Contacts of the helix formed by residues 950 - 967 (chain A) in PDB entry 1JQO
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 GLY 950 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A PRO* 4.0 17.1 - - - +
95A ALA* 5.7 0.9 - - - -
96A ILE* 3.4 23.7 - - - +
939A VAL* 4.6 4.8 - - - +
949A PRO* 1.3 79.2 - - - +
951A LEU* 1.3 62.9 + - - +
952A GLU 3.0 1.3 + - - -
953A ASP* 3.4 3.9 + - - -
954A THR* 2.6 32.6 + - - -
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Residues in contact with LEU 951 (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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908A THR* 3.7 18.2 - - + +
911A ARG* 3.9 49.6 - - + +
912A ILE* 3.6 32.3 - - + +
947A TYR* 4.3 2.0 - - + -
948A PRO* 3.3 39.3 - - + +
949A PRO* 2.9 3.1 + - + -
950A GLY* 1.3 74.4 - - - +
952A GLU* 1.3 65.3 + - - +
954A THR* 3.6 6.1 - - + +
955A LEU* 3.0 20.8 + - - +
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Residues in contact with GLU 952 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753A ARG* 2.6 32.9 + - - +
942A ASN* 3.8 18.9 + - - +
945A SER* 2.4 44.7 + - - +
946A GLU* 3.4 10.7 + - - +
947A TYR* 3.9 21.5 + - + +
948A PRO 4.1 0.8 + - - -
949A PRO 3.7 4.6 + - - +
950A GLY 3.0 2.0 + - - -
951A LEU* 1.3 75.0 - - - +
953A ASP* 1.3 58.2 + - - +
955A LEU* 2.6 27.6 + - - +
956A ILE* 2.9 30.1 + - + +
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Residues in contact with ASP 953 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ILE* 3.3 28.2 - - + +
228A ASP* 5.1 0.7 - - - +
230A ILE* 3.3 19.7 - - + +
232A ARG* 2.7 35.4 + - - -
938A LEU* 4.3 13.0 - - - +
939A VAL* 5.2 1.7 - - - +
941A LEU* 4.6 1.2 - - - +
942A ASN* 3.1 24.4 + - - +
949A PRO 5.0 0.8 + - - -
950A GLY* 3.4 2.5 + - - +
952A GLU* 1.3 78.1 - - - +
954A THR* 1.3 63.2 + - - +
956A ILE* 3.4 6.4 + - - +
957A LEU* 2.9 28.9 + - - +
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Residues in contact with THR 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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95A ALA* 4.0 12.8 - - + +
96A ILE* 3.4 11.0 + - - +
99A ALA* 4.2 6.1 - - + -
904A PHE* 3.8 38.1 - - + -
908A THR* 4.2 14.8 - - - +
950A GLY 2.6 30.3 + - - -
951A LEU* 3.6 7.9 - - + +
953A ASP* 1.3 76.5 - - - +
955A LEU* 1.3 65.0 + - - +
957A LEU* 3.1 12.5 + - - +
958A THR* 2.9 22.9 + - + +
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Residues in contact with LEU 955 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747A PRO* 5.5 0.9 - - + -
750A GLU* 3.4 41.5 - - + +
753A ARG* 5.1 3.8 - - - -
905A GLN* 3.9 20.9 - - + -
908A THR* 4.0 17.7 - - + +
909A LEU* 3.9 18.8 - - + -
912A ILE* 4.1 12.6 - - + -
947A TYR* 4.9 4.0 - - + -
951A LEU 3.0 13.9 + - - +
952A GLU* 2.6 15.0 + - - +
954A THR* 1.3 70.4 - - - +
956A ILE* 1.3 65.9 + - + +
958A THR* 2.5 35.5 + - - +
959A MET* 3.0 16.7 + - + +
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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
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230A ILE* 4.0 25.6 - - + -
753A ARG* 4.0 35.0 - - + +
754A MET* 4.3 15.0 - - + +
942A ASN* 5.8 0.7 - - - +
952A GLU* 2.9 58.2 + - + +
953A ASP* 3.8 8.7 - - - +
955A LEU* 1.3 77.9 - - + +
957A LEU* 1.3 57.2 + - - +
959A MET* 3.5 13.4 + - + +
960A LYS* 3.0 50.3 + - + +
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Residues in contact with LEU 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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96A ILE* 3.8 34.8 - - + +
99A ALA* 3.8 16.4 - - + -
100A SER* 4.2 17.5 - - - +
103A LEU* 4.6 15.6 - - + +
229A GLU* 3.9 18.4 - - + +
230A ILE* 3.7 27.6 - - + -
901A LEU* 4.9 1.0 - - - +
953A ASP 2.9 25.4 + - - +
954A THR* 3.3 7.6 - - - +
955A LEU 2.9 0.2 + - - -
956A ILE* 1.3 74.1 - - - +
958A THR* 1.3 66.9 + - - +
960A LYS* 2.8 11.5 + - + +
961A GLY* 2.8 21.1 + - - -
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Residues in contact with THR 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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99A ALA* 5.0 1.8 - - + -
901A LEU* 3.8 31.5 - - + +
904A PHE* 4.1 21.3 - - + -
905A GLN* 3.7 37.6 + - - +
908A THR* 5.5 0.2 - - - +
954A THR* 2.9 19.5 + - + +
955A LEU* 2.5 28.1 + - - +
957A LEU* 1.3 74.9 - - - +
959A MET* 1.3 59.8 + - - +
962A ILE* 2.8 36.6 + - - +
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Residues in contact with MET 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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747A PRO* 4.6 7.6 - - + +
