Contacts of the helix formed by residues 951 - 966 (chain Z) in PDB entry 5WTI
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 951 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879Z SER* 4.8 5.3 - - - +
891Z ARG* 3.7 21.8 - - - +
934Z GLY 3.4 20.0 - - - +
935Z GLU* 2.8 23.9 + - - +
936Z LYS 4.1 6.7 - - - +
937Z PHE* 4.0 13.7 - - + +
949Z THR 3.5 1.4 + - - -
950Z HIS* 1.3 71.3 + - - +
952Z ASP* 1.3 60.8 + - - +
954Z ASN* 3.2 6.2 + - - +
955Z ALA* 2.9 26.9 + - - +
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Residues in contact with ASP 952 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574Z ASP* 3.6 22.1 - - - +
576Z GLY* 4.3 6.4 - - - -
577Z GLN* 4.1 16.2 + - - +
579Z GLN* 3.6 32.2 + - - +
582Z ALA* 3.6 10.1 - - + +
879Z SER* 5.6 0.9 - - - -
891Z ARG* 3.8 24.0 + - - -
935Z GLU* 6.4 0.7 - - - -
950Z HIS* 3.2 8.2 + - + -
951Z ALA* 1.3 74.1 - - - +
953Z ILE* 1.3 60.6 + - - +
955Z ALA* 3.7 8.1 - - - +
956Z ALA* 3.0 27.5 + - - +
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Residues in contact with ILE 953 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B U 3.4 33.7 - - + +
18B G 4.2 3.8 - - - +
19B U 3.5 23.8 - - - -
582Z ALA* 3.9 9.6 - - + -
583Z ALA 4.8 3.1 - - - +
584Z SER* 5.5 0.2 - - - -
615Z SER* 3.7 27.1 - - - +
616Z PHE 4.3 9.9 - - - -
617Z ASN* 3.4 18.4 - - - +
950Z HIS* 3.1 22.5 + - + +
952Z ASP* 1.3 73.4 - - - +
954Z ASN* 1.3 65.4 + - - +
956Z ALA* 3.4 5.4 + - - +
957Z GLN* 3.1 30.0 + - - +
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Residues in contact with ASN 954 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878Z SER 4.0 5.3 + - - -
879Z SER* 4.4 3.8 - - - +
881Z PHE 3.0 18.9 + - - -
882Z HIS* 3.6 6.6 - - + -
883Z ALA* 2.9 30.8 + - - +
937Z PHE* 3.8 28.5 - - - +
949Z THR* 3.7 14.9 + - + -
950Z HIS 2.9 19.9 + - - +
951Z ALA* 3.5 5.0 + - - +
953Z ILE* 1.3 77.0 - - - +
955Z ALA* 1.3 63.2 + - - +
957Z GLN* 3.3 15.2 + - - +
958Z ASN* 3.1 19.6 + - - -
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Residues in contact with ALA 955 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574Z ASP* 3.5 24.9 - - - +
878Z SER* 3.5 29.8 - - - +
879Z SER* 4.0 13.0 - - - -
951Z ALA 2.9 15.8 + - - +
952Z ASP* 3.7 6.5 - - - +
953Z ILE 3.3 0.2 - - - -
954Z ASN* 1.3 78.2 - - - +
956Z ALA* 1.3 61.6 + - - +
958Z ASN* 3.1 13.3 + - - +
959Z LEU* 3.3 15.2 + - - +
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Residues in contact with ALA 956 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572Z SER* 2.8 31.9 + - - +
574Z ASP* 4.2 11.8 - - - +
582Z ALA 3.5 27.1 - - - +
583Z ALA 4.5 0.7 - - - -
584Z SER* 4.3 10.3 - - - +
952Z ASP 3.0 15.0 + - - +
953Z ILE 3.7 5.6 - - - +
954Z ASN 3.3 0.2 - - - -
955Z ALA* 1.3 75.3 - - - +
957Z GLN* 1.3 61.7 + - - +
959Z LEU* 3.3 15.0 + - - +
960Z GLN 3.4 4.2 + - - -
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Residues in contact with GLN 957 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B U 3.0 40.1 + - - +
584Z SER* 3.5 20.0 - - - +
586Z PHE* 4.6 1.1 - - + -
599Z LEU* 3.4 27.5 - - + +
601Z PHE* 3.9 4.9 - - + -
612Z HIS* 3.6 12.9 + - - -
615Z SER* 3.6 5.2 + - - +
882Z HIS* 5.9 0.3 - - - -
883Z ALA* 3.7 15.6 - - + +
884Z LYS 5.6 0.3 + - - -
949Z THR* 5.5 1.6 + - - -
953Z ILE* 3.1 20.5 + - - +
954Z ASN* 3.6 16.7 - - - +
955Z ALA 3.2 0.4 - - - -
956Z ALA* 1.3 73.4 - - - +
958Z ASN* 1.3 59.8 + - - +
960Z GLN* 3.2 11.4 + - - +
961Z LYS* 2.9 24.3 + - - +
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Residues in contact with ASN 958 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878Z SER* 2.4 44.3 + - - +
881Z PHE* 3.0 27.8 + - - +
882Z HIS 4.4 1.2 - - - +
883Z ALA* 3.4 20.8 + - - +
954Z ASN 3.1 11.5 + - - -
955Z ALA 3.1 10.2 + - - +
957Z GLN* 1.3 75.6 - - - +
959Z LEU* 1.3 60.3 + - - +
961Z LYS* 2.9 18.8 + - - +
962Z ARG* 2.9 45.1 + - - +
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Residues in contact with LEU 959 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572Z SER* 4.1 6.7 - - - -
