Contacts of the helix formed by residues 118 - 135 (chain F) in PDB entry 4Q44
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 SER 118 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115F CYS* 2.9 17.4 + - - +
116F HIS* 3.1 4.2 - - - -
117F GLY* 1.3 74.0 - - - +
119F ALA* 1.3 58.8 + - - +
120F THR* 3.7 6.8 + - - -
121F LEU* 3.1 32.7 + - - +
122F ILE* 2.9 31.6 + - - +
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Residues in contact with ALA 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3F LYS* 4.2 19.2 - - + +
5F ILE* 3.3 17.2 - - + +
109F VAL* 4.1 17.9 - - + -
117F GLY 3.4 5.9 + - - -
118F SER* 1.3 70.9 - - - +
120F THR* 1.3 56.7 + - - +
122F ILE* 4.2 7.4 - - - +
123F ALA* 2.9 28.1 + - - +
142F VAL* 3.7 25.7 - - + +
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Residues in contact with THR 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118F SER* 3.1 7.2 - - - -
119F ALA* 1.3 80.1 - - - +
121F LEU* 1.3 66.5 + - + +
124F GLN* 2.9 30.8 + - - +
142F VAL* 4.4 6.9 - - - +
161F GLN* 3.2 25.1 + - - +
163F VAL* 3.4 32.6 - - + +
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Residues in contact with LEU 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115F CYS* 3.5 26.4 - - + +
118F SER* 3.1 21.4 + - - +
120F THR* 1.3 89.1 - - + +
122F ILE* 1.3 57.9 + - - +
124F GLN* 3.4 13.0 - - + +
125F GLU* 2.9 34.6 + - - +
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Residues in contact with ILE 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F ILE* 3.9 13.2 - - + -
93F TYR* 3.8 24.2 - - + -
109F VAL* 4.0 23.1 - - + +
112F SER* 3.4 33.7 - - - +
114F HIS* 4.9 0.9 - - + -
115F CYS* 3.9 26.7 - - + +
117F GLY* 4.9 1.3 - - - -
118F SER 2.9 28.2 + - - +
119F ALA 3.6 5.2 - - - +
121F LEU* 1.3 72.6 - - - +
123F ALA* 1.3 66.9 + - - +
125F GLU* 2.9 4.7 + - - +
126F ILE* 2.9 36.3 + - + +
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Residues in contact with ALA 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F ILE* 3.9 25.5 - - + +
7F VAL* 5.9 0.8 - - - +
119F ALA 2.9 17.8 + - - +
120F THR 3.8 3.6 - - - +
122F ILE* 1.3 75.9 - - - +
124F GLN* 1.3 57.4 + - - +
126F ILE* 3.1 10.3 + - - +
127F ARG* 2.9 34.5 + - - +
140F ALA* 4.0 16.8 - - + -
142F VAL* 4.2 7.9 - - + -
161F GLN* 4.0 9.4 - - - +
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Residues in contact with GLN 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120F THR* 2.9 21.0 + - - +
121F LEU* 3.4 18.0 - - + +
123F ALA* 1.3 78.7 - - - +
125F GLU* 1.3 57.0 + - - +
127F ARG* 2.8 25.8 + - - +
128F GLN* 2.9 33.3 + - + +
161F GLN* 3.1 31.7 + - - +
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Residues in contact with GLU 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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93F TYR* 3.1 36.9 + - + +
115F CYS* 3.1 25.3 - - - -
121F LEU* 2.9 19.9 + - - +
122F ILE 2.9 5.3 + - - +
124F GLN* 1.3 72.9 - - - +
126F ILE* 1.3 53.8 + - - +
128F GLN* 2.7 24.0 - - + +
129F THR* 3.6 12.1 + - - +
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Residues in contact with ILE 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F ILE* 5.2 1.8 - - + -
7F VAL* 4.6 11.2 - - + -
89F ILE* 4.2 9.9 - - + +
90F PHE* 3.4 33.7 - - + -
93F TYR* 4.0 24.7 - - + -
107F LEU* 3.7 29.6 - - + -
122F ILE* 2.9 32.2 + - + +
123F ALA* 3.6 9.9 - - - +
124F GLN 3.1 0.2 - - - -
125F GLU* 1.3 79.6 - - - +
127F ARG* 1.3 60.5 + - + +
128F GLN 2.8 13.1 - - - +
129F THR* 3.8 0.7 - - - -
130F ILE* 3.0 32.2 + - + +
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Residues in contact with ARG 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F VAL* 5.4 3.8 - - + -
123F ALA 2.9 15.6 + - - +
