Contacts of the strand formed by residues 1039 - 1054 (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 PRO1039 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1032C GLY 3.3 9.6 - - - +
1033C ASN* 3.7 11.4 - - - +
1037C GLY 3.5 5.3 - - - +
1038C ASN* 1.3 92.4 - - + +
1040C ILE* 1.3 60.1 + - - +
1041C LYS* 3.9 29.1 + - + +
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Residues in contact with ILE1040 (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* 3.6 61.9 - - + -
176A TYR* 4.7 6.1 - - - +
1030C ASP* 4.1 0.2 - - - -
1031C SER* 2.8 34.8 + - - +
1032C GLY 2.6 13.6 + - - +
1033C ASN* 3.4 11.4 - - - +
1034C ASP* 3.3 41.3 - - + +
1038C ASN 3.9 1.1 - - - +
1039C PRO* 1.3 75.2 - - - +
1041C LYS* 1.3 71.8 + - - +
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Residues in contact with LYS1041 (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* 5.1 0.7 - - - -
176A TYR* 4.7 2.6 + - - -
1028C GLU* 3.5 41.5 + - + +
1029C VAL 3.3 9.9 - - - +
1030C ASP* 2.2 39.9 + - - +
1031C SER* 4.1 0.4 - - - -
1039C PRO* 3.9 27.7 + - + +
1040C ILE* 1.3 87.7 + - - +
1042C ARG* 1.3 66.6 + - - +
1067C PRO* 3.2 31.3 - - + +
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Residues in contact with ARG1042 (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* 4.0 28.8 - - + -
1028C GLU* 3.7 2.4 - - - +
1029C VAL* 2.8 35.7 + - + +
1031C SER* 3.4 20.2 - - - +
1041C LYS* 1.3 77.4 - - - +
1043C ILE* 1.3 65.9 + - - +
1044C GLN 3.7 0.3 + - - -
1064C TYR* 3.6 38.1 - - + +
1065C THR 3.8 9.4 - - - +
1066C ALA* 5.9 1.1 - - - -
1067C PRO* 4.4 0.4 - - - -
1091C GLU* 2.6 41.2 + - - -
1097C HIS* 3.0 28.1 + - - -
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Residues in contact with ILE1043 (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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1026C LYS* 4.1 21.5 - - + +
1027C LYS 3.6 6.7 - - - +
1028C GLU* 4.2 25.1 - - + +
1042C ARG* 1.3 76.9 - - - +
1044C GLN* 1.3 61.4 + - - +
1045C TYR* 3.8 24.2 - - + +
1063C ILE 3.5 1.4 - - - +
1064C TYR* 3.2 7.3 - - - +
1065C THR* 2.8 46.2 + - + +
1066C ALA 4.3 2.0 - - - +
1067C PRO* 3.7 34.5 - - + -
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Residues in contact with GLN1044 (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 3.8 0.7 - - - +
1026C LYS* 3.5 2.8 - - - -
1027C LYS* 2.7 58.8 + - - +
1029C VAL* 3.8 18.1 - - + +
1042C ARG 3.7 0.4 + - - -
1043C ILE* 1.3 72.7 - - - +
1045C TYR* 1.3 61.9 + - - +
1046C GLU* 3.9 2.3 + - - +
1062C PHE* 3.6 40.8 - - + -
1063C ILE 3.6 2.7 - - - -
1064C TYR* 3.0 42.0 + - + -
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Residues in contact with TYR1045 (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* 4.0 8.5 - - + -
1025C ASN 3.3 4.0 - - - -
1026C LYS* 3.1 34.1 - - + +
1043C ILE* 3.8 16.0 - - + +
1044C GLN* 1.3 74.4 - - - +
1046C GLU* 1.3 60.8 - - - +
1047C ILE* 3.6 14.6 + - + +
1062C PHE* 3.2 9.5 - - - -
1063C ILE* 2.7 50.2 + - + +
1065C THR* 3.8 21.1 - - + -
1074C VAL 3.7 4.6 + - - -
1075C SER* 3.5 10.6 + - - -
1076C LEU* 2.9 49.4 + - + -
1078C ILE* 3.5 26.0 - - + -
1098C ILE* 5.6 0.4 - - + -
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Residues in contact with GLU1046 (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* 3.6 1.2 - - - -
1024C VAL* 2.9 41.5 + - + +
1025C ASN* 2.9 32.6 + - + +
1044C GLN* 3.9 3.4 + - - +
1045C TYR* 1.3 71.5 - - - +
1047C ILE* 1.3 67.0 + - - +
1061C GLU* 3.5 10.1 - - + +
1062C PHE* 4.0 23.2 - - + -
