Contacts of the helix formed by residues 956 - 975 (chain A) in PDB entry 1WER
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 VAL 956 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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830A LEU* 4.3 3.1 - - + -
845A LEU* 4.2 7.6 - - + -
848A LEU* 3.9 27.8 - - + -
849A LEU* 4.3 6.3 - - + -
852A LEU* 3.9 5.4 - - + -
936A SER* 3.7 18.4 - - - +
946A PHE* 4.2 7.0 - - + -
953A MET* 3.0 28.8 + - + +
955A GLY* 1.3 78.0 - - - +
957A ASN* 1.3 66.5 + - - +
958A PRO 3.4 1.1 - - - -
959A PHE* 3.0 36.2 + - + +
960A ILE* 3.1 14.9 + - + +
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Residues in contact with ASN 957 (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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945A GLU* 3.5 24.1 - - - +
946A PHE* 2.8 58.7 - - - +
954A GLU* 3.2 30.8 - - - +
956A VAL* 1.3 79.0 - - - +
958A PRO* 1.3 62.0 - - + +
960A ILE* 3.3 5.3 + - - +
961A LYS* 2.9 35.8 + - + +
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Residues in contact with PRO 958 (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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849A LEU* 6.1 3.6 - - + -
954A GLU 3.8 5.2 - - - +
955A GLY* 3.6 14.1 - - - +
956A VAL 3.6 2.5 - - - -
957A ASN* 1.3 93.3 - - + +
959A PHE* 1.3 61.8 + - - +
961A LYS* 3.7 10.2 - - + +
962A SER* 3.0 27.8 + - - -
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Residues in contact with PHE 959 (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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849A LEU* 3.8 23.2 - - + +
852A LEU* 3.8 49.4 - - + -
853A SER* 4.3 11.2 - - - -
856A VAL* 4.0 14.8 - - + -
936A SER 4.6 5.8 - - - -
937A VAL* 5.6 1.1 - - + -
940A LEU* 3.7 31.0 - - + -
956A VAL* 3.0 27.0 + - + +
958A PRO* 1.3 79.7 - - - +
960A ILE* 1.3 70.8 + - + +
962A SER* 3.1 10.1 + - - -
963A ASN* 2.5 53.5 + - - +
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Residues in contact with ILE 960 (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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936A SER 4.4 2.0 - - - +
939A ASN* 3.7 29.2 - - + -
940A LEU* 3.7 23.3 - - + +
944A VAL 3.7 20.2 - - - +
945A GLU* 4.4 2.9 - - + +
946A PHE* 3.8 24.0 - - + -
956A VAL* 3.1 12.0 + - + +
957A ASN* 3.3 14.1 + - - +
959A PHE* 1.3 91.0 - - + +
961A LYS* 1.3 63.4 + - - +
963A ASN 3.1 2.3 + - - -
964A LYS* 3.0 46.8 + - + +
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Residues in contact with LYS 961 (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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945A GLU* 3.1 43.3 + - + +
957A ASN* 2.9 25.7 + - + +
958A PRO* 3.7 7.6 - - + +
960A ILE* 1.3 73.0 - - - +
962A SER* 1.3 63.2 + - - +
963A ASN 3.2 1.0 + - - -
964A LYS* 3.5 23.3 + - - +
965A HIS 5.0 0.5 + - - -
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Residues in contact with SER 962 (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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958A PRO 3.0 18.2 + - - -
959A PHE* 3.1 12.3 + - - -
961A LYS* 1.3 77.0 - - - +
963A ASN* 1.3 67.6 + - - +
964A LYS 3.6 0.4 - - - -
965A HIS* 5.0 4.1 + - - +
966A ARG* 4.9 5.7 + - - +
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Residues in contact with ASN 963 (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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853A SER* 6.4 0.2 - - - +
856A VAL* 4.5 2.2 - - + +
860A PHE* 4.8 0.7 - - + -
940A LEU* 3.7 20.9 - - + +
959A PHE* 2.5 47.9 + - - +
960A ILE 3.1 3.8 + - - +
962A SER* 1.3 86.6 + - - +
964A LYS* 1.3 64.5 + - - +
965A HIS 3.3 2.7 - - - -
966A ARG* 2.6 48.5 + - + +
967A MET* 3.0 22.3 + - - +
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Residues in contact with LYS 964 (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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940A LEU* 3.9 7.0 - - + -
943A LEU* 3.1 51.1 + - + +
944A VAL* 4.1 5.6 - - - +
945A GLU* 4.3 17.6 + - - +
960A ILE* 3.0 38.1 + - + +
961A LYS* 3.5 18.6 + - - +
963A ASN* 1.3 78.7 - - - +
965A HIS* 1.3 57.8 + - - +
967A MET* 3.3 3.5 + - - +
968A ILE* 3.0 36.3 + - + +
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Residues in contact with HIS 965 (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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961A LYS 5.0 0.6 + - - -
962A SER 5.0 3.7 + - - +
963A ASN 3.3 0.6 - - - -
964A LYS* 1.3 76.0 - - - +
966A ARG* 1.3 62.2 + - + +
968A ILE* 3.3 18.0 + - + +
969A MET* 2.9 62.8 + - + +
