Contacts of the helix formed by residues 952 - 966 (chain A) in PDB entry 2XT6
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 GLU 952 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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656A GLU* 4.1 2.0 + - - -
901A GLN* 2.9 30.4 + - - +
950A LEU* 4.3 9.3 - - - +
951A SER* 1.3 78.2 - - - +
953A PHE* 1.3 61.4 + - - +
954A ALA 3.5 0.2 - - - -
955A ALA 4.1 0.2 - - - -
956A VAL* 2.9 39.6 + - - +
973A TRP* 4.4 17.3 - - + -
980A PHE* 3.4 43.0 - - + +
981A VAL* 4.9 0.7 - - - -
983A GLY* 4.1 15.8 - - - -
984A ALA* 3.8 7.6 - - + +
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Residues in contact with PHE 953 (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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608A ALA* 4.1 16.8 - - + -
611A PRO* 4.2 0.4 - - + +
651A GLN* 5.5 6.3 - - - -
653A VAL* 3.4 38.6 - - + -
656A GLU* 3.5 15.7 + - - +
952A GLU* 1.3 77.1 - - - +
954A ALA* 1.4 55.7 + - - +
956A VAL* 4.2 0.2 - - - -
957A GLY* 3.1 22.9 + - - -
983A GLY 3.4 22.2 + - - +
984A ALA* 4.0 8.3 - - - -
986A SER* 3.7 31.0 - - - -
987A ILE* 3.5 33.1 - - + +
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Residues in contact with ALA 954 (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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611A PRO* 3.3 18.7 - - + +
653A VAL* 4.7 0.9 - - + +
656A GLU* 3.1 41.9 + - + +
657A THR* 4.3 2.0 - - - +
660A LEU* 3.9 16.5 - - + +
951A SER* 3.5 11.2 + - - +
952A GLU 3.5 0.2 - - - -
953A PHE* 1.4 71.6 - - - +
955A ALA* 1.4 56.2 + - - +
958A PHE* 2.7 36.8 + - - +
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Residues in contact with ALA 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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660A LEU* 5.2 2.0 - - + +
666A TYR* 4.8 10.1 - - + +
948A SER* 4.6 15.0 - - - -
949A ALA 6.1 0.2 - - - +
951A SER* 3.4 27.2 + - - +
952A GLU 4.0 0.7 - - - +
953A PHE 3.5 0.6 - - - -
954A ALA* 1.4 75.1 - - - +
956A VAL* 1.4 64.4 + - - +
958A PHE* 3.3 6.7 + - - +
959A GLU* 3.0 29.8 + - - +
973A TRP* 3.4 25.1 - - + +
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Residues in contact with VAL 956 (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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952A GLU 2.9 30.4 + - - +
953A PHE 4.3 0.2 - - - +
955A ALA* 1.4 70.9 - - - +
957A GLY* 1.3 57.2 + - - +
959A GLU* 3.3 3.8 + - - +
960A TYR* 2.9 28.6 + - - +
973A TRP* 3.6 40.6 - - + -
981A VAL* 4.6 1.1 - - + -
984A ALA* 3.5 22.7 - - + -
987A ILE* 3.7 8.3 - - + -
988A ILE* 4.8 1.8 - - + -
992A ILE* 3.7 28.0 - - + -
1005A VAL* 5.3 0.9 - - - +
1007A LEU* 4.1 16.2 - - + -
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Residues in contact with GLY 957 (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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611A PRO* 3.9 10.3 - - - -
612A VAL* 3.5 13.0 - - - +
953A PHE 3.1 18.1 + - - -
954A ALA 3.7 0.7 - - - -
956A VAL* 1.3 75.9 - - - +
958A PHE* 1.3 54.1 - - - +
960A TYR* 3.3 2.9 + - - +
961A GLY 3.0 24.6 + - - -
987A ILE* 3.8 26.6 - - - +
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Residues in contact with PHE 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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611A PRO 3.4 11.3 + - - -
614A GLU* 3.5 27.8 - - + -
615A GLY* 3.1 24.4 - - - -
618A ARG* 3.4 31.4 - - + -
660A LEU* 4.1 8.3 - - + -
665A GLY 3.9 0.4 - - - -
666A TYR* 3.4 50.0 - + + -
897A ARG* 3.4 24.2 - - - -
954A ALA 2.7 21.4 + - - +
955A ALA 3.3 6.3 + - - +
957A GLY* 1.3 72.4 - - - +
959A GLU* 1.4 72.2 + - - +
961A GLY 3.4 0.3 + - - -
962A TYR* 2.9 26.5 + + - +
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Residues in contact with GLU 959 (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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666A TYR* 3.6 7.3 + - - -
897A ARG* 2.7 50.4 + - - +