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Residues in contact with ILE1047 (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* 3.7 9.6 - - + -
1021C ALA* 3.7 24.9 - - + -
1022C LYS 3.3 13.0 - - - +
1023C ALA* 4.2 7.9 - - + -
1024C VAL* 4.5 5.8 - - - -
1045C TYR* 3.7 19.7 - - + +
1046C GLU* 1.3 82.3 - - - +
1048C LYS* 1.3 59.7 + - - +
1049C GLN* 4.1 3.3 + - - +
1060C ILE* 3.6 38.6 - - + +
1061C GLU* 2.9 39.3 + - - +
1062C PHE 4.3 0.2 - - - +
1063C ILE* 3.8 21.8 - - + -
1076C LEU* 5.3 1.6 - - + -
1086C ILE* 5.7 1.3 - - + -
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Residues in contact with LYS1048 (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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1021C ALA* 3.4 3.0 - - - -
1022C LYS* 2.8 58.8 + - + +
1024C VAL* 4.9 11.1 - - + +
1047C ILE* 1.3 73.1 - - - +
1049C GLN* 1.3 71.8 + - - +
1050C ILE* 3.4 13.1 + - + +
1061C GLU* 4.7 3.8 - - - -
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Residues in contact with GLN1049 (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* 3.7 19.3 - - + +
1020C ARG 3.9 4.3 - - - +
1021C ALA* 4.1 4.3 - - - -
1047C ILE* 4.0 4.8 + - + +
1048C LYS* 1.3 78.6 - - - +
1050C ILE* 1.3 63.3 + - - +
1051C LYS* 4.0 10.9 - - - +
1052C MET* 3.5 35.7 + - - +
1059C ASP* 3.6 27.8 - - + +
1060C ILE* 2.9 52.1 + - - +
1061C GLU* 5.2 1.4 + - - -
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Residues in contact with ILE1050 (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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1020C ARG* 2.9 40.5 + - + +
1021C ALA* 4.1 12.1 - - - -
1022C LYS* 3.8 16.6 - - - +
1048C LYS* 3.8 18.6 - - + +
1049C GLN* 1.3 77.9 - - - +
1051C LYS* 1.3 90.7 + - + +
1083C GLU* 3.3 41.3 - - + +
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Residues in contact with LYS1051 (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* 3.3 5.4 - - - +
1020C ARG* 2.8 40.4 + - + +
1049C GLN* 4.1 7.0 - - - -
1050C ILE* 1.3 108.2 + - + +
1052C MET* 1.3 61.6 + - - +
1053C PHE* 4.1 20.7 + - + -
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Residues in contact with MET1052 (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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1017C ILE* 4.3 7.4 - - + -
1018C VAL 3.7 4.9 - - - +
1019C ILE* 3.8 9.9 - - + -
1049C GLN* 3.5 37.2 + - - +
1051C LYS* 1.3 72.5 - - - +
1053C PHE* 1.3 62.4 + - - +
1054C LYS 3.4 19.1 - - - +
1055C GLY* 3.5 20.6 - - - +
1056C PRO* 3.0 30.1 - - + +
1057C ASP* 5.1 2.5 - - - -
1058C GLN 4.4 4.5 - - - +
1059C ASP* 4.9 0.9 - - - -
1060C ILE* 4.1 13.5 - - + -
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Residues in contact with PHE1053 (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* 4.0 17.5 - - + -
1018C VAL* 2.8 28.4 + - + +
1019C ILE* 4.3 0.7 - - - -
1020C ARG* 4.0 26.0 - - + -
1051C LYS* 4.2 20.2 - - + -
1052C MET* 1.3 75.2 - - - +
1054C LYS* 1.3 63.1 + - - +
1085C LEU* 4.3 1.3 - - + -
1107C TRP* 3.9 21.5 - + - -
1115C LYS 4.9 2.0 - - - -
1118C LEU* 3.6 44.0 - - + +
1119C ASN* 3.5 33.5 - - - +
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Residues in contact with LYS1054 (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* 3.0 33.8 + - + +
1013C CYS* 3.0 27.1 + - - +
1015C ALA 2.9 29.4 + - - +
1016C ASP* 3.7 10.8 - - - +
1017C ILE* 3.3 3.5 - - - +
1018C VAL* 3.0 34.8 + - + +
1052C MET* 3.4 13.3 - - - +
1053C PHE* 1.3 83.9 - - - +
1055C GLY* 1.3 61.3 + - - +
1123C GLN* 4.9 11.3 - - - +
1126C CYS* 5.6 0.2 - - - -
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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