Contacts of the helix formed by residues 118 - 138 (chain B) in PDB entry 4F4W
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 ASN 118 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2B ILE* 4.9 0.2 - - - -
115B VAL* 3.1 19.5 + - - +
116B GLU* 2.7 11.6 + - + +
117B GLY* 1.3 75.4 - - - +
119B PHE* 1.3 61.6 + - - +
120B GLU* 3.4 12.7 - - - +
121B ASN* 2.1 59.3 + - - +
122B GLY 3.1 13.7 + - - -
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Residues in contact with PHE 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B ILE* 3.3 37.5 - - + -
117B GLY 3.7 3.6 + - - +
118B ASN* 1.3 73.3 - - - +
120B GLU* 1.3 62.8 + - + +
122B GLY* 3.0 16.8 + - - +
123B ILE* 3.0 21.3 + - + +
145B VAL* 3.8 19.9 - - + +
146B ALA 4.0 18.6 - - - -
147B PRO* 4.2 2.0 - - + -
166B VAL* 3.8 24.2 - - + -
167B ILE 3.3 23.6 - - - -
168B ARG* 3.9 18.4 - - + -
169B PRO* 3.8 25.1 - - + -
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Residues in contact with GLU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ASN* 3.4 9.2 - - - +
119B PHE* 1.3 80.4 - - + +
121B ASN* 1.3 63.2 + - - +
123B ILE* 3.0 15.6 + - - +
124B GLU* 3.0 20.3 + - - +
127B ARG* 4.7 2.3 + - - -
168B ARG* 2.7 46.6 + - - +
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Residues in contact with ASN 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B VAL* 3.8 17.7 + - + +
116B GLU* 5.4 4.8 + - - +
118B ASN* 2.1 40.2 + - - +
120B GLU* 1.3 75.9 - - - +
122B GLY* 1.3 60.6 + - - +
124B GLU* 3.8 9.7 - - - +
125B LEU* 2.9 28.6 + - - +
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Residues in contact with GLY 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B ILE* 4.5 11.7 - - - -
4B ILE* 3.8 6.6 - - - +
111B VAL* 4.8 3.4 - - - -
115B VAL* 3.9 18.3 - - - +
118B ASN 3.1 8.7 + - - -
119B PHE 3.0 10.3 + - - -
121B ASN* 1.3 78.0 - - - +
123B ILE* 1.3 61.6 + - - +
125B LEU* 3.3 4.9 + - - +
126B ALA* 3.0 21.5 + - - +
145B VAL* 4.4 6.0 - - - +
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Residues in contact with ILE 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B PHE* 3.0 26.3 + - + +
120B GLU* 3.0 17.9 + - - +
122B GLY* 1.3 74.9 - - - +
124B GLU* 1.3 64.8 + - - +
126B ALA* 3.1 16.5 + - - +
127B ARG* 3.1 43.4 + - - +
145B VAL* 4.4 5.6 - - + -
164B LEU* 4.5 5.3 - - + +
166B VAL* 3.6 36.8 - - + -
168B ARG* 3.5 29.2 - - - +
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Residues in contact with GLU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B GLU 3.0 12.0 + - - +
121B ASN* 3.8 12.8 - - - +
123B ILE* 1.3 76.6 - - - +
125B LEU* 1.3 63.3 + - - +
127B ARG* 3.0 38.0 + - - +
128B LYS* 3.0 52.4 + - + +
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Residues in contact with LEU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ILE* 4.0 2.9 - - + -
95B HIS* 3.8 48.0 - - + +
111B VAL* 3.9 23.8 - - + -
114B LYS* 4.5 7.4 - - + -
115B VAL* 4.0 15.0 - - + -
121B ASN 2.9 17.0 + - - +
122B GLY* 3.4 7.6 - - - +
123B ILE 3.2 0.2 - - - -
124B GLU* 1.3 76.8 - - - +
126B ALA* 1.3 57.1 + - - +
128B LYS* 3.1 9.1 + - + -
129B ILE* 2.8 37.1 + - + +
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Residues in contact with ALA 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ILE* 4.1 12.1 - - + +
122B GLY 3.0 7.4 + - - +
123B ILE 3.1 11.2 + - - +
125B LEU* 1.3 77.7 - - - +
127B ARG* 1.3 61.1 + - - +
129B ILE* 3.2 6.5 + - - +
130B LYS* 3.0 26.2 + - - +
143B VAL* 3.9 15.6 - - + +
145B VAL* 3.6 30.5 - - + -
164B LEU* 4.2 9.2 - - + -
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Residues in contact with ARG 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B GLU* 4.7 2.0 + - - -
123B ILE* 3.1 40.2 + - - +
124B GLU* 3.0 46.2 + - - +
126B ALA* 1.3 75.8 - - - +
128B LYS* 1.3 66.1 + - - +
130B LYS* 3.4 6.5 + - - +
131B GLN* 3.0 23.6 + - - +
164B LEU* 3.3 28.7 - - + +
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Residues in contact with LYS 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B HIS* 5.7 5.6 - - + -
124B GLU* 3.0 35.4 + - + +
