Contacts of the helix formed by residues 124 - 133 (chain F) in PDB entry 2ZJQ
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 ALA 124 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104F VAL* 4.9 9.8 - - + +
108F ALA* 5.8 0.9 - - + -
120F VAL* 3.3 15.5 - - + +
121F GLU* 2.9 9.1 + - - +
123F ALA* 1.3 79.2 - - - +
125F ASN* 1.3 67.9 + - - +
126F THR 3.1 1.8 - - - -
127F VAL* 3.2 17.8 + - - +
128F ALA* 3.4 10.9 + - - +
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Residues in contact with ASN 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121F GLU* 3.0 26.5 + - - +
122F ALA* 4.2 2.6 - - - +
124F ALA* 1.3 77.0 - - - +
126F THR* 1.3 60.5 + - - +
128F ALA* 3.5 8.9 + - - +
129F GLY 3.3 12.8 + - - -
1090X C 4.9 0.2 + - - -
1091X C 2.7 45.5 + - - +
1092X U 3.6 15.9 + - - -
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Residues in contact with THR 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74F MET* 5.1 1.5 - - + +
115F LEU* 5.1 11.0 - - + -
117F ALA* 4.7 2.9 - - - +
122F ALA 3.2 7.4 + - - -
123F ALA* 4.8 7.9 - - - -
124F ALA 3.1 0.4 - - - -
125F ASN* 1.3 74.0 - - - +
127F VAL* 1.3 65.4 + - + +
129F GLY 3.2 8.0 + - - -
130F THR* 3.5 7.1 + - - -
1069X G 3.3 16.0 + - - +
1070X G 3.3 32.6 + - - +
1091X C 2.4 49.1 + - - +
1092X U 3.1 13.7 + - - -
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Residues in contact with VAL 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74F MET* 3.5 31.2 - - + -
78F ILE* 5.8 2.1 - - + +
104F VAL* 3.5 38.4 - - + -
107F ILE* 4.7 15.7 - - + -
108F ALA* 5.1 4.3 - - + -
115F LEU* 5.6 5.2 - - + -
123F ALA 3.6 21.5 - - - +
124F ALA 3.2 6.7 + - - +
126F THR* 1.3 78.8 - - + +
128F ALA* 1.3 61.7 + - - +
130F THR* 3.2 5.7 + - - -
131F ALA* 3.2 23.1 + - + +
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Residues in contact with ALA 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124F ALA 3.4 8.4 + - - +
125F ASN* 3.8 11.7 - - - +
126F THR 3.3 0.4 - - - -
127F VAL* 1.3 79.3 - - - +
129F GLY* 1.3 57.2 + - - +
131F ALA* 3.9 6.6 - - - +
132F ARG* 3.0 31.4 + - - +
138F VAL* 4.2 27.6 - - + +
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Residues in contact with GLY 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125F ASN 3.3 9.3 + - - -
126F THR 3.2 7.4 + - - -
127F VAL 3.1 1.4 - - - -
128F ALA* 1.3 79.2 - - - +
130F THR* 1.3 58.5 + - - +
132F ARG* 3.7 6.9 + - - +
133F SER 3.5 8.8 + - - -
1070X G 4.1 1.6 - - - -
1090X C 3.4 35.0 - - - +
1099X A 3.2 19.7 + - - -
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Residues in contact with THR 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74F MET* 4.2 30.8 - - + -
75F SER* 4.9 9.9 - - - +
78F ILE* 5.1 4.0 - - + +
126F THR* 3.5 8.4 + - - +
127F VAL 3.2 7.7 + - - -
129F GLY* 1.3 75.0 - - - +
131F ALA* 1.3 65.2 + - - +
132F ARG 3.2 0.2 - - - -
133F SER* 2.7 21.9 + - - -
134F MET* 3.4 10.5 + - + +
1070X G 4.1 0.9 + - - -
1071X U 2.5 36.0 + - + -
1073X G 3.8 18.6 - - - +
1074X G 6.0 0.7 - - - -
1099X A 4.6 0.2 - - - +
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Residues in contact with ALA 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78F ILE* 3.8 22.8 - - + +
99F LEU* 6.0 3.6 - - + -
127F VAL* 3.2 17.1 + - + +
128F ALA* 4.0 7.0 - - - +
130F THR* 1.3 78.6 - - - +
132F ARG* 1.3 62.1 + - - +
134F MET* 3.2 10.0 + - - +
135F GLY 3.3 11.4 + - - -
136F VAL* 3.4 31.6 - - + +
137F THR 6.0 0.4 - - - +
138F VAL* 5.8 5.4 - - + -
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Residues in contact with ARG 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F PRO* 5.3 4.0 - - - +
128F ALA 3.0 19.6 + - - +
129F GLY* 3.8 7.6 - - - +
130F THR 3.2 0.2 - - - -
131F ALA* 1.3 76.9 - - - +
133F SER* 1.3 59.1 + - - +
134F MET 3.1 2.8 + - - -
135F GLY* 4.1 6.4 + - - -
136F VAL 4.4 7.9 - - - +
138F VAL* 6.3 2.2 - - + -
1088X A 3.2 30.1 + - - -
1089X C 3.9 23.9 + - - -
1090X C 4.9 21.9 + - - -
1099X A 5.9 1.0 + - - -
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Residues in contact with SER 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F PRO* 5.0 7.1 - - - +
129F GLY 3.5 1.0 + - - -
130F THR 2.7 20.8 + - - -
132F ARG* 1.3 79.6 - - - +
134F MET* 1.3 60.1 + - - +
1073X G 3.6 43.7 + - - +
1074X G 4.0 14.4 + - - +
1087X C 4.8 1.4 - - - +
1088X A 5.1 8.3 - - - -
1099X A 2.9 34.5 + - - -
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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