124F GLN* 2.8 20.5 + - - +
126F ILE* 1.3 74.8 - - + +
128F GLN* 1.3 59.1 + - - +
130F ILE* 3.2 8.7 + - - +
131F PHE* 2.9 29.0 + - - +
138F ALA* 3.1 35.6 + - + +
139F SER* 4.0 0.4 - - - +
140F ALA* 3.8 18.2 - - + +
159F ASN* 2.9 46.2 + - - +
160F GLY* 4.0 8.3 - - - -
161F GLN* 2.5 47.7 + - - +
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Residues in contact with GLN 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124F GLN* 2.9 18.8 + - + +
125F GLU* 2.7 32.3 - - + +
126F ILE 2.8 8.5 - - - +
127F ARG* 1.3 75.5 - - - +
129F THR* 1.3 58.2 + - - +
131F PHE* 4.3 18.0 - - - +
132F ASN* 3.0 33.0 + - - +
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Residues in contact with THR 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89F ILE* 3.2 27.1 - - + +
92F ARG* 3.6 27.4 - - - +
93F TYR* 5.0 4.2 + - + +
125F GLU* 3.6 16.0 + - - +
126F ILE 4.2 1.1 - - - -
127F ARG 3.7 0.2 + - - -
128F GLN* 1.3 80.5 + - - +
130F ILE* 1.3 55.0 + - - +
132F ASN* 2.6 43.5 + - - +
133F GLU* 3.7 10.9 - - + +
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Residues in contact with ILE 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F VAL* 4.3 3.6 - - + -
9F MET* 3.8 30.7 - - + -
86F ILE* 4.2 9.4 - - + -
89F ILE* 3.9 20.4 - - + -
90F PHE* 4.1 13.0 - - + -
126F ILE* 3.0 42.6 + - + +
127F ARG 3.3 5.2 - - - +
129F THR* 1.3 73.1 - - - +
131F PHE* 1.3 58.2 + - - +
132F ASN 2.6 16.7 - - - +
134F LEU* 3.0 30.2 + - + +
135F GLN 3.4 0.7 + - - -
136F LEU 3.5 13.6 - - - +
137F THR 4.7 0.2 - - - -
138F ALA* 4.0 22.2 - - + -
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Residues in contact with PHE 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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127F ARG 2.9 16.0 + - - +
128F GLN* 4.3 15.3 - - - +
130F ILE* 1.3 75.0 - - - +
132F ASN* 1.3 68.2 + - - +
135F GLN* 2.9 41.1 + - + +
136F LEU 3.1 17.5 + - - +
137F THR* 3.6 31.9 - - + -
159F ASN* 5.4 6.3 - - - +
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Residues in contact with ASN 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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128F GLN* 3.0 34.7 + - - +
129F THR* 2.6 38.2 + - + +
130F ILE 2.6 8.0 - - - +
131F PHE* 1.3 82.0 - - - +
133F GLU* 1.3 57.0 + - + +
134F LEU 2.6 18.1 + - - -
135F GLN* 5.8 0.2 - - - -
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Residues in contact with GLU 133 (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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19F ARG* 5.4 0.3 + - - -
85F HIS* 2.8 38.4 + - + +
89F ILE* 3.8 3.6 - - - +
92F ARG* 2.9 39.2 + - - -
129F THR* 3.7 15.5 - - - +
131F PHE 4.1 0.2 + - - -
132F ASN* 1.3 75.2 - - + +
134F LEU* 1.3 61.3 + - + +
135F GLN* 3.7 17.9 + - - +
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Residues in contact with LEU 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F ARG* 2.8 31.4 + - - +
81F GLU* 6.3 0.2 - - + -
82F ALA* 3.6 40.2 - - + +
85F HIS* 3.6 42.4 - - + +
86F ILE* 3.8 17.7 - - + -
89F ILE* 3.6 20.2 - - + -
129F THR 4.5 0.2 - - - +
130F ILE* 3.0 17.3 - - + +
132F ASN 2.6 11.7 + - - -
133F GLU* 1.3 73.4 - - - +
135F GLN* 1.3 68.7 + - - +
136F LEU* 3.2 14.8 - - + +
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Residues in contact with GLN 135 (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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19F ARG* 3.9 23.4 + - + +
25F ARG* 5.8 2.1 + - - -
130F ILE 3.4 0.6 + - - -
131F PHE* 2.9 38.5 + - + +
133F GLU* 3.9 21.9 + - - +
134F LEU* 1.3 79.7 - - - +
136F LEU* 1.3 67.3 + - - +
137F THR* 5.6 0.2 - - - +
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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