 - - - -
880N ILE* 3.4 11.7 - - + +
881N LEU* 2.9 28.1 + - - +
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Residues in contact with GLY 878 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792N ILE* 3.3 32.7 - - - +
860N LEU* 3.1 26.0 + - - +
876N SER 3.0 1.4 - - - -
877N PRO* 1.3 76.2 - - - +
879N ARG* 1.3 59.0 + - - +
881N LEU* 3.2 5.8 + - - +
882N PHE* 2.9 27.4 + - - +
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Residues in contact with ARG 879 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793N THR* 2.8 37.4 + - + +
795N VAL* 3.4 39.8 - - - +
875N THR* 3.2 27.9 + - - +
876N SER* 3.2 12.3 + - - +
878N GLY* 1.3 72.2 - - - +
880N ILE* 1.3 61.3 + - - +
882N PHE* 3.3 8.1 + - - +
883N ALA 2.9 23.7 + - - -
902N LEU* 3.1 36.8 + - + +
903N ASP* 3.0 37.4 + - - +
904N VAL 4.2 2.8 - - - -
905N PRO* 3.5 21.2 - - - +
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Residues in contact with ILE 880 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
846N PRO* 3.6 37.0 - - + +
849N ALA* 5.8 0.9 - - + -
850N LEU* 5.0 6.5 - - + -
866N VAL* 4.5 24.7 - - + -
868N TYR* 4.5 22.6 - - + -
873N LEU* 4.7 9.6 - - + -
875N THR* 3.8 20.2 - - + -
876N SER 3.3 13.7 + - - +
877N PRO* 3.4 13.2 - - + +
879N ARG* 1.3 77.5 - - - +
881N LEU* 1.3 57.9 + - - +
883N ALA* 3.2 7.5 + - + +
884N ARG* 2.9 29.6 + - + +
897N TRP* 5.8 0.2 - - + -
902N LEU* 5.2 4.5 - - + -
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Residues in contact with LEU 881 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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792N ILE* 4.4 6.3 - - + -
850N LEU* 3.8 28.3 - - + -
860N LEU* 4.3 22.0 - - + -
877N PRO 2.9 14.7 + - - +
878N GLY 3.2 9.4 - - - +
880N ILE* 1.3 77.2 - - - +
882N PHE* 1.3 57.6 + - - +
884N ARG* 3.2 20.5 + - - +
885N ILE* 2.9 46.8 + - + +
937N TYR* 5.4 5.4 - - + -
941N PHE* 3.5 32.5 - - + -
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Residues in contact with PHE 882 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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789N LEU* 4.1 22.0 - - + -
792N ILE* 4.6 2.9 - - + +
793N THR* 3.8 19.7 - - + -
878N GLY 2.9 13.3 + - - +
879N ARG* 3.6 8.3 - - - +
880N ILE 3.3 0.2 - - - -
881N LEU* 1.3 74.5 - - - +
883N ALA* 1.3 66.5 + - - +
885N ILE* 2.9 23.3 + - + +
886N VAL* 2.9 25.1 + - + +
900N ILE* 3.5 20.9 - - + -
902N LEU* 5.8 1.6 - - + -
906N GLN* 3.4 31.4 - - + -
911N LEU* 3.6 27.1 - - + -
914N LEU* 3.7 16.8 - - + -
934N LEU* 3.7 23.8 - - + -
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Residues in contact with ALA 883 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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868N TYR* 4.4 19.9 + - + -
879N ARG 2.9 13.8 + - - +
880N ILE* 3.4 11.7 - - - +
882N PHE* 1.3 77.7 - - - +
884N ARG* 1.3 57.9 + - - +
886N VAL* 3.5 2.6 + - - +
887N ALA* 2.9 29.0 + - - +
896N ALA* 4.9 0.2 - - - +
897N TRP* 4.7 6.7 - - + -
900N ILE* 3.6 26.2 - - + +
902N LEU* 4.3 12.6 - - + -
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Residues in contact with ARG 884 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176L ARG* 3.1 40.6 - - - +
846N PRO* 5.2 6.5 - - + +
847N ASP* 3.1 28.3 + - - +
850N LEU* 3.3 36.7 - - - +
868N TYR* 4.9 7.8 + - + +
880N ILE* 2.9 16.0 + - + +
881N LEU* 3.5 20.5 - - - +
883N ALA* 1.3 73.2 - - - +
885N ILE* 1.3 62.3 + - - +
887N ALA* 3.6 6.7 - - + +
888N GLU* 2.9 55.1 + - + +
