Contacts of the helix formed by residues 951 - 968 (chain A) in PDB entry 2DFS
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 MET 951 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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952A ASN* 1.3 76.6 + - + +
953A ASN 2.9 9.5 + - - -
954A LEU* 3.1 13.2 + - - +
955A GLU 4.0 0.9 + - - -
52G ILE 5.4 0.2 - - - -
53G ASN 5.1 0.8 - - - +
54G GLU* 2.6 43.0 + - - +
55G VAL* 3.3 22.8 - - + +
56G ASP* 3.2 42.2 - - - +
57G ALA* 2.7 20.5 - - - +
58G ASP* 2.7 29.6 - - - +
59G GLY* 3.2 36.6 - - - +
60G ASN* 3.5 13.0 - - + +
77S LYS* 5.5 5.2 - - - +
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Residues in contact with ASN 952 (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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951A MET* 1.3 90.3 - - - +
953A ASN* 1.3 59.2 + - - +
954A LEU 3.6 0.4 - - - -
955A GLU* 3.0 31.2 + - - -
956A ILE* 3.9 22.9 + - - +
55G VAL* 3.5 9.8 - - - +
59G GLY* 3.0 27.7 - - - +
77S LYS* 4.5 2.4 - - - +
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Residues in contact with ASN 953 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
951A MET 2.9 0.4 + - - -
952A ASN* 1.3 79.1 - - - +
954A LEU* 1.4 59.5 + - - +
956A ILE* 3.2 28.1 - - - +
957A THR* 4.4 4.5 + - - -
58G ASP* 3.1 39.7 + - - +
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Residues in contact with LEU 954 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
951A MET 3.1 7.3 + - - +
953A ASN* 1.4 77.6 - - - +
955A GLU* 1.4 66.7 + - - +
956A ILE 3.1 2.2 - - - -
957A THR* 2.8 29.8 + - - -
958A TYR* 3.4 56.4 + - + -
53G ASN* 2.9 38.8 - - + +
54G GLU 2.7 33.9 - - - +
55G VAL* 4.2 1.8 - - + +
58G ASP* 4.0 3.6 + - - +
954M LEU* 4.9 3.8 - - + -
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Residues in contact with GLU 955 (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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951A MET 4.0 0.8 + - - -
952A ASN* 3.0 29.9 + - - +
953A ASN 3.6 0.4 - - - -
954A LEU* 1.4 86.9 - - - +
956A ILE* 1.3 67.2 + - + +
958A TYR* 3.6 2.2 + - - +
959A SER* 3.1 28.8 + - - -
55G VAL* 3.4 33.5 - - + +
77S LYS* 2.8 28.9 + - - -
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Residues in contact with ILE 956 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
952A ASN* 3.9 16.4 - - - +
953A ASN* 3.2 36.8 - - + +
955A GLU* 1.3 84.3 - - + +
957A THR* 1.3 62.8 + - - +
959A SER* 3.5 7.9 - - - -
960A THR* 3.4 23.9 + - - +
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Residues in contact with THR 957 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
953A ASN 4.4 3.5 + - - -
954A LEU* 2.8 16.0 + - - -
956A ILE* 1.3 79.3 - - - +
958A TYR* 1.4 67.6 + - + -
959A SER 3.2 1.3 - - - -
960A THR* 2.7 25.9 + - - +
961A GLU* 2.9 17.6 + - + +
958M TYR* 5.3 9.6 - - + +
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Residues in contact with TYR 958 (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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954A LEU* 3.4 44.5 + - + +
955A GLU* 4.4 3.4 - - - +
957A THR* 1.4 77.0 - - - +
959A SER* 1.4 61.5 + - - +
961A GLU* 3.2 8.9 + - - +
962A THR* 3.0 31.2 + - + +
53G ASN* 4.7 10.6 + - - +
954M LEU* 3.8 26.5 + - + -
955M GLU* 4.3 8.3 - - - -
957M THR* 4.8 8.3 - - + -
958M TYR* 3.3 61.8 - + + +
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Residues in contact with SER 959 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
955A GLU* 3.1 22.9 + - - -
956A ILE* 3.5 9.6 - - - -
958A TYR* 1.4 74.1 - - - +
960A THR* 1.4 60.9 + - - +