573Z ILE 3.6 33.4 - - - +
574Z ASP* 4.7 3.6 - - - +
826Z LEU* 4.4 5.8 - - + +
827Z PHE 4.1 4.0 - - - -
828Z GLU* 3.7 19.7 - - + +
873Z VAL* 3.9 33.4 - - + +
874Z GLY 4.0 3.1 - - - +
875Z ALA* 3.6 30.1 - - + -
878Z SER* 4.5 3.6 - - - -
955Z ALA 3.3 14.8 + - - +
956Z ALA* 3.4 11.2 - - - +
957Z GLN 3.3 0.2 - - - -
958Z ASN* 1.3 77.1 - - - +
960Z GLN* 1.3 61.4 + - - +
962Z ARG* 3.3 2.3 + - - -
963Z PHE* 3.0 23.9 + - - +
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Residues in contact with GLN 960 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570Z VAL* 2.8 38.1 + - - +
571Z MET 3.7 1.0 - - - -
572Z SER* 3.2 25.1 - - - +
584Z SER* 3.1 16.5 + - - +
586Z PHE* 3.3 38.4 - - + +
601Z PHE* 4.4 0.4 - - + -
826Z LEU* 4.9 1.6 - - - -
956Z ALA 3.4 4.0 + - - +
957Z GLN* 3.2 9.9 + - - +
959Z LEU* 1.3 75.8 - - - +
961Z LYS* 1.3 62.6 + - - +
963Z PHE* 3.3 4.0 + - - +
964Z TRP* 2.7 66.3 + - + -
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Residues in contact with LYS 961 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601Z PHE* 3.7 33.0 - - + -
881Z PHE* 6.3 0.6 - - - +
882Z HIS 4.2 3.2 + - - -
883Z ALA 3.7 13.4 + - - +
884Z LYS 5.5 0.4 - - - -
885Z THR 2.9 28.5 + - - -
886Z GLY* 4.1 8.1 - - - -
957Z GLN 2.9 12.9 + - - +
958Z ASN* 2.9 26.7 + - - +
960Z GLN* 1.3 77.2 - - - +
962Z ARG* 1.3 57.0 + - + +
964Z TRP* 4.2 0.2 - - - -
965Z THR* 2.3 49.8 + - + +
967Z THR 5.2 2.2 - - - +
968Z HIS 5.7 6.8 + - - +
969Z GLY* 5.7 8.0 - - - +
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Residues in contact with ARG 962 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873Z VAL* 3.9 16.8 - - + -
874Z GLY 2.9 28.7 + - - -
875Z ALA* 3.5 12.7 - - - +
876Z GLN 3.5 7.5 - - - +
877Z PHE 3.3 33.5 + - - +
878Z SER* 3.3 11.9 - - - +
881Z PHE* 5.7 1.4 - - - +
958Z ASN* 2.9 26.0 + - - +
959Z LEU* 4.9 1.1 - - - +
960Z GLN 3.2 0.2 - - - -
961Z LYS* 1.3 77.9 - - + +
963Z PHE* 1.3 62.0 + - - +
965Z THR* 4.0 0.2 - - - -
966Z ARG* 3.1 26.9 + - - -
967Z THR 3.7 22.5 + - - +
968Z HIS* 3.6 44.2 + - + +
971Z TYR* 4.0 10.7 + - - -
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Residues in contact with PHE 963 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568Z LEU* 5.9 0.9 - - + -
570Z VAL* 4.4 8.3 - - + -
824Z ILE* 4.2 18.8 - - + -
826Z LEU* 3.7 35.2 - - + -
873Z VAL* 4.5 10.5 - - + +
959Z LEU 3.0 16.8 + - - +
960Z GLN* 3.3 3.1 + - - +
962Z ARG* 1.3 79.2 - - - +
964Z TRP* 1.3 102.8 + + - +
966Z ARG* 3.4 44.7 + - - +
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Residues in contact with TRP 964 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545Z LEU* 4.9 3.8 - - + -
568Z LEU* 4.2 12.1 - - + -
570Z VAL* 3.5 38.1 - - + -
586Z PHE* 4.0 7.2 - + + +
588Z VAL* 3.4 31.6 - - + -
601Z PHE* 4.5 12.8 - + + -
602Z PRO 4.1 4.7 - - - +
603Z ILE* 3.5 38.0 - - + +
604Z LYS* 3.0 26.3 + - - +
610Z ALA* 3.5 26.8 - - + +
960Z GLN* 2.7 50.7 + - + +
961Z LYS 4.4 1.1 - - - +
963Z PHE* 1.3 99.1 - + - +
965Z THR* 1.3 62.0 + - - +
966Z ARG* 3.5 2.7 + - - +
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Residues in contact with THR 965 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601Z PHE* 4.2 17.7 - - + -
602Z PRO* 3.5 27.6 - - + +
604Z LYS* 4.3 13.6 - - - +
961Z LYS* 2.3 41.6 + - + +
964Z TRP* 1.3 75.7 - - - +
966Z ARG* 1.3 68.6 + - - +
967Z THR* 3.1 30.5 + - - +
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Residues in contact with ARG 966 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604Z LYS* 4.3 23.1 - - + -
962Z ARG 3.1 14.9 + - - -
963Z PHE* 3.4 49.6 + - - +
964Z TRP 4.5 4.0 - - - +
965Z THR* 1.3 78.6 - - - +
967Z THR* 1.3 58.7 + - - +
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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
------------------------------------------------------------
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