937N TYR* 6.4 0.2 - - - -
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Residues in contact with ILE 885 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789N LEU* 5.0 1.6 - - + -
792N ILE* 4.6 4.5 - - + -
881N LEU* 2.9 29.2 + - + +
882N PHE* 3.2 19.5 - - + +
884N ARG* 1.3 78.4 - - - +
886N VAL* 1.3 58.4 + - - +
888N GLU* 4.1 2.7 - - - +
889N ALA* 2.9 31.9 + - + +
930N LEU* 5.7 0.2 - - + -
933N ALA* 4.5 10.9 - - + +
934N LEU* 4.6 17.9 - - + -
937N TYR* 3.5 64.6 - - + -
941N PHE* 4.2 12.6 - - + -
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Residues in contact with VAL 886 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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882N PHE* 2.9 44.3 + - + +
883N ALA 3.8 5.2 - - - +
885N ILE* 1.3 75.2 - - + +
887N ALA* 1.3 63.8 + - - +
889N ALA* 3.2 0.5 + - - +
890N VAL* 2.9 35.6 + - + +
896N ALA* 4.0 16.2 - - + -
899N LEU* 5.0 2.5 - - + -
900N ILE* 3.9 17.9 - - + -
914N LEU* 4.1 19.5 - - + -
930N LEU* 4.0 23.1 - - + -
934N LEU* 4.9 2.5 - - + -
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Residues in contact with ALA 887 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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868N TYR* 4.5 4.9 - - - +
883N ALA 2.9 19.2 + - - +
884N ARG* 3.6 9.2 - - + +
886N VAL* 1.3 76.3 - - - +
888N GLU* 1.3 59.3 + - + +
890N VAL* 3.5 2.8 + - - +
891N GLU* 2.9 28.4 + - - -
892N ASP 3.6 3.9 + - - -
893N GLU* 4.2 26.2 - - + +
896N ALA* 3.5 19.3 - - + +
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Residues in contact with GLU 888 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176L ARG* 2.3 40.6 + - - -
198L ARG* 3.9 20.0 + - - -
200L TRP* 4.6 1.1 - - - -
884N ARG* 2.9 37.6 + - + +
885N ILE* 4.2 2.9 - - - +
887N ALA* 1.3 74.3 - - + +
889N ALA* 1.3 64.9 + - - +
890N VAL 3.6 0.2 + - - -
891N GLU* 3.6 16.5 + - - +
937N TYR* 4.9 6.8 + - - -
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Residues in contact with ALA 889 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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885N ILE 2.9 20.0 + - - +
886N VAL 3.2 4.2 + - - +
888N GLU* 1.3 80.1 - - - +
890N VAL* 1.3 61.1 + - - +
891N GLU* 3.6 5.4 + - - +
926N LYS* 4.7 1.0 - - - +
929N ARG* 4.1 23.8 + - - +
930N LEU* 3.9 24.0 - - + +
933N ALA* 3.7 27.8 - - + -
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Residues in contact with VAL 890 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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886N VAL* 2.9 25.4 + - + +
887N ALA 3.6 1.3 - - - +
889N ALA* 1.3 75.8 - - - +
891N GLU* 1.3 69.8 + - - +
892N ASP* 3.1 31.1 + - + +
896N ALA* 3.8 9.4 - - + +
899N LEU* 5.2 0.9 - - + -
922N LEU* 3.5 32.3 - - + -
926N LYS* 3.3 32.6 + - + +
930N LEU* 4.0 31.2 - - + -
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Residues in contact with GLU 891 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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887N ALA 2.9 12.0 + - - -
888N GLU* 3.6 15.2 + - - +
889N ALA 3.3 4.0 - - - +
890N VAL* 1.3 78.4 - - - +
892N ASP* 1.3 58.1 + - - +
893N GLU 4.2 0.4 - - - -
926N LYS* 4.1 16.0 + - - +
929N ARG* 3.7 29.0 + - - -
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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
------------------------------------------------------------
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