Contacts of the strand formed by residues 711 - 728 (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 SER 711 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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895A GLN* 3.2 23.2 + - - +
897A PRO* 3.3 14.2 - - - +
706C ALA 5.3 0.6 + - - -
708C SER* 3.6 27.3 - - - +
710C ASN* 1.3 82.1 - - - +
712C ILE* 1.3 61.4 + - - +
1074C ASN* 4.5 15.1 + - - +
1075C PHE 3.0 14.7 + - - -
1076C THR* 4.9 1.8 - - - -
1077C THR* 3.4 2.5 + - - -
1Q NAG 5.2 0.5 - - - -
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Residues in contact with ILE 712 (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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894A LEU* 5.7 1.1 - - + -
895A GLN* 3.1 11.7 - - - +
896A ILE* 3.8 31.6 - - + -
897A PRO* 4.5 3.1 - - + -
900A MET* 5.2 1.6 - - + -
711C SER* 1.3 74.0 - - - +
713C ALA* 1.3 70.6 + - - +
714C ILE* 3.8 25.6 - - + -
1073C LYS 3.9 0.2 - - - +
1074C ASN* 4.3 0.8 - - - -
1075C PHE* 2.7 39.3 + - + +
1077C THR* 3.3 28.8 + - + +
1094C VAL* 4.1 22.2 - - + -
1096C VAL* 3.9 4.0 - - + -
1107C ARG* 5.1 5.2 - - + +
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Residues in contact with ALA 713 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894A LEU* 3.5 44.5 - - + +
895A GLN* 3.2 21.9 + - - +
712C ILE* 1.3 78.4 - - - +
714C ILE* 1.3 63.8 + - - +
1072C GLU* 4.2 0.2 - - + -
1073C LYS 3.4 8.1 - - - +
1107C ARG 5.6 0.2 - - - +
1Q NAG 3.5 26.9 - - + -
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Residues in contact with ILE 714 (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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712C ILE* 3.8 18.7 + - + -
713C ALA* 1.3 80.4 - - - +
715C PRO* 1.3 85.1 - - + +
716C THR* 3.5 6.2 + - - +
1072C GLU* 3.2 16.7 - - - +
1073C LYS 3.3 11.9 + - - -
1075C PHE* 4.1 16.1 - - + -
1094C VAL* 4.2 8.5 - - + -
1096C VAL* 3.4 33.7 - - + -
1105C THR* 4.0 13.2 - - + -
1106C GLN 4.2 4.5 - - - +
1107C ARG* 4.1 15.0 - - - +
1109C PHE 4.2 2.2 - - - -
1110C TYR* 3.7 20.2 - - + +
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Residues in contact with PRO 715 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894A LEU* 3.7 23.6 - - + -
714C ILE* 1.3 88.3 - - + +
716C THR* 1.3 54.9 + - - +
717C ASN 3.5 11.7 - - - +
1069C PRO* 3.5 28.9 - - + -
1070C ALA 3.9 4.5 - - - +
1072C GLU* 3.5 13.4 - - + -
1107C ARG 4.2 5.6 - - - +
1108C ASN 3.1 29.4 - - - +
1109C PHE* 3.5 1.9 - - - -
1110C TYR* 2.8 32.1 + - - +
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Residues in contact with THR 716 (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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714C ILE 3.5 9.4 - - - +
715C PRO* 1.3 73.0 - - - +
717C ASN* 1.3 62.7 + - - +
1071C GLN* 2.3 35.9 + - - +
1073C LYS* 3.8 28.2 - - + +
1075C PHE* 4.6 0.4 - - + -
1109C PHE* 3.7 14.9 - - - -
1110C TYR* 3.5 38.1 - - + -
1S NAG 4.7 10.4 - - - +
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Residues in contact with ASN 717 (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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715C PRO* 3.8 9.2 - - - +
716C THR* 1.3 78.4 - - - +
718C PHE* 1.3 92.6 + - - +
719C THR* 5.6 0.9 - - - -
922C LEU* 4.6 5.4 - - - +
1067C TYR* 4.6 0.2 + - - -
1069C PRO* 4.0 0.3 - - - +
1070C ALA* 2.8 29.2 + - + +
1071C GLN* 3.1 23.4 + - + +
1109C PHE* 3.4 13.6 - - - -
1S NAG 1.4 63.5 + - - +
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Residues in contact with PHE 718 (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* 1.3 95.3 + - - +
719C THR* 1.3 64.9 + - - +
720C ILE* 4.0 17.3 - - + -
906C PHE* 4.1 4.3 - + - -
915C VAL* 4.0 21.8 - - + -
919C ASN* 4.7 11.4 - - + -
922C LEU* 5.2 6.5 - - + +
923C ILE* 3.3 43.3 - - + -
926C GLN* 3.4 16.4 + - - +
1067C TYR* 3.3 45.3 - + + -
1068C VAL 3.4 11.2 - - - +
1069C PRO* 4.4 0.2 - - + -
1070C ALA 4.1 2.9 - - - +
1109C PHE* 3.8 20.0 - + - -
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Residues in contact with THR 719 (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* 5.6 0.4 - - - -
718C PHE* 1.3 77.9 - - - +
720C ILE* 1.3 64.7 + - - +
721C SER* 3.8 3.5 + - - -
926C GLN* 3.2 15.0 - - - +
1068C VAL* 2.9 40.7 + - - +
1070C ALA* 4.4 17.8 - - + +
1S NAG 4.9 16.6 - - - +
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Residues in contact with ILE 720 (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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718C PHE* 4.0 26.2 - - + -
