Contacts of the strand formed by residues 1059 - 1078 (chain C) in PDB entry 6VSB
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 GLY1059 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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727C LEU 3.2 13.0 - - - -
728C PRO* 3.8 1.3 - - - -
729C VAL* 3.7 14.8 - - - +
782C PHE* 4.1 9.5 - - - -
948C LEU* 3.8 7.8 - - - +
1056C ALA* 3.0 30.4 + - - +
1057C PRO 3.6 1.2 + - - -
1058C HIS* 1.3 80.8 - - - +
1060C VAL* 1.3 60.8 + - - +
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Residues in contact with VAL1060 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725C GLU 3.9 1.0 - - - +
726C ILE* 3.8 1.1 - - - +
727C LEU* 2.7 38.3 + - + +
729C VAL* 4.2 4.9 - - + -
781C VAL* 4.7 3.1 - - + -
782C PHE* 4.0 25.8 - - + -
948C LEU* 4.9 0.4 - - - +
1025C ALA* 3.8 21.3 - - + -
1029C MET* 4.5 3.1 - - + -
1053C PRO* 4.4 8.7 - - + -
1054C GLN 3.7 12.3 - - - +
1056C ALA* 4.4 0.2 - - - -
1059C GLY* 1.3 74.6 - - - +
1061C VAL* 1.3 68.7 + - - +
1062C PHE* 3.5 37.4 - - + -
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Residues in contact with VAL1061 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724C THR* 4.9 9.2 - - + -
725C GLU 3.3 10.3 - - - +
726C ILE* 4.1 16.6 - - + -
818C ILE* 6.2 0.9 - - + -
822C LEU* 4.0 34.5 - - + -
938C LEU* 5.7 5.2 - - + -
945C LEU* 4.1 22.2 - - + -
948C LEU* 4.5 0.2 - - + -
1053C PRO* 3.6 0.7 - - - +
1054C GLN* 2.7 43.9 + - + +
1055C SER 4.6 0.2 + - - -
1056C ALA* 4.3 11.4 - - + -
1060C VAL* 1.3 77.6 - - - +
1062C PHE* 1.3 70.3 + - - +
1063C LEU* 5.6 3.4 - - + -
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Residues in contact with PHE1062 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724C THR* 3.2 7.8 - - - -
725C GLU* 2.8 37.7 + - - +
727C LEU* 4.1 20.4 - - + -
1025C ALA 3.9 19.3 - - - -
1028C LYS* 4.6 4.9 - - + -
1029C MET* 4.0 21.3 - - + -
1033C VAL* 3.6 31.9 - - + -
1051C SER* 4.9 1.1 - - - -
1052C PHE 3.6 3.1 - - - -
1053C PRO* 4.1 16.8 - - + -
1060C VAL* 3.5 35.2 - - + -
1061C VAL* 1.3 76.6 - - - +
1063C LEU* 1.3 62.7 + - - +
1064C HIS* 3.5 32.1 - + + +
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Residues in contact with LEU1063 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722C VAL* 3.7 14.8 - - + -
723C THR 3.4 4.7 - - - +
724C THR* 4.6 4.3 - - + +
805C ILE* 4.7 6.3 - - + -
818C ILE* 4.2 20.4 - - + -
931C ILE* 4.2 12.8 - - + -
934C ILE* 3.6 31.2 - - + -
1051C SER* 3.1 6.1 - - - -
1052C PHE* 3.0 52.2 + - + +
1054C GLN* 3.4 34.3 - - + -
1061C VAL* 4.7 3.4 - - + +
1062C PHE* 1.3 75.2 - - - +
1064C HIS* 1.3 62.4 + - - +
1065C VAL 3.8 0.9 + - - -
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Residues in contact with HIS1064 (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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721C SER 3.4 2.6 - - - +
722C VAL* 3.3 1.5 - - - -
723C THR* 2.7 50.3 + - - +
724C THR 4.7 0.4 - - - -
725C GLU* 2.8 42.0 + - + -
1028C LYS* 5.3 2.7 - - + -
1032C CYS* 4.3 3.1 - - + -
1043C CYS* 3.4 45.2 - - + +
1044C GLY* 3.8 11.7 - - - -
1048C HIS* 4.8 0.2 - - + -
1051C SER* 2.4 32.1 + - - +
1062C PHE* 3.5 29.3 - + + +
1063C LEU* 1.3 70.7 - - - +
1065C VAL* 1.3 61.9 + - - +
1066C THR* 3.8 2.1 + - + +
