Contacts of the strand formed by residues 1017 - 1033 (chain C) in PDB entry 2E2D
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 ILE1017 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1015C ALA* 3.6 0.7 - - - +
1016C ASP* 1.3 84.9 - - + +
1018C VAL* 1.3 69.5 + - - +
1019C ILE* 3.9 22.4 - - + -
1052C MET* 4.3 6.3 - - + -
1054C LYS 3.3 8.3 - - - +
1056C PRO* 3.9 17.5 - - + -
1060C ILE* 3.7 25.1 - - + -
1086C ILE 3.7 0.2 - - - +
1087C ALA* 3.1 4.0 - - - -
1088C GLY 2.9 33.0 + - - +
1090C ALA* 3.4 36.6 - - + +
1095C ASN 4.6 0.9 - - - +
1096C MET* 3.9 25.1 - - + -
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Residues in contact with VAL1018 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1012C PHE* 3.8 53.6 - - + +
1015C ALA* 4.2 2.7 - - + -
1017C ILE* 1.3 79.0 - - - +
1019C ILE* 1.3 60.4 + - - +
1053C PHE* 2.8 38.3 + - + -
1054C LYS* 3.0 18.8 + - + +
1085C LEU* 4.1 22.9 - - + -
1086C ILE 3.4 5.8 - - - +
1087C ALA* 4.1 16.2 - - + -
1118C LEU* 4.2 7.9 - - + -
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Residues in contact with ILE1019 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1017C ILE* 3.9 13.9 - - + -
1018C VAL* 1.3 78.8 - - - +
1020C ARG* 1.3 61.2 + - - +
1021C ALA* 3.8 10.8 - - + -
1047C ILE* 3.7 29.2 - - + -
1049C GLN* 3.7 23.8 - - + +
1051C LYS 3.3 12.1 - - - +
1052C MET* 3.8 10.1 - - + -
1053C PHE* 4.3 6.7 - - - -
1060C ILE* 4.2 7.2 - - + -
1063C ILE* 4.7 1.3 - - + -
1084C TYR 3.5 0.2 - - - +
1085C LEU* 3.5 5.3 - - - +
1086C ILE* 2.7 57.4 + - + +
1096C MET* 4.0 20.9 - - - -
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Residues in contact with ARG1020 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1019C ILE* 1.3 72.1 - - - +
1021C ALA* 1.3 65.5 + - - +
1049C GLN* 3.8 1.2 - - - -
1050C ILE* 2.9 49.2 + - + +
1051C LYS* 2.8 28.6 + - + +
1053C PHE* 4.0 14.5 - - + -
1083C GLU* 2.8 33.3 + - + +
1084C TYR 3.3 7.0 - - - +
1085C LEU* 4.7 0.9 - - - +
1107C TRP* 3.4 57.0 - - + +
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Residues in contact with ALA1021 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1019C ILE* 3.8 14.1 - - + -
1020C ARG* 1.3 79.1 - - - +
1022C LYS* 1.3 61.6 + - - +
1047C ILE* 3.7 25.4 - - + -
1048C LYS 3.4 14.8 - - - +
1049C GLN* 4.1 1.3 - - - -
1050C ILE* 4.1 7.4 - - - -
1083C GLU* 3.5 1.6 - - - -
1084C TYR* 2.8 39.1 + - - +
1086C ILE* 4.4 11.0 - - + -
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Residues in contact with LYS1022 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1021C ALA* 1.3 77.4 - - - +
1023C ALA* 1.3 61.8 + - - +
1024C VAL* 4.0 7.0 + - + +
1047C ILE* 3.3 5.1 - - - +
1048C LYS* 2.8 56.6 + - + +
1050C ILE* 3.8 18.0 - - + +
1080C GLY* 2.9 43.7 + - - +
1081C LYS* 3.9 8.4 + - - +
1082C LYS 3.8 14.6 - - - +
1083C GLU* 3.5 20.9 + - + +
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Residues in contact with ALA1023 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1022C LYS* 1.3 75.3 - - - +
1024C VAL* 1.3 62.5 + - - +
1045C TYR* 4.0 26.2 - - + -
1046C GLU 3.6 7.6 - - - +
1047C ILE* 4.2 6.3 - - + -
1076C LEU* 4.3 17.0 - - + -
1077C ASP 3.5 26.9 + - - +
1078C ILE* 3.5 8.0 - - + -
1080C GLY* 3.6 12.1 + - - -
1082C LYS 4.4 2.4 + - - +
1084C TYR* 5.1 3.9 - - + -
