Contacts of the strand formed by residues 1059 - 1067 (chain A) in PDB entry 7CN9
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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727A LEU 3.5 11.7 - - - -
728A PRO* 4.2 2.5 - - - -
729A VAL* 3.5 13.6 - - - +
782A PHE* 5.0 1.7 - - - -
870A ILE* 5.7 1.6 - - - +
948A LEU* 5.1 5.8 - - - +
1056A ALA* 2.9 27.2 + - - +
1057A PRO 3.5 0.2 - - - -
1058A HIS* 1.3 81.1 - - - +
1060A VAL* 1.3 71.5 + - - +
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Residues in contact with VAL1060 (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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726A ILE* 3.3 4.2 - - - +
727A LEU* 2.9 46.6 + - + +
729A VAL* 3.5 16.8 - - + -
781A VAL* 4.2 4.3 - - + -
782A PHE* 3.3 37.2 - - + -
948A LEU* 4.9 0.8 - - - +
1025A ALA* 4.6 6.1 - - + -
1054A GLN 4.8 5.4 - - - +
1055A SER* 4.7 0.9 - - - -
1056A ALA* 3.3 9.2 - - - +
1059A GLY* 1.3 81.5 - - - +
1061A VAL* 1.3 60.8 + - - +
1062A PHE* 3.2 29.8 - - + -
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Residues in contact with VAL1061 (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* 4.9 4.3 - - - +
725A GLU 3.3 15.7 - - - +
726A ILE* 3.6 17.0 - - + -
822A LEU* 4.2 15.3 - - + -
938A LEU* 5.4 8.1 - - + -
945A LEU* 5.7 2.0 - - + -
948A LEU* 5.7 0.2 - - + -
1054A GLN* 3.0 45.8 + - + +
1055A SER 3.1 24.5 - - - +
1056A ALA* 3.8 3.9 - - + +
1060A VAL* 1.3 74.7 - - - +
1062A PHE* 1.3 80.2 + - - +
1063A LEU* 5.4 6.3 - - + -
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Residues in contact with PHE1062 (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 3.5 5.9 - - - +
725A GLU* 3.0 29.0 + - - +
727A LEU* 4.0 18.2 - - + -
781A VAL* 6.1 1.8 - - + -
782A PHE* 6.1 2.2 - + - -
1025A ALA* 4.9 7.0 - - + -
1028A LYS* 5.6 2.5 - - + -
1029A MET* 4.4 27.4 - - + -
1033A VAL* 5.0 5.6 - - + -
1051A SER* 3.5 4.9 - - - +
1052A PHE 3.9 4.3 - - - +
1053A PRO* 4.2 21.5 - - + -
1054A GLN 4.7 1.1 - - - +
1060A VAL* 3.2 46.9 - - + -
1061A VAL* 1.3 83.0 - - - +
1063A LEU* 1.3 77.6 + - - +
1064A HIS* 3.1 30.5 - + + +
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Residues in contact with LEU1063 (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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722A VAL* 5.4 7.6 - - + -
723A THR 3.2 25.1 - - - +
724A THR* 4.1 6.3 - - - +
805A ILE* 5.3 10.3 - - + -
818A ILE* 5.3 11.9 - - + -
931A ILE* 5.8 7.9 - - + -
934A ILE* 4.3 26.9 - - + -
938A LEU* 5.4 5.6 - - + -
1051A SER* 3.1 3.4 + - - -
1052A PHE* 2.9 46.2 + - + +
1054A GLN* 4.7 16.2 - - + -
1061A VAL* 5.4 6.3 - - + -
1062A PHE* 1.3 84.0 - - - +
1064A HIS* 1.3 60.2 + - - +
1065A VAL* 3.3 8.8 + - + +
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Residues in contact with HIS1064 (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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722A VAL* 4.0 0.5 - - - -
723A THR* 3.7 33.4 + - + -
725A GLU* 3.7 28.9 + - + +
727A LEU* 6.2 1.1 - - + -
1028A LYS* 5.8 9.9 - - + -
1032A CYS* 5.5 0.9 - - + +
1042A PHE 5.6 2.6 + - - -
1043A CYS* 4.7 12.1 - - + +
1044A GLY* 4.2 20.2 - - - +
1048A HIS* 4.4 3.1 - - - +
1050A MET 3.5 5.4 - - - +
1051A SER* 2.3 35.4 + - - -
1062A PHE* 3.1 28.9 - + + +
1063A LEU* 1.3 70.7 - - - +
1065A VAL* 1.3 69.1 + - - +
1066A THR* 3.7 8.1 + - - +
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Residues in contact with VAL1065 (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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720A ILE* 5.2 5.8 - - + -
721A SER 3.2 9.0 - - - +
722A VAL* 4.0 19.3 - - + +
902A MET* 6.3 0.4 - - - -
927A PHE* 4.2 24.9 - - + -
1044A GLY* 4.2 0.3 - - - -
1048A HIS* 4.1 10.2 - - - -
1049A LEU* 3.4 35.1 + - + -
1050A MET* 3.0 33.1 + - + +
1052A PHE* 5.1 5.2 - - + -
1063A LEU* 4.4 7.0 - - + +
1064A HIS* 1.3 79.9 - - - +
1066A THR* 1.3 63.7 + - - +
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Residues in contact with THR1066 (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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720A ILE* 3.3 10.7 - - - +
721A SER* 2.6 64.8 + - - -
722A VAL* 4.6 1.4 + - - -
723A THR* 5.0 7.2 + - - +
1044A GLY* 3.5 6.3 - - - -
1045A LYS* 3.2 47.1 - - + +
1047A TYR 4.1 4.0 - - - -
1049A LEU* 4.1 5.6 - - - -
1064A HIS 3.8 7.0 - - - +
1065A VAL* 1.3 83.4 - - - +
1067A TYR* 1.3 62.4 + - - +
1068A VAL* 4.1 3.3 - - - +
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Residues in contact with TYR1067 (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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718A PHE* 3.5 33.6 - + + -
720A ILE* 3.7 20.4 - - + -
906A PHE* 4.6 10.3 - + + -
909A ILE* 3.4 28.7 - - + -
911A VAL* 5.8 5.1 - - + +
1045A LYS 4.2 0.3 - - - +
1046A GLY* 4.3 0.2 - - - -
1047A TYR* 3.1 43.5 + + + +
1049A LEU* 4.2 19.3 - - + +
1066A THR* 1.3 73.8 - - - +
1068A VAL* 1.3 69.2 + - - +
1069A PRO* 4.2 15.2 - - + +
1108A ASN* 2.7 43.4 + - + +
890B ALA* 4.4 2.0 - - + +
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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