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Residues in contact with VAL1065 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720C ILE* 4.2 18.8 - - + -
721C SER 3.9 3.1 - - - +
722C VAL* 3.6 31.0 - - + +
902C MET* 4.8 4.7 - - + -
927C PHE* 3.8 30.1 - - + -
1049C LEU* 3.0 25.8 + - + +
1050C MET* 2.9 44.2 + - + +
1052C PHE* 4.1 10.3 - - + -
1063C LEU 4.5 2.5 - - - +
1064C HIS* 1.3 71.7 - - - +
1066C THR* 1.3 62.6 + - - +
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Residues in contact with THR1066 (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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720C ILE* 3.2 25.0 - - - +
721C SER* 3.3 17.5 + - - -
723C THR* 5.2 2.2 - - - +
1043C CYS 3.7 23.1 - - - +
1044C GLY* 4.0 4.5 - - - +
1045C LYS 2.7 28.8 + - - +
1047C TYR 3.2 18.4 - - - +
1048C HIS* 3.9 7.9 - - + -
1049C LEU* 4.0 6.1 - - - +
1064C HIS 4.3 7.4 + - - +
1065C VAL* 1.3 81.3 - - - +
1067C TYR* 1.3 60.9 + - - +
1068C VAL* 3.8 8.1 + - - +
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Residues in contact with TYR1067 (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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717C ASN 4.6 1.2 + - - -
718C PHE* 3.3 50.3 - + + +
720C ILE* 4.5 4.5 - - + -
906C PHE* 3.6 22.0 - + - -
909C ILE* 3.6 24.9 - - + -
911C VAL* 4.0 22.7 - - + +
1047C TYR* 2.9 43.8 + + - +
1049C LEU* 3.7 15.4 - - + +
1066C THR* 1.3 72.0 - - - +
1068C VAL* 1.3 62.7 + - - +
1069C PRO* 4.2 14.5 - - + +
1108C ASN* 3.4 25.9 + - + -
1109C PHE* 3.7 17.5 - - - +
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Residues in contact with VAL1068 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
890A ALA 4.0 14.8 - - - +
891A GLY* 4.1 6.7 - - - -
718C PHE* 3.4 1.9 - - - -
719C THR* 2.9 49.0 + - - +
721C SER* 4.2 11.7 - - - +
1045C LYS* 4.4 2.9 - - + +
1046C GLY* 4.3 10.8 - - - -
1066C THR* 3.8 18.6 - - - +
1067C TYR* 1.3 83.6 - - - +
1069C PRO* 1.3 81.2 - - + +
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Residues in contact with PRO1069 (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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887A THR* 6.1 1.6 - - - +
890A ALA* 5.0 0.9 - - + -
891A GLY* 4.7 15.0 - - - +
892A ALA* 4.9 13.4 + - + +
894A LEU* 5.3 9.6 - - + -
715C PRO* 3.5 29.8 - - + -
717C ASN 4.0 6.5 - - - +
718C PHE* 4.3 3.8 - - + -
719C THR* 5.0 0.2 + - - -
1047C TYR* 4.3 24.9 - - + -
1067C TYR* 4.2 9.6 - - + +
1068C VAL* 1.3 102.2 - - + +
1070C ALA* 1.3 61.4 + - - +
1108C ASN 4.8 0.7 - - - +
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Residues in contact with ALA1070 (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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892A ALA* 6.1 2.0 - - - -
715C PRO* 3.9 1.7 - - - +
716C THR 3.6 2.1 + - - -
717C ASN* 2.8 27.2 + - + +
718C PHE* 4.6 2.0 - - - -
719C THR* 4.4 25.1 - - + +
1068C VAL 3.8 0.2 + - - -
1069C PRO* 1.3 78.5 - - - +
1071C GLN* 1.3 79.5 + - + +
1072C GLU* 3.6 6.5 - - - -
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Residues in contact with GLN1071 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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716C THR* 2.3 45.5 + - - +
717C ASN* 3.1 34.2 + - + +
1070C ALA* 1.3 79.8 - - + +
1072C GLU* 1.3 58.5 + - - +
1073C LYS* 5.4 0.2 - - - -
1S NAG 3.8 21.6 + - - +