719C THR* 1.3 76.4 - - - +
721C SER* 1.3 59.6 + - - +
722C VAL* 5.7 0.9 - - + -
800C PHE* 5.0 1.3 - - + -
902C MET* 5.1 4.5 - - + -
906C PHE* 4.8 2.0 - - + -
923C ILE* 3.9 22.4 - - + -
926C GLN* 3.2 22.6 + - + +
927C PHE* 3.6 50.5 - - + +
930C ALA* 4.5 3.1 - - - +
1049C LEU* 4.7 9.0 - - + -
1065C VAL* 4.2 11.7 - - + -
1066C THR 3.2 16.2 - - - +
1067C TYR* 4.5 7.9 - - - +
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Residues in contact with SER 721 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719C THR* 3.8 5.5 + - - -
720C ILE* 1.3 75.8 - - - +
722C VAL* 1.3 63.8 + - - +
723C THR* 3.4 14.0 + - - +
930C ALA* 4.6 4.5 - - - -
1045C LYS 5.4 0.2 + - - -
1064C HIS 3.4 3.3 - - - +
1066C THR* 3.3 34.5 + - - -
1068C VAL* 4.2 10.6 - - - +
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Residues in contact with VAL 722 (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 5.5 0.9 - - - +
721C SER* 1.3 71.8 - - - +
723C THR* 1.3 61.6 + - - +
724C THR* 4.4 0.3 - - - +
927C PHE* 4.5 9.0 - - + +
930C ALA* 3.6 26.5 - - + +
931C ILE* 4.0 16.4 - - + -
934C ILE* 3.3 36.9 - - + +
1063C LEU* 3.7 24.9 - - + -
1064C HIS 3.3 4.3 - - - +
1065C VAL* 3.6 34.8 - - + -
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Residues in contact with THR 723 (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* 4.3 17.7 - - - +
722C VAL* 1.3 77.8 - - - +
724C THR* 1.3 61.2 + - - +
1044C GLY* 3.7 14.2 - - - -
1045C LYS* 4.9 18.2 - - + +
1063C LEU* 3.4 4.2 - - - -
1064C HIS* 2.7 51.5 + - - +
1066C THR* 5.3 0.7 - - - +
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Residues in contact with THR 724 (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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722C VAL 4.4 0.2 - - - +
723C THR* 1.3 85.0 + - - +
725C GLU* 1.3 63.2 + - - +
726C ILE* 5.4 7.4 - - - +
934C ILE* 3.8 39.3 - - + -
938C LEU* 5.6 9.4 - - + +
1061C VAL* 4.9 10.1 - - + -
1062C PHE 3.2 10.1 - - - +
1063C LEU* 4.8 5.4 - - + -
1064C HIS* 4.7 2.2 - - - -
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Residues in contact with GLU 725 (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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724C THR* 1.3 77.8 - - - +
726C ILE* 1.3 72.3 + - - +
727C LEU* 4.2 16.1 - - + +
947C LYS* 5.7 1.5 + - - +
1024C LEU* 5.4 0.3 - - - +
1028C LYS* 2.9 43.8 + - - +
1042C PHE 4.2 0.9 - - - +
1044C GLY 4.9 0.9 + - - -
1060C VAL 3.9 0.7 - - - +
1061C VAL* 3.3 5.9 - - - +
1062C PHE* 2.8 34.8 + - + +
1064C HIS* 2.8 34.7 + - + +
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Residues in contact with ILE 726 (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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724C THR* 5.4 7.0 - - - +
725C GLU* 1.3 82.8 - - - +
727C LEU* 1.3 69.0 + - - +
938C LEU* 5.7 3.1 - - + -
944C ALA 3.2 27.8 - - - +
945C LEU* 3.5 19.1 - - + -
946C GLY 5.3 0.7 - - - +
947C LYS* 3.0 46.7 + - + +
948C LEU* 3.6 36.6 - - + +
1060C VAL 3.8 2.9 - - - +
1061C VAL* 4.1 13.0 - - + -
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Residues in contact with LEU 727 (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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725C GLU* 4.2 15.5 - - + +
726C ILE* 1.3 83.9 - - - +
728C PRO* 1.3 66.8 - - + +
947C LYS* 4.0 12.3 - - - +
948C LEU* 4.1 3.3 - - - +
1021C SER* 4.2 12.8 - - - +
1024C LEU* 4.2 20.0 - - + -
1025C ALA* 3.8 37.0 - - + +
1028C LYS* 3.8 22.2 - - + -
1059C GLY* 3.2 1.5 - - - -
1060C VAL* 2.7 40.2 + - + +
1062C PHE* 4.1 16.8 - - + -
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Residues in contact with PRO 728 (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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726C ILE 4.6 2.2 - - - +
727C LEU* 1.3 85.2 - - + +
729C VAL* 1.3 66.9 + - - +
730C SER 3.8 4.3 - - - +
947C LYS* 4.7 19.3 - - + +
948C LEU* 4.0 10.1 - - + -
951C VAL* 3.8 30.1 - - + -
1017C GLU* 5.5 3.4 - - - +
1018C ILE* 4.5 9.3 - - + +
1021C SER* 2.9 40.2 + - - +
1022C ALA 3.9 0.5 + - - -
1058C HIS 3.4 14.6 - - - +
1059C GLY* 3.8 0.9 - - - -
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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
------------------------------------------------------------
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