750A GLU* 3.4 41.7 - - + +
753A ARG* 4.8 0.4 - - + -
754A MET* 3.7 29.4 - - + -
779A PHE* 4.0 21.5 - - + -
783A GLN* 3.3 24.9 - - - +
905A GLN* 3.8 7.0 - - - +
955A LEU* 3.0 12.4 + - + +
956A ILE* 3.6 33.7 - - + +
958A THR* 1.3 81.0 + - - +
960A LYS* 1.3 64.9 + - - +
963A ALA* 3.1 28.2 + - - +
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Residues in contact with LYS 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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103A LEU* 4.1 17.3 - - + +
181A SER* 3.2 43.6 + - - +
182A ALA* 4.7 5.2 - - - +
183A ARG* 5.1 1.1 - - - -
229A GLU* 2.9 34.7 + - - +
230A ILE* 3.9 10.1 - - - +
231A ARG* 4.1 6.5 - - - +
754A MET* 4.4 22.2 + - - +
956A ILE* 3.0 34.6 + - + +
957A LEU* 2.8 20.6 + - + +
959A MET* 1.3 78.1 - - - +
961A GLY* 1.3 55.4 + - - +
963A ALA* 3.6 5.2 - - - +
964A ALA* 3.1 23.0 + - - +
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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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103A LEU* 3.6 24.1 - - - +
106A LEU* 3.4 5.2 - - - +
901A LEU* 3.6 19.3 - - - -
957A LEU 2.8 14.9 + - - -
960A LYS* 1.3 70.0 - - - +
962A ILE* 1.3 53.4 + - - +
963A ALA 3.1 1.8 - - - -
964A ALA* 2.7 21.6 + - - +
965A GLY 2.7 16.6 + - - -
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Residues in contact with ILE 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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106A LEU* 5.1 0.4 - - - -
783A GLN* 3.1 37.5 - - - +
785A ARG* 6.1 0.2 - - + -
898A ILE* 4.5 18.0 - - + +
901A LEU* 3.6 34.4 - - + +
902A ASN* 3.5 25.4 - - - +
905A GLN* 3.4 27.6 - - - +
958A THR 2.8 19.9 + - - +
961A GLY* 1.3 70.3 - - - -
963A ALA* 1.3 57.1 + - - +
965A GLY* 3.4 1.1 + - - +
966A MET* 2.9 46.3 + - + +
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Residues in contact with ALA 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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181A SER* 4.1 18.4 - - - +
675A GLU* 5.2 1.3 - - - +
754A MET* 6.1 0.2 - - - -
779A PHE* 5.3 2.9 - - + -
782A THR* 6.1 0.2 - - - -
783A GLN* 4.0 8.1 - - - +
959A MET 3.1 19.6 + - - +
960A LYS 3.6 4.5 - - - +
962A ILE* 1.3 78.3 - - - +
964A ALA* 1.3 57.3 + - - +
966A MET* 4.4 0.9 - - - -
967A GLN* 2.9 23.6 + - - -
968A ASN 3.0 29.7 + - - +
969A THR* 4.1 11.9 - - + +
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Residues in contact with ALA 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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103A LEU* 4.4 11.0 - - + -
106A LEU* 4.7 8.1 - - + -
107A ASN* 4.9 6.1 - - + +
110A ASN* 3.1 27.4 + - - +
181A SER* 6.2 0.2 - - - -
960A LYS 3.1 13.8 + - - +
961A GLY* 2.7 21.5 + - - +
963A ALA* 1.3 70.4 - - - +
965A GLY* 1.3 57.9 + - - +
967A GLN* 3.0 19.3 + - - +
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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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106A LEU* 3.7 20.1 - - - +
110A ASN* 4.8 0.4 - - - -
835A LYS* 5.5 1.0 - - - -
891A LEU* 6.1 1.0 - - - +
894A ARG* 3.4 18.1 - - - -
898A ILE* 3.6 24.6 - - - +
961A GLY 2.7 14.7 + - - -
962A ILE 3.9 0.2 - - - -
964A ALA* 1.3 73.9 - - - +
966A MET* 1.3 57.3 + - - +
967A GLN* 2.9 16.3 + - - -
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Residues in contact with MET 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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782A THR* 3.8 30.7 - - + +
785A ARG* 3.8 30.7 - - + -
787A HIS* 4.6 4.3 - - - -
835A LYS* 3.1 50.3 + - + +
891A LEU* 5.6 3.4 - - + -
895A ASN* 5.4 3.4 - - - +
898A ILE* 3.8 22.9 - - + -
962A ILE* 2.9 37.4 + - + +
963A ALA* 3.8 4.0 - - - +
965A GLY* 1.3 76.7 - - - +
967A GLN* 1.3 70.0 + - - +
968A ASN* 3.1 17.1 + - + +
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Residues in contact with GLN 967 (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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110A ASN* 3.5 22.1 + - + +
113A GLU* 3.3 11.8 - - - +
675A GLU* 4.8 1.1 - - - -
679A PHE* 3.2 31.8 - - + -
835A LYS* 4.2 13.5 - - - +
894A ARG* 3.1 26.9 + - - +
963A ALA 2.9 6.4 + - - -
964A ALA* 3.0 11.3 + - - +
965A GLY 2.9 26.9 + - - -
966A MET* 1.3 80.0 - - - +
968A ASN* 1.3 71.4 + - - +
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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
------------------------------------------------------------
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