Contacts of the strand formed by residues 711 - 728 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708A SER* 3.0 31.2 + - - +
709A ASN 3.5 1.0 - - - -
710A ASN* 1.3 86.2 - - - +
712A ILE* 1.3 60.0 + - - +
1074A ASN* 5.7 5.9 - - - -
1075A PHE 3.1 17.0 - - - -
1076A THR* 4.3 3.8 - - - -
1077A THR* 3.7 3.5 + - - -
895B GLN* 4.1 14.4 + - - +
896B ILE* 4.3 0.3 - - - -
897B PRO* 3.1 19.5 - - - +
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Residues in contact with ILE 712 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711A SER* 1.3 74.9 - - - +
713A ALA* 1.3 67.9 + - - +
714A ILE* 4.4 13.7 - - + -
1074A ASN* 3.7 1.7 - - - -
1075A PHE* 2.6 43.4 + - + +
1077A THR* 3.3 28.2 + - + +
1094A VAL* 4.0 25.1 - - + -
1096A VAL* 4.2 16.2 - - + -
1107A ARG* 5.2 2.7 - - + +
894B LEU* 6.0 0.2 - - + -
895B GLN* 3.5 14.6 - - - +
896B ILE* 3.6 31.9 - - + -
897B PRO* 4.6 2.5 - - + -
900B MET* 4.7 1.1 - - + -
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Residues in contact with ALA 713 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712A ILE* 1.3 80.9 - - - +
714A ILE* 1.3 67.5 + - - +
1072A GLU* 4.5 7.2 - - + -
1073A LYS 3.1 11.9 - - - +
1074A ASN* 4.1 1.6 - - - +
894B LEU* 3.5 33.2 - - + +
895B GLN* 3.2 43.5 + - + +
1F NAG 6.1 0.7 - - + -
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Residues in contact with ILE 714 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712A ILE* 4.1 11.1 + - + -
713A ALA* 1.3 80.5 - - - +
715A PRO* 1.3 86.3 - - + +
716A THR* 3.9 3.3 - - - +
1072A GLU* 3.5 5.2 - - - -
1073A LYS* 2.9 29.0 + - - +
1075A PHE* 4.5 8.1 - - + -
1094A VAL* 3.7 30.7 - - + -
1096A VAL* 4.0 11.2 - - + -
1105A THR* 3.8 15.0 - - - +
1106A GLN 4.3 2.2 - - - +
1107A ARG* 3.6 19.7 - - - +
1109A PHE 4.1 2.5 - - - -
1110A TYR* 3.7 26.7 - - + +
894B LEU* 4.5 0.7 - - + -
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Residues in contact with PRO 715 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714A ILE* 1.3 94.2 - - + +
716A THR* 1.3 59.7 + - - +
717A ASN 3.6 13.5 - - - +
1067A TYR* 5.6 0.2 - - - +
1069A PRO* 3.6 29.2 - - + -
1070A ALA 3.9 4.0 - - - +
1071A GLN 3.9 0.2 - - - +
1072A GLU* 3.7 11.8 - - + -
1107A ARG 3.8 10.1 - - - +
1108A ASN* 3.3 29.2 - - - +
1109A PHE* 3.7 1.2 - - + -
1110A TYR* 2.8 26.7 + - - +
894B LEU* 3.8 17.0 - - + -
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Residues in contact with THR 716 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714A ILE 3.9 5.6 - - - +
715A PRO* 1.3 76.4 - - - +
717A ASN* 1.3 62.9 + - - +
1071A GLN* 2.5 28.9 + - - +
1073A LYS* 3.8 33.6 - - + +
1075A PHE* 4.6 0.9 - - + -
1109A PHE* 4.7 9.4 - - - -
1110A TYR* 3.4 38.8 - - + +
1D NAG 4.1 15.9 - - - +
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Residues in contact with ASN 717 (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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715A PRO* 3.6 9.4 - - - +
716A THR* 1.3 78.1 - - - +
718A PHE* 1.3 92.7 + - - +
719A THR* 5.9 1.6 - - - -
919A ASN* 5.4 2.4 + - - -
922A LEU* 4.5 5.4 - - - +
1067A TYR* 4.6 1.6 + - - -
1069A PRO* 4.1 0.2 - - - +
1070A ALA* 2.9 26.4 + - + +
1071A GLN* 3.0 26.0 + - + +
1109A PHE* 4.4 11.6 - - - -
1D NAG 1.4 65.0 + - - +
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Residues in contact with PHE 718 (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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717A ASN* 1.3 95.7 + - - +
719A THR* 1.3 65.2 + - - +
720A ILE* 4.2 16.8 - - + -
906A PHE* 4.1 13.9 - + - -
915A VAL* 4.2 13.9 - - + -
919A ASN* 3.8 25.8 - - + -
922A LEU* 4.8 6.5 - - + +
923A ILE* 3.4 39.5 - - + -
926A GLN* 3.6 17.3 + - - -
1067A TYR* 3.3 41.1 - + + +
1068A VAL 3.6 9.0 - - - +
1069A PRO* 4.6 0.7 - - + -
1070A ALA 4.2 2.7 - - - +
1109A PHE* 3.8 16.4 - + - -
1D NAG 5.0 0.2 - - - +
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Residues in contact with THR 719 (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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717A ASN* 5.9 1.3 - - - -
718A PHE* 1.3 77.7 - - - +
720A ILE* 1.3 64.5 + - - +
721A SER* 3.8 4.1 + - - -
926A GLN* 3.3 9.6 - - - +
1068A VAL* 2.9 45.4 + - - +
1070A ALA* 3.7 23.5 - - + +
1D NAG 5.7 6.7 - - - +
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Residues in contact with ILE 720 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718A PHE* 4.1 13.0 + - + -