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Residues in contact with VAL1024 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1022C LYS* 4.5 12.1 - - + +
1023C ALA* 1.3 78.6 - - - +
1025C ASN* 1.3 68.8 + - + +
1046C GLU* 2.9 39.9 + - + +
1047C ILE* 4.5 6.1 - - - -
1048C LYS* 5.1 10.3 - - + -
1078C ILE* 3.6 17.9 - - - +
1080C GLY* 4.3 15.9 - - - +
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Residues in contact with ASN1025 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1023C ALA 3.8 0.6 - - - -
1024C VAL* 1.3 83.8 - - - +
1026C LYS* 1.3 79.3 + - - +
1027C LYS* 5.5 1.2 - - - +
1044C GLN 4.4 0.2 - - - -
1045C TYR* 3.3 10.2 - - - -
1046C GLU* 2.9 51.4 + - + +
1078C ILE* 3.7 11.6 - - - +
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Residues in contact with LYS1026 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1025C ASN* 1.3 87.1 + - - +
1027C LYS* 1.3 64.7 + - - +
1043C ILE* 4.1 15.0 - - + +
1044C GLN 3.5 3.8 - - - -
1045C TYR* 3.1 45.1 - - + +
1076C LEU 5.4 1.3 - - - +
1078C ILE* 3.6 29.1 - - + +
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Residues in contact with LYS1027 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1025C ASN* 5.5 1.3 - - - +
1026C LYS* 1.3 76.8 - - - +
1028C GLU* 1.3 75.2 + - - +
1029C VAL* 4.7 7.0 - - + -
1043C ILE* 3.6 5.9 - - - +
1044C GLN* 2.7 57.5 + - + +
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Residues in contact with GLU1028 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1027C LYS* 1.3 88.0 - - - +
1029C VAL* 1.3 63.5 + - - +
1030C ASP* 4.8 2.2 - - - +
1041C LYS* 3.5 47.0 + - + +
1042C ARG 3.7 3.4 - - - +
1043C ILE* 4.2 18.6 - - + +
1067C PRO* 5.8 1.6 - - + +
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Residues in contact with VAL1029 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1027C LYS* 4.3 10.5 - - + +
1028C GLU* 1.3 81.0 - - - +
1030C ASP* 1.3 76.5 + - - +
1031C SER* 3.3 4.3 + - - +
1041C LYS* 3.3 6.7 - - - -
1042C ARG* 2.8 35.8 + - + +
1044C GLN* 3.8 39.3 - - + +
1064C TYR* 4.6 11.2 - - + +
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Residues in contact with ASP1030 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1028C GLU* 4.8 2.9 - - - +
1029C VAL* 1.3 84.1 - - - +
1031C SER* 1.3 62.1 + - - +
1032C GLY 3.7 3.1 - - - +
1040C ILE 4.1 3.8 - - - -
1041C LYS* 2.2 35.4 + - - +
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Residues in contact with SER1031 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A PHE* 4.2 20.7 - - - -
1029C VAL* 3.3 12.6 + - - +
1030C ASP* 1.3 77.3 + - - +
1032C GLY* 1.3 60.8 + - - +
1040C ILE* 2.8 27.9 + - - +
1042C ARG* 3.4 31.3 + - - +
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Residues in contact with GLY1032 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1030C ASP* 3.7 3.8 - - - +
1031C SER* 1.3 78.8 - - - +
1033C ASN* 1.3 66.2 + - - +
1039C PRO* 3.3 4.7 - - - +
1040C ILE* 2.6 30.8 + - - +
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Residues in contact with ASN1033 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1032C GLY* 1.3 80.7 - - - +
1034C ASP* 1.3 69.3 + - - +
1037C GLY* 3.0 26.7 + - - +
1038C ASN 3.1 6.1 - - - +
1039C PRO* 3.7 17.6 - - - +
1040C ILE* 3.4 10.1 - - - +
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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