899A SER* 3.4 13.8 + - - +
955A ALA 3.0 19.1 + - - +
956A VAL* 3.9 3.4 - - - +
958A PHE* 1.4 82.4 - - - +
960A TYR* 1.3 67.0 + - - +
962A TYR* 3.1 12.5 + - - +
963A SER* 3.1 13.2 + - - -
971A VAL* 3.4 19.9 - - + +
972A LEU 4.5 2.5 - - - +
973A TRP* 3.6 29.8 - - + -
1005A VAL* 3.8 18.9 - - + +
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Residues in contact with TYR 960 (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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612A VAL* 3.7 17.5 - - + -
956A VAL 2.9 17.8 + - - +
957A GLY 3.3 4.0 + - - +
959A GLU* 1.3 74.3 - - - +
961A GLY* 1.3 62.4 + - - +
963A SER* 2.7 24.2 + - - -
964A VAL* 3.2 23.1 - - + +
987A ILE* 4.4 4.3 - - + -
991A PHE* 3.6 53.0 + + + +
992A ILE* 3.7 29.4 - - + -
995A GLY* 4.4 0.3 - - - -
999A TRP* 4.4 4.5 - - - -
1001A GLN* 3.0 43.5 + - - +
1003A SER* 3.3 30.1 - - - -
1005A VAL* 3.9 7.7 - - + +
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Residues in contact with GLY 961 (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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612A VAL* 3.4 33.0 - - - -
616A LEU* 3.3 16.0 - - - -
957A GLY 3.0 11.2 + - - -
958A PHE 3.7 2.2 - - - -
960A TYR* 1.3 75.3 - - - +
962A TYR* 1.3 62.5 + - - +
964A VAL* 3.2 7.8 + - - +
965A GLY 3.0 18.4 + - - -
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Residues in contact with TYR 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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615A GLY 3.3 21.0 - - - -
618A ARG* 3.9 13.5 - - + -
619A ALA* 3.2 28.7 + - + +
622A ASP* 2.5 39.1 + - - +
895A LEU* 3.9 19.3 - - + +
897A ARG* 3.7 31.2 - - - +
944A LEU* 3.9 1.7 - - - +
958A PHE* 2.9 17.4 + + - +
959A GLU* 3.1 13.9 + - - +
961A GLY* 1.3 74.8 - - - +
963A SER* 1.4 56.5 + - - +
965A GLY 3.1 2.8 + - - -
966A ASN* 2.9 27.4 + - + -
969A ALA* 4.2 20.2 - - + -
971A VAL* 3.6 20.2 - - + -
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Residues in contact with SER 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 GLU 3.1 9.7 + - - -
960A TYR 2.7 16.6 + - - -
962A TYR* 1.4 74.2 - - - +
964A VAL* 1.3 58.9 + - - +
966A ASN 3.1 24.5 - - - +
967A PRO* 3.4 9.9 - - - +
969A ALA 5.4 1.3 - - - -
971A VAL* 4.0 16.9 - - - +
1002A LEU 4.8 1.7 - - - +
1003A SER* 2.6 26.7 + - - -
1004A ASP* 3.7 20.9 - - - -
1005A VAL* 3.8 10.0 + - - +
1061A GLN* 4.1 4.0 - - - +
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Residues in contact with VAL 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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612A VAL* 6.0 0.9 - - + -
616A LEU* 4.3 17.6 - - + +
960A TYR* 3.2 44.9 - - + +
961A GLY* 3.2 10.0 + - - +
963A SER* 1.3 75.1 - - - +
965A GLY* 1.3 62.7 + - - +
966A ASN 3.6 0.3 + - - -
967A PRO* 4.0 11.1 - - - +
1001A GLN* 3.7 28.3 - - + +
1002A LEU 3.6 21.1 - - - +
1003A SER* 4.0 4.0 - - - -
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Residues in contact with GLY 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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616A LEU* 3.4 25.5 - - - +
619A ALA* 3.7 12.6 - - - -
620A LYS* 4.3 10.4 - - - +
623A LEU* 3.8 13.3 - - - +
961A GLY 3.0 10.1 + - - -
962A TYR 3.1 4.7 + - - -
964A VAL* 1.3 78.0 - - - +
966A ASN* 1.3 57.9 + - - +
967A PRO* 3.9 4.8 - - - +
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Residues in contact with ASN 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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619A ALA* 3.9 14.4 + - + -
623A LEU* 3.7 36.7 - - + +
895A LEU* 4.0 19.4 - - - +
962A TYR* 2.9 10.2 + - + +
963A SER* 3.1 15.2 - - - +
965A GLY* 1.3 79.1 - - - +
967A PRO* 1.4 64.1 - - - +
968A ASP* 3.2 25.4 + - - +
969A ALA* 3.3 37.7 + - + +
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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
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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