Contacts of the strand formed by residues 958 - 972 (chain A) in PDB entry 2W18
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 GLN 958 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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912A TRP* 4.3 4.3 - - + +
913A HIS 2.9 35.4 + - - +
914A PHE* 3.6 19.3 - - - -
945A ARG* 3.4 38.2 + - - +
946A ALA 3.2 7.2 - - - +
947A LEU* 4.1 11.7 - - + -
956A GLU* 3.4 20.8 + - - +
957A LYS* 1.3 79.8 - - - +
959A VAL* 1.3 66.3 + - - +
960A LEU 4.3 0.7 + - - -
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Residues in contact with VAL 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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945A ARG* 3.3 7.4 - - - -
946A ALA* 2.8 34.9 + - + +
948A PHE* 4.0 22.9 - - + -
957A LYS 5.7 0.2 - - - -
958A GLN* 1.3 76.8 - - - +
960A LEU* 1.3 73.9 + - - +
961A LEU* 3.3 16.2 + - + +
1000A GLY 6.3 0.7 - - - +
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Residues in contact with LEU 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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943A GLU* 3.8 33.2 - - + +
944A ILE 3.8 7.2 - - - +
945A ARG* 3.9 27.0 - - + +
958A GLN 4.3 0.2 + - - -
959A VAL* 1.3 79.5 - - - +
961A LEU* 1.3 58.7 + - - +
962A LYS 3.3 23.3 - - - +
963A SER* 4.1 9.6 - - - +
2190A GOL 3.8 38.4 + - - +
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Residues in contact with LEU 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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933A CYS* 4.5 3.6 - - - -
944A ILE* 2.8 25.0 + - + +
945A ARG 4.2 5.4 - - - -
946A ALA* 3.9 20.6 - - + +
959A VAL* 4.0 25.1 - - + +
960A LEU* 1.3 73.8 - - - +
962A LYS* 1.3 68.3 + - + +
992A MET* 3.2 41.0 - - + +
994A PHE* 3.6 28.5 - - + -
998A GLY 5.4 1.6 - - - +
1000A GLY* 5.0 12.6 - - - +
2190A GOL 3.3 17.4 + - - -
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Residues in contact with LYS 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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943A GLU* 3.4 0.9 - - - -
944A ILE* 2.9 39.9 + - + -
960A LEU* 3.3 9.4 - - - +
961A LEU* 1.3 85.1 - - + +
963A SER* 1.3 63.7 + - - +
966A ILE* 3.9 20.2 - - + -
977A LEU* 5.5 1.5 + - + -
979A SER* 3.9 19.0 + - - +
990A GLU* 3.3 36.3 + - - +
992A MET* 4.1 26.6 - - + +
1003A ASN* 3.0 30.7 + - - +
2190A GOL 3.9 5.6 - - - +
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Residues in contact with SER 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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942A ARG 3.4 9.5 + - - -
943A GLU* 4.9 4.0 + - - +
960A LEU* 4.1 16.3 - - - +
962A LYS* 1.3 80.2 - - - +
964A GLY* 1.3 60.1 + - - +
966A ILE* 4.0 5.2 - - - +
2190A GOL 2.9 24.1 + - - -
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Residues in contact with GLY 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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941A ILE 3.2 12.5 - - - +
942A ARG* 3.0 20.8 + - - +
963A SER* 1.3 79.3 + - - +
965A ASN* 1.3 60.8 + - - -
966A ILE* 3.2 9.2 + - - +
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Residues in contact with ASN 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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940A GLU* 4.1 12.0 - - - +
941A ILE 4.3 1.6 - - - -
964A GLY* 1.3 69.8 - - - -
966A ILE* 1.3 61.4 + - - +
967A LYS* 2.9 39.4 + - - +
981A SER* 3.1 24.2 - - - -
982A GLY* 3.6 17.5 + - - +
983A THR* 4.7 3.2 - - - +