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Residues in contact with ARG 966 (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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853A SER* 5.0 4.0 + - - +
856A VAL* 3.6 19.8 - - - +
857A GLU* 3.7 23.0 - - - +
860A PHE* 3.6 33.4 - - + +
861A MET* 6.2 2.2 - - - +
962A SER 4.9 4.5 + - - +
963A ASN* 2.6 49.9 + - - +
965A HIS* 1.3 78.6 - - + +
967A MET* 1.3 56.3 + - - +
969A MET* 3.3 8.4 + - - +
970A PHE* 3.0 29.3 + - - +
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Residues in contact with MET 967 (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 PHE* 3.7 21.9 - - + -
897A SER* 4.0 0.4 - - - +
901A PHE* 3.1 41.7 - - + -
940A LEU* 3.5 26.9 - - + +
941A ALA* 3.2 28.5 - - + +
943A LEU* 3.8 11.7 - - + -
963A ASN 3.0 13.4 + - - +
964A LYS 3.5 9.2 - - - +
966A ARG* 1.3 76.7 - - - +
968A ILE* 1.3 56.0 + - - +
970A PHE* 3.3 3.6 + - - +
971A LEU* 2.9 59.5 + - + +
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Residues in contact with ILE 968 (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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893A THR* 3.6 20.1 - - + +
943A LEU* 3.7 30.1 - - + -
964A LYS* 3.0 25.3 + - + +
965A HIS* 3.3 19.7 + - + +
967A MET* 1.3 74.1 - - - +
969A MET* 1.3 64.7 + - - +
971A LEU* 3.3 2.4 + - - -
972A ASP* 2.9 32.5 + - + +
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Residues in contact with MET 969 (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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965A HIS* 2.9 51.9 + - + +
966A ARG* 3.7 7.4 - - - +
968A ILE* 1.3 79.7 - - - +
970A PHE* 1.3 64.7 - - - +
972A ASP* 4.5 5.4 - - + -
973A GLU* 3.1 57.9 + - + +
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Residues in contact with PHE 970 (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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809A PHE* 4.3 13.0 - + - -
859A ILE* 3.6 30.5 - - + -
860A PHE* 3.5 42.6 - + + -
863A SER* 4.1 12.6 + - - -
900A VAL* 4.4 2.7 - - + -
901A PHE* 3.6 27.6 - + - -
966A ARG 3.0 14.3 + - - +
967A MET* 3.5 7.2 - - - +
969A MET* 1.3 77.5 - - - +
971A LEU* 1.3 75.2 + - + +
973A GLU* 4.0 2.1 - - - +
974A LEU* 3.1 58.2 + - + +
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Residues in contact with LEU 971 (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 GLN* 3.4 10.7 + - - -
893A THR* 3.7 39.3 - - + +
894A ARG* 5.4 0.2 - - - -
896A VAL* 3.9 8.5 - - + +
897A SER* 3.7 29.6 - - - +
900A VAL* 4.1 7.4 - - + -
901A PHE* 4.0 10.1 - - + -
941A ALA 4.3 3.4 - - - +
943A LEU* 5.1 6.1 - - + -
967A MET* 2.9 60.1 + - + +
968A ILE* 4.7 1.8 - - - -
970A PHE* 1.3 77.5 - - + +
972A ASP* 1.3 68.6 + - - +
974A LEU* 3.5 15.4 + - - +
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Residues in contact with ASP 972 (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 GLN* 3.1 23.5 + - - +
892A ARG* 3.0 40.9 + - - -
893A THR* 3.7 11.6 - - + +
968A ILE* 2.9 21.5 + - + +
969A MET* 3.8 8.1 - - + +
971A LEU* 1.3 78.3 - - - +
973A GLU* 1.3 68.5 + - + +
974A LEU 3.4 0.5 + - - -
975A GLY* 3.6 3.1 + - - -
976A ASN* 4.6 2.3 + - - +
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Residues in contact with GLU 973 (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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863A SER* 5.3 3.4 - - - +
871A ARG* 3.0 18.9 + - - +
969A MET* 3.1 41.0 + - + +
970A PHE* 4.4 2.0 - - - +
972A ASP* 1.3 83.6 - - + +
974A LEU* 1.3 64.4 + - - +
975A GLY 3.1 4.4 + - - -
976A ASN* 3.1 25.4 + - + +
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Residues in contact with LEU 974 (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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809A PHE* 5.7 0.4 - - + -
863A SER* 3.7 27.8 + - - +
866A LEU* 3.9 22.0 - - + -
871A ARG* 3.0 37.4 + - - +
874A TYR* 4.0 7.8 - - + -
896A VAL* 3.7 23.3 - - + -
900A VAL* 3.9 19.1 - - + -
970A PHE* 3.1 54.0 + - + +
971A LEU* 3.6 8.7 - - - +
972A ASP 3.2 0.8 - - - -
973A GLU* 1.3 76.2 - - - +
975A GLY* 1.3 56.5 + - - +
976A ASN 3.3 0.2 - - - -
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Residues in contact with GLY 975 (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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871A ARG 3.4 14.2 - - - +
874A TYR* 4.0 5.8 - - - +
875A GLY* 3.2 25.2 - - - -
878A GLN* 3.6 20.9 + - - +
896A VAL* 5.4 0.2 - - - +
971A LEU 4.2 1.6 + - - -
972A ASP 3.6 5.8 + - - -
973A GLU 3.1 0.8 - - - -
974A LEU* 1.3 79.5 - - - +
976A ASN* 1.3 54.9 + - - +
977A VAL 2.8 14.3 + - - +
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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