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Residues in contact with GLU1072 (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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892A ALA* 3.9 21.1 - - - +
893A ALA 4.5 1.6 - - - +
894A LEU* 3.5 20.9 - - + +
713C ALA* 4.2 1.1 - - + -
714C ILE 3.2 25.6 - - - +
715C PRO* 3.5 7.4 - - + -
1070C ALA* 3.8 3.8 - - - -
1071C GLN* 1.3 87.8 + - - +
1073C LYS* 1.3 61.6 + - - +
1Q NAG 3.4 38.3 - - + +
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Residues in contact with LYS1073 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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713C ALA* 3.4 26.7 - - - +
714C ILE 3.3 7.4 + - - -
716C THR* 3.8 24.2 - - + +
1071C GLN 5.4 0.2 - - - -
1072C GLU* 1.3 78.8 - - - +
1074C ASN* 1.3 66.5 + - - +
1075C PHE* 3.8 39.8 + - + -
1098C ASN* 6.1 1.6 - - - +
1110C TYR* 5.0 6.5 + - + -
1Q NAG 4.4 4.4 - - - +
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Residues in contact with ASN1074 (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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895A GLN* 3.8 3.6 - - - +
711C SER* 4.5 9.1 + - - +
712C ILE 4.3 1.7 - - - -
1073C LYS* 1.3 76.3 - - - +
1075C PHE* 1.3 69.5 + - - +
1097C SER 5.0 0.2 - - - +
1Q NAG 1.5 71.9 + - - +
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Residues in contact with PHE1075 (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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711C SER* 3.0 10.4 + - - -
712C ILE* 2.7 46.4 + - + +
714C ILE* 4.1 33.9 - - + -
716C THR* 4.6 0.2 - - + -
1073C LYS* 3.8 44.6 - - + -
1074C ASN* 1.3 80.5 - - - +
1076C THR* 1.3 59.3 + - - +
1096C VAL* 4.1 17.9 - - + -
1097C SER 3.6 18.2 - - - +
1098C ASN* 4.8 7.9 - - + -
1110C TYR* 3.5 53.2 - + - -
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Residues in contact with THR1076 (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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710C ASN* 3.1 23.1 + - + +
711C SER* 4.2 1.7 - - - +
1075C PHE* 1.3 74.1 - - - +
1077C THR* 1.3 70.6 + - - +
1096C VAL* 3.2 4.9 - - - -
1097C SER* 2.6 51.1 + - - +
1099C GLY* 5.5 4.4 + - - -
1102C TRP* 4.2 11.9 - - + -
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Residues in contact with THR1077 (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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897A PRO* 3.8 4.2 - - - +
900A MET* 3.7 27.0 - - + -
710C ASN* 2.9 35.0 + - - +
711C SER* 3.4 4.2 + - - -
712C ILE* 3.3 35.9 - - + -
1076C THR* 1.3 80.1 - - - +
1078C ALA* 1.3 66.4 + - - +
1079C PRO* 4.8 0.6 - - - +
1094C VAL* 4.8 0.7 - - + -
1095C PHE 3.1 18.8 - - - +
1096C VAL* 3.9 4.5 - - + -
1102C TRP* 3.4 10.2 - - - -
1133C VAL* 4.8 3.1 - - - +
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Residues in contact with ALA1078 (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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900A MET* 4.4 7.1 - - - +
1077C THR* 1.3 80.8 - - - +
1079C PRO* 1.3 76.4 - - + +
1080C ALA 3.1 10.0 + - - +
1081C ILE* 3.9 3.6 - - + -
1095C PHE* 3.7 23.3 + - - +
1102C TRP* 3.6 18.8 - - + -
1131C GLY 4.2 0.9 - - - +
1133C VAL* 3.6 26.9 - - + -
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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