Contacts of the helix formed by residues 945 - 965 (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 LEU 945 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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726C ILE* 3.5 30.3 - - + -
822C LEU* 3.5 53.8 - - + +
825C LYS* 4.0 15.1 + - + +
826C VAL* 3.9 21.0 - - + +
938C LEU* 4.9 5.4 - - + -
943C SER* 4.3 1.5 - - - +
944C ALA* 1.3 79.8 - - + +
946C GLY* 1.3 63.5 + - - +
947C LYS 3.2 3.1 - - - -
948C LEU* 3.0 36.5 + - + -
949C GLN* 3.1 13.4 + - - +
1057C PRO* 5.6 1.1 - - + -
1061C VAL* 4.1 3.4 - - + -
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Residues in contact with GLY 946 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726C ILE* 5.3 0.8 - - - +
943C SER* 4.0 17.0 + - - -
944C ALA 3.6 3.2 + - - -
945C LEU* 1.3 75.7 - - - +
947C LYS* 1.3 62.0 + - - +
949C GLN* 3.9 7.5 - - - +
950C ASP* 3.0 32.7 + - - +
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Residues in contact with LYS 947 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725C GLU* 5.7 1.8 + - - +
726C ILE* 3.0 47.9 + - + +
727C LEU* 4.0 14.1 - - - +
728C PRO* 4.7 16.4 - - + +
945C LEU 3.2 1.2 - - - -
946C GLY* 1.3 76.7 - - - +
948C LEU* 1.3 62.7 + - - +
950C ASP* 3.9 7.0 - - - +
951C VAL* 3.7 22.9 + - - +
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Residues in contact with LEU 948 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726C ILE* 3.6 21.5 - - + -
728C PRO* 4.0 14.8 - - + -
826C VAL* 4.6 8.5 - - + -
945C LEU* 3.0 39.2 + - + +
947C LYS* 1.3 75.2 - - - +
949C GLN* 1.3 67.5 + - - +
951C VAL* 3.4 7.1 + - - +
952C VAL* 3.4 24.2 + - - +
1056C ALA* 3.8 26.7 - - + -
1057C PRO* 4.1 10.3 - - + -
1058C HIS* 3.9 13.6 - - + +
1059C GLY* 3.8 26.0 - - - +
1061C VAL* 4.5 1.6 - - + -
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Residues in contact with GLN 949 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
825C LYS 4.4 2.1 - - - +
826C VAL* 3.6 17.1 - - + +
827C THR* 2.7 46.3 + - - +
945C LEU 3.1 14.6 + - - +
946C GLY* 3.9 7.2 - - - +
948C LEU* 1.3 74.4 - - - +
950C ASP* 1.3 61.4 + - - +
952C VAL* 3.2 13.3 + - - +
953C ASN* 2.8 65.1 + - - +
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Residues in contact with ASP 950 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
946C GLY* 3.0 21.9 + - - +
947C LYS* 3.9 8.3 - - - +
948C LEU 3.3 0.2 - - - -
949C GLN* 1.3 77.9 - - - +
951C VAL* 1.3 58.8 + - + +
953C ASN* 3.3 11.2 + - - +
954C GLN* 2.8 52.1 + - - +
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Residues in contact with VAL 951 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728C PRO* 3.8 27.1 - - + -
730C SER 3.6 22.9 - - - +
731C MET* 4.3 12.1 - - + -
947C LYS 3.7 13.2 + - - +
948C LEU* 3.4 8.6 + - + +
949C GLN 3.3 0.6 - - - -
950C ASP* 1.3 77.0 - - + +
952C VAL* 1.3 66.2 + - + +
954C GLN* 3.4 9.6 + - - +
955C ASN* 3.1 22.4 + - + +
1014C ARG* 5.4 3.9 - - - +
1017C GLU* 5.8 1.1 - - - +
1018C ILE* 4.0 20.9 - - + -
1058C HIS* 5.1 5.8 - - + -
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Residues in contact with VAL 952 (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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732C THR* 6.2 1.6 - - + -
826C VAL* 6.2 4.0 - - + -
827C THR 5.1 1.1 - - - +
828C LEU* 4.2 28.5 - - + +
948C LEU* 3.4 13.4 + - + +
949C GLN* 3.2 22.4 + - - +
951C VAL* 1.3 77.8 - - + +
953C ASN* 1.3 65.7 + - - +
955C ASN* 3.3 8.0 + - - +
956C ALA* 3.0 25.2 + - + +
1057C PRO* 6.2 0.9 - - + -
1058C HIS* 3.4 35.4 - - + +
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Residues in contact with ASN 953 (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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949C GLN* 2.8 55.9 + - - +
950C ASP* 3.7 11.7 + - - +
952C VAL* 1.3 76.4 - - - +
954C GLN* 1.3 57.5 + - + +
956C ALA* 3.3 6.4 + - - +
957C GLN* 2.8 31.3 + - - +
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Residues in contact with GLN 954 (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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950C ASP* 2.8 43.9 + - - +
951C VAL* 3.9 7.6 - - - +
953C ASN* 1.3 73.9 - - + +
955C ASN* 1.3 63.4 + - - +
957C GLN* 3.3 6.2 + - - +
958C ALA* 3.0 23.7 + - - +
1014C ARG* 3.1 45.2 + - - +
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Residues in contact with ASN 955 (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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731C MET* 5.0 14.7 - - + +
732C THR* 2.3 43.0 + - + +
734C THR* 4.7 1.9 - - - -
860C VAL* 5.9 0.6 - - - +
951C VAL 3.1 17.1 + - - +
952C VAL* 3.7 7.0 + - - +
954C GLN* 1.3 77.4 - - - +
956C ALA* 1.3 64.5 + - - +
958C ALA* 3.3 6.7 + - - +
959C LEU* 3.2 38.1 + - - +
1007C TYR* 4.5 2.4 + - - -
1011C GLN* 3.7 24.8 + - - +
1014C ARG* 4.9 2.8 - - - +