125B LEU* 3.1 16.4 + - + +
127B ARG* 1.3 82.3 + - - +
129B ILE* 1.3 63.4 + - - +
131B GLN* 3.4 14.6 + - + +
132B GLU* 3.0 27.3 + - - +
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Residues in contact with ILE 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ILE* 4.0 15.3 - - + -
6B VAL* 4.7 7.9 - - + -
92B LEU* 3.4 28.3 - - + -
95B HIS* 3.8 36.3 - - + +
109B LEU* 4.0 18.6 - - + -
125B LEU* 2.8 35.9 + - + +
126B ALA* 3.2 8.9 + - - +
128B LYS* 1.3 77.7 - - - +
130B LYS* 1.3 62.5 + - - +
132B GLU* 3.3 6.9 + - - +
133B ILE* 3.1 32.2 + - + +
143B VAL* 5.2 4.3 - - + -
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Residues in contact with LYS 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B ALA 3.0 14.0 + - - +
127B ARG* 3.7 7.6 - - - +
129B ILE* 1.3 76.0 - - - +
131B GLN* 1.3 62.8 + - - +
133B ILE* 3.5 2.4 + - - +
134B LEU* 3.1 23.6 + - - +
139B ILE 4.9 1.0 - - - +
141B VAL* 2.7 35.0 + - + +
143B VAL* 3.8 19.1 - - + -
162B ASN* 2.6 38.1 + - - -
163B GLY 3.0 24.0 + - - +
164B LEU* 4.2 24.5 - - + -
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Residues in contact with GLN 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B ARG 3.0 16.8 + - - +
128B LYS* 3.8 20.6 - - + +
129B ILE 3.2 0.2 - - - -
130B LYS* 1.3 78.5 - - - +
132B GLU* 1.3 56.4 + - - +
134B LEU* 3.3 21.6 + - - +
135B GLU* 2.9 61.8 + - - +
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Residues in contact with GLU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B LEU* 3.8 26.0 - - + +
94B LYS* 4.5 6.8 + - - -
95B HIS* 2.7 37.3 + - - -
128B LYS 3.0 16.9 + - - +
129B ILE* 3.3 3.6 + - - +
131B GLN* 1.3 78.1 - - - +
133B ILE* 1.3 59.8 + - + +
135B GLU* 4.4 10.1 - - - +
136B LYS* 2.9 63.4 + - + +
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Residues in contact with ILE 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B VAL* 4.6 3.6 - - + -
88B ILE* 3.9 36.1 - - + -
91B LEU* 4.6 18.6 - - + -
92B LEU* 3.9 9.9 - - + -
129B ILE* 3.1 36.0 + - + +
130B LYS* 4.0 4.0 - - - +
131B GLN 3.3 0.2 - - - -
132B GLU* 1.3 75.3 - - + +
134B LEU* 1.3 58.0 + - - +
137B GLU* 2.9 25.6 + - + +
138B LYS 3.4 3.8 + - - -
139B ILE* 3.4 25.9 + - + +
141B VAL* 4.0 29.8 - - + -
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Residues in contact with LEU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B LYS 3.1 19.2 + - - +
131B GLN* 3.6 23.1 - - - +
133B ILE* 1.3 74.7 - - - +
135B GLU* 1.3 62.3 + - - +
138B LYS* 2.9 45.3 + - + +
139B ILE 3.6 16.3 + - - +
140B THR* 4.0 22.2 - - + -
162B ASN* 6.2 1.3 - - - +
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Residues in contact with GLU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B GLN* 2.9 47.5 + - - +
132B GLU* 3.7 9.9 - - - +
134B LEU* 1.3 75.7 - - - +
136B LYS* 1.3 69.1 + - + +
138B LYS* 3.0 27.3 + - - +
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Residues in contact with LYS 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B LEU* 3.9 33.2 - - + -
132B GLU* 2.9 49.7 + - + +
135B GLU* 1.3 87.4 + - + +
137B GLU* 1.3 68.4 + - + +
138B LYS* 4.7 2.9 - - - +
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Residues in contact with GLU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B VAL* 4.0 11.4 - - - +
84B PHE* 3.8 14.3 - - + -
87B ARG* 2.8 54.8 + - - +
88B ILE* 4.0 22.4 - - + -
91B LEU* 4.7 8.9 - - + +
133B ILE* 2.9 13.3 + - + +
136B LYS* 1.3 90.0 - - + +
138B LYS* 1.3 74.4 + - - +
139B ILE* 3.3 21.5 + - + +
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Residues in contact with LYS 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B GLN* 3.7 5.9 - - - +
18B VAL* 3.5 28.6 - - + +
134B LEU* 2.9 32.3 + - + +
135B GLU* 3.0 24.2 + - - +
136B LYS 4.7 2.2 - - - +
137B GLU* 1.3 82.5 - - - +
139B ILE* 1.3 58.8 + - - +
140B THR* 4.2 0.5 + - - +
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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
------------------------------------------------------------
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