719A THR* 1.3 74.3 - - - +
721A SER* 1.3 63.3 + - - +
722A VAL* 6.2 0.2 - - + -
902A MET* 4.0 14.1 - - + -
906A PHE* 5.2 2.7 - - + -
923A ILE* 4.1 23.6 - - + +
926A GLN* 3.1 40.5 + - + +
927A PHE* 4.0 18.4 - - + +
930A ALA* 4.6 2.1 - - - +
1049A LEU* 3.8 18.6 - - + -
1065A VAL* 3.6 27.4 - - + -
1066A THR 3.5 15.5 - - - +
1067A TYR* 4.7 2.9 - - + +
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Residues in contact with SER 721 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719A THR* 3.8 5.1 + - - -
720A ILE* 1.3 75.5 - - - +
722A VAL* 1.3 68.6 + - - +
723A THR* 4.8 3.1 + - - -
930A ALA* 4.4 7.9 - - - -
1064A HIS 3.7 0.2 - - - +
1065A VAL* 3.3 6.0 - - - +
1066A THR* 3.0 41.2 + - - -
1068A VAL* 4.3 10.9 - - - +
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Residues in contact with VAL 722 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721A SER* 1.3 80.8 - - - +
723A THR* 1.3 67.6 + - - +
927A PHE* 4.4 5.2 - - + -
930A ALA* 3.3 39.4 - - + +
931A ILE* 3.8 21.8 - - + +
934A ILE* 3.6 24.3 - - + +
1063A LEU* 5.3 4.7 - - + -
1064A HIS 3.2 7.0 - - - +
1065A VAL* 3.6 28.5 - - + -
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Residues in contact with THR 723 (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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721A SER* 4.8 5.0 + - - -
722A VAL* 1.3 80.3 + - - +
724A THR* 1.3 75.8 + - - +
725A GLU* 5.6 1.1 - - + -
934A ILE* 5.3 0.9 - - - -
1044A GLY* 4.3 19.7 - - - -
1045A LYS* 4.6 14.5 + - + +
1062A PHE 3.2 3.8 - - - +
1063A LEU* 3.2 1.9 - - - -
1064A HIS* 2.7 49.3 + - + +
1066A THR* 5.1 2.1 + - - -
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Residues in contact with THR 724 (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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723A THR* 1.3 81.3 - - - +
725A GLU* 1.3 60.3 + - - +
726A ILE* 4.3 12.0 - - - +
934A ILE* 3.6 32.4 - - + +
938A LEU* 5.0 15.8 - - + +
1061A VAL* 4.6 9.2 - - + -
1062A PHE 3.2 5.4 - - - -
1063A LEU* 3.5 25.1 - - + -
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Residues in contact with GLU 725 (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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723A THR* 5.6 1.8 - - + -
724A THR* 1.3 74.9 - - - +
726A ILE* 1.3 63.0 + - - +
727A LEU* 4.3 17.2 - - + +
947A LYS* 6.0 1.3 - - - +
1028A LYS* 2.2 46.0 + - - +
1042A PHE 4.1 3.6 - - - +
1043A CYS* 4.3 0.5 - - - -
1044A GLY 4.3 2.2 + - - -
1060A VAL 3.8 1.7 - - - +
1061A VAL* 3.5 1.4 - - - +
1062A PHE* 3.0 34.3 + - + +
1064A HIS* 2.5 45.0 + - + +
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Residues in contact with ILE 726 (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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724A THR* 5.0 10.3 - - - +
725A GLU* 1.3 79.9 - - - +
727A LEU* 1.3 70.9 + - - +
728A PRO* 4.7 0.7 - - + -
938A LEU* 5.8 2.7 - - + -
944A ALA 3.2 26.9 - - - +
945A LEU* 3.6 16.4 - - + -
947A LYS* 3.3 41.3 + - + +
948A LEU* 4.1 33.2 - - + +
1060A VAL 3.7 3.4 - - - +
1061A VAL* 3.9 28.9 - - + -
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Residues in contact with LEU 727 (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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725A GLU* 4.3 15.0 - - + +
726A ILE* 1.3 86.2 - - - +
728A PRO* 1.3 68.2 - - + +
947A LYS* 4.3 11.4 - - - +
1021A SER* 4.2 13.0 - - - +
1024A LEU* 4.3 17.9 - - + -
1025A ALA* 3.8 39.3 - - + +
1028A LYS* 3.9 23.6 - - + -
1059A GLY* 3.2 0.8 - - - -
1060A VAL* 2.7 44.2 + - + +
1062A PHE* 4.4 11.0 - - + -
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Residues in contact with PRO 728 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726A ILE* 4.6 2.9 - - + +
727A LEU* 1.3 86.8 - - + +
729A VAL* 1.3 66.7 + - - +
730A SER 3.8 1.8 - - - +
947A LYS* 4.9 21.3 - - + +
948A LEU* 4.3 10.9 - - + -
951A VAL* 4.5 13.2 - - + -
1017A GLU* 5.5 2.7 - - - +
1018A ILE* 4.2 23.7 - - + +
1021A SER* 2.9 38.1 + - - +
1022A ALA 4.0 0.3 + - - -
1058A HIS 3.4 13.5 - - - +
1059A GLY* 3.7 1.8 - - - -
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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
------------------------------------------------------------
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