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Residues in contact with ILE 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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940A GLU* 4.8 4.5 - - - +
941A ILE* 3.2 51.6 + - + +
942A ARG 4.2 13.7 - - - +
944A ILE* 4.1 24.5 - - + -
962A LYS* 3.9 34.8 - - + +
963A SER 4.0 13.0 - - - +
964A GLY 4.2 5.2 - - - +
965A ASN* 1.3 75.0 - - - +
967A LYS* 1.3 64.7 + - - +
968A ALA 3.8 20.4 - - - +
979A SER* 4.3 6.5 - - - -
980A SER 3.6 5.8 - - - +
981A SER* 4.3 7.2 - - - -
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Residues in contact with LYS 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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940A GLU* 3.3 25.0 + - + +
941A ILE* 5.4 2.7 - - - -
965A ASN* 2.9 43.3 + - - +
966A ILE* 1.3 76.1 - - - +
968A ALA* 1.3 59.7 + - + +
980A SER* 2.7 22.7 + - - +
982A GLY 3.6 17.0 - - - +
983A THR* 3.9 20.9 - - - +
1012A THR* 3.8 15.3 - - + -
1013A ILE 3.9 17.7 - - - +
1014A LEU* 4.4 4.5 - - - +
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Residues in contact with ALA 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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941A ILE* 5.1 3.1 - - - +
966A ILE* 3.6 5.1 - - - +
967A LYS* 1.3 80.5 - - + +
969A VAL* 1.3 64.2 + - - +
979A SER* 3.2 5.4 - - - -
980A SER* 3.0 25.2 + - - -
1013A ILE* 3.7 24.7 - - + +
1014A LEU 3.8 14.4 - - - +
1015A THR* 4.7 1.3 - - - -
1016A PHE* 3.8 20.9 - - + -
2188A GOL 4.9 0.9 - - - +
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Residues in contact with VAL 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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921A GLN* 4.1 13.2 + - - +
923A VAL* 4.0 24.9 - - + +
935A ALA* 4.9 0.2 - - + -
941A ILE* 3.8 24.2 - - + -
944A ILE* 3.7 20.9 - - + -
966A ILE* 4.9 0.2 - - + -
968A ALA* 1.3 77.4 - - - +
970A LEU* 1.3 68.2 + - - +
977A LEU* 3.6 29.6 - - + -
978A VAL 3.2 13.7 - - - +
979A SER* 4.5 0.7 - - - -
1016A PHE* 4.0 3.3 - - - -
2188A GOL 3.1 20.4 + - - -
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Residues in contact with LEU 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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923A VAL* 4.2 7.9 - - - -
969A VAL* 1.3 76.7 - - - +
971A GLY* 1.3 72.4 + - - +
972A LEU* 3.9 18.8 - - + -
977A LEU* 3.5 2.2 - - - -
978A VAL* 2.9 38.5 + - + +
1016A PHE* 3.6 40.2 - - + +
1017A ALA* 3.9 10.3 - - - -
1018A GLU* 4.0 5.4 - - + +
2188A GOL 3.7 33.9 - - - +
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Residues in contact with GLY 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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923A VAL* 3.9 4.8 - - - +
924A PRO 3.3 24.6 + - - -
925A VAL* 4.2 7.9 - - - -
926A PRO* 3.7 13.4 - - - +
970A LEU* 1.3 90.8 - - - +
972A LEU* 1.3 60.8 + - - +
976A ARG 3.6 8.1 - - - -
977A LEU* 4.4 1.3 - - - -
1018A GLU* 4.6 1.6 - - - +
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Residues in contact with LEU 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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926A PRO* 3.5 15.0 - - - +
970A LEU* 3.9 15.7 - - + +
971A GLY* 1.3 82.4 - - - +
973A THR* 1.3 71.7 + - - +
974A LYS 3.6 0.5 + - - -
975A ARG 3.6 2.4 + - - -
976A ARG* 2.8 47.2 + - + +
978A VAL* 3.9 28.0 - - + +
991A VAL* 4.4 4.9 - - + -
1018A GLU* 3.4 20.4 - - + +
1026A LEU* 3.8 24.0 - - + -
1040A LEU* 4.2 31.4 - - + -
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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