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Residues in contact with ALA 956 (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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952C VAL* 3.0 20.2 + - + +
953C ASN* 3.7 7.2 - - - +
955C ASN* 1.3 80.6 - - - +
957C GLN* 1.3 57.8 + - - +
959C LEU* 3.2 9.0 + - - +
960C ASN* 2.9 30.3 + - - +
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Residues in contact with GLN 957 (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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765A ARG* 3.6 35.2 - - - +
953C ASN 2.8 17.5 + - - +
954C GLN* 3.7 7.6 - - - +
955C ASN 3.3 0.2 - - - -
956C ALA* 1.3 77.4 - - - +
958C ALA* 1.3 61.1 + - - +
960C ASN* 3.3 12.9 + - - +
961C THR* 2.9 39.9 + - - -
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Residues in contact with ALA 958 (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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765A ARG* 5.2 4.2 - - - +
954C GLN 3.0 13.3 + - - +
955C ASN 3.6 7.6 - - - +
956C ALA 3.3 0.2 - - - -
957C GLN* 1.3 76.6 - - - +
959C LEU* 1.3 59.0 + - - +
961C THR* 3.5 6.1 + - - -
962C LEU* 3.0 28.2 + - - +
1007C TYR* 3.5 27.6 - - + -
1010C GLN* 6.1 2.9 - - + -
1011C GLN* 4.3 12.6 - - - +
1014C ARG* 4.6 9.2 - - - +
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Residues in contact with LEU 959 (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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734C THR* 3.8 15.3 - - - +
853C GLN 5.1 16.2 - - - +
858C LEU* 4.1 23.3 - - + -
860C VAL* 4.9 13.9 - - + -
955C ASN* 3.2 32.5 + - - +
956C ALA* 3.2 8.3 + - - +
958C ALA* 1.3 75.4 - - - +
960C ASN* 1.3 65.6 + - - +
962C LEU* 3.2 5.7 + - + +
963C VAL* 2.9 32.0 + - + +
1007C TYR* 3.2 31.6 - - + +
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Residues in contact with ASN 960 (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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569B ILE* 5.1 7.4 - - - +
956C ALA 2.9 17.2 + - - +
957C GLN* 3.3 15.2 + - - +
959C LEU* 1.3 75.4 - - - +
961C THR* 1.3 58.1 + - - +
963C VAL* 3.4 6.0 + - - +
964C LYS* 2.9 38.4 + - - +
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Residues in contact with THR 961 (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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758A SER* 3.7 11.0 - - - +
762A GLN* 3.3 43.1 - - + +
765A ARG* 3.4 19.0 + - - +
957C GLN* 2.9 25.3 + - - +
958C ALA* 3.8 5.2 - - - -
960C ASN* 1.3 73.5 - - - +
962C LEU* 1.3 66.7 + - - +
964C LYS* 3.2 8.0 + - + +
965C GLN* 3.1 22.6 + - + +
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Residues in contact with LEU 962 (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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736C VAL* 4.7 2.0 - - + -
741C TYR* 2.5 61.1 + - + +
858C LEU* 4.1 26.9 - - + -
958C ALA 3.0 17.5 + - - +
959C LEU* 3.5 6.7 - - + +
961C THR* 1.3 79.1 - - - +
963C VAL* 1.3 61.3 + - - +
965C GLN* 3.4 6.2 + - - +
966C LEU* 3.4 1.6 - - - +
1003C SER* 3.9 29.4 - - - +
1004C LEU* 4.2 11.9 - - + -
1007C TYR* 3.9 37.5 - - + -
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Residues in contact with VAL 963 (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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569B ILE* 4.7 8.5 - - + -
570B ALA* 3.2 25.9 - - + +
853C GLN 5.8 1.6 - - - +
855C PHE* 4.2 32.3 - - + -
856C ASN* 5.2 4.0 - - - +
858C LEU* 3.5 30.7 - - + -
959C LEU* 2.9 22.4 + - + +
960C ASN* 3.8 7.4 - - - +
962C LEU* 1.3 73.3 - - - +
964C LYS* 1.3 67.9 + - - +
966C LEU* 3.0 28.5 + - + +
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Residues in contact with LYS 964 (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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758A SER* 5.7 2.5 - - - +
569B ILE* 3.5 32.3 - - + +
570B ALA* 4.5 6.0 - - - +
49C HIS* 5.4 11.7 + - - -
960C ASN* 2.9 30.4 + - - +
961C THR* 3.2 9.8 + - + +
963C VAL* 1.3 75.9 - - - +
965C GLN* 1.4 59.0 + - - +
966C LEU 3.1 0.2 - - - -
967C SER* 2.9 52.7 + - - -
968C SER* 4.2 0.7 + - - -
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Residues in contact with GLN 965 (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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756A TYR 3.7 12.2 + - - +
757A GLY* 4.2 3.2 - - - -
758A SER* 2.9 42.8 + - - +
759A PHE* 3.9 11.1 - - - +
762A GLN* 3.5 12.8 - - - +
741C TYR* 4.1 3.6 - - - +
961C THR* 3.1 17.1 + - + +
962C LEU 3.5 9.2 - - - +
963C VAL 3.1 0.6 - - - -
964C LYS* 1.4 75.4 - - - +
966C LEU* 1.3 62.2 + - - +
967C SER 3.1 0.4 - - - -
968C SER* 3.1 23.6 + - - -
970C PHE* 3.7 29.5 - - + -
1000C ARG* 5.1 2.7 - - + +
1003C SER* 3.0 29.7 + - - +
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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