962A THR* 2.8 25.7 + - - -
963A GLU* 3.7 5.9 + - - +
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Residues in contact with THR 960 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
956A ILE 3.4 10.3 + - - +
957A THR* 2.7 33.9 + - - +
959A SER* 1.4 75.0 - - - +
961A GLU* 1.3 60.9 + - - +
963A GLU* 3.3 11.9 - - - +
964A LYS* 3.3 28.9 + - - +
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Residues in contact with GLU 961 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
957A THR* 2.9 17.6 + - - +
958A TYR* 3.2 13.4 + - - +
960A THR* 1.3 74.7 + - - +
962A THR* 1.4 57.9 + - + +
964A LYS* 2.9 34.2 + - - +
965A LEU* 3.2 15.8 + - - +
958M TYR* 3.1 39.5 + - + -
961M GLU* 5.0 11.2 - - + -
962M THR* 4.3 5.0 - - + +
965M LEU* 4.7 26.3 - - + +
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Residues in contact with THR 962 (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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958A TYR* 3.0 21.4 + - + +
959A SER* 2.8 20.8 + - - -
961A GLU* 1.4 74.6 - - + +
963A GLU* 1.4 58.8 + - - +
965A LEU* 3.6 9.2 - - - +
966A ARG* 3.1 31.6 + - - +
961M GLU* 4.7 11.4 - - + +
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Residues in contact with GLU 963 (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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959A SER 3.7 3.8 + - - +
960A THR* 3.3 15.2 + - - +
962A THR* 1.4 76.5 + - - +
964A LYS* 1.4 85.9 + - - +
966A ARG* 2.9 23.7 + - - +
967A SER* 3.0 35.3 + - - -
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Residues in contact with LYS 964 (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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960A THR* 3.3 22.1 + - - +
961A GLU* 2.9 25.8 + - - +
963A GLU* 1.4 108.0 + - - +
965A LEU* 1.3 56.0 + - - +
967A SER* 3.5 6.9 + - - -
968A ASP* 3.1 42.0 + - - +
965M LEU* 5.3 13.7 - - + -
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Residues in contact with LEU 965 (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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961A GLU* 3.2 19.8 + - + +
962A THR* 3.6 15.3 - - - +
964A LYS* 1.3 73.2 - - - +
966A ARG* 1.3 92.8 + - - +
968A ASP* 4.7 5.4 - - - -
969A VAL* 3.4 22.4 - - + +
961M GLU* 3.5 39.0 - - + +
964M LYS* 5.7 4.5 - - + -
965M LEU* 4.3 24.1 - - + +
968M ASP* 5.0 8.7 - - - +
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Residues in contact with ARG 966 (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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962A THR* 3.1 32.1 + - - +
963A GLU* 2.9 18.9 + - - +
965A LEU* 1.3 113.0 + - - +
967A SER* 1.3 65.6 + - - +
968A ASP 3.4 0.9 - - - -
969A VAL* 3.1 32.0 - - - +
970A GLU* 3.4 8.8 + - - +
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Residues in contact with SER 967 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
963A GLU* 3.0 37.4 + - - -
964A LYS* 3.5 9.7 + - - -
966A ARG* 1.3 74.4 - - - +
968A ASP* 1.3 57.3 + - - +
970A GLU* 3.2 8.3 + - - +
971A ARG* 2.7 44.5 + - - -
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Residues in contact with ASP 968 (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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964A LYS* 3.1 32.3 + - - +
965A LEU* 4.7 3.8 - - - -
967A SER* 1.3 75.4 + - - +
969A VAL* 1.4 58.2 + - - +
971A ARG* 3.0 22.8 + - - +
972A LEU* 2.9 29.7 + - - +
965M LEU* 6.4 1.6 - - + -
968M ASP* 5.4 7.6 - - - +
972M LEU* 5.2 15.4 - - + +
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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