Contacts of the helix formed by residues 122 - 138 (chain B) in PDB entry 6E7P
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 ARG 122 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B THR* 1.3 74.3 - - - +
123B GLU* 1.3 62.0 + - - +
124B GLN 3.4 0.2 - - - -
125B LEU* 3.5 6.6 + - - +
126B TYR* 3.2 30.5 + - + -
225B PHE* 3.2 43.9 - - + +
140C PRO 2.9 24.0 + - - -
141C ASP* 3.6 21.3 + - - +
142C VAL 2.7 15.8 + - - +
143C SER 3.3 17.9 + - - -
144C LEU* 3.5 25.8 - - + +
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Residues in contact with GLU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B THR* 3.2 26.1 + - - +
122B ARG* 1.3 79.1 + - - +
124B GLN* 1.3 64.1 + - + +
125B LEU 3.2 1.1 - - - -
126B TYR* 3.8 12.6 - - + +
127B GLN* 3.2 37.6 + - + +
141C ASP 5.2 0.3 - - - +
142C VAL* 3.7 20.1 - - - +
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Residues in contact with GLN 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B LEU* 5.7 0.5 - - - +
118B ALA 5.2 1.6 - - - -
119B ALA* 3.3 16.9 - - + +
120B TYR* 2.5 43.0 + - - +
121B THR* 2.8 31.0 + - + +
123B GLU* 1.3 78.9 - - + +
125B LEU* 1.3 59.0 + - - +
127B GLN* 3.8 5.8 + - - +
128B ALA* 3.2 27.9 + - - +
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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
----------------------------------------------------------
119B ALA* 4.4 12.1 - - + +
121B THR 4.0 8.4 + - - +
122B ARG 3.5 11.6 + - - +
123B GLU 3.2 0.4 - - - -
124B GLN* 1.3 79.2 - - - +
126B TYR* 1.3 62.8 + - - +
128B ALA* 3.5 1.4 + - - +
129B ILE* 3.2 34.6 + - + +
223B LEU* 3.8 15.9 - - + -
225B PHE* 3.6 27.6 - - + -
228B LEU* 4.5 5.6 - - + -
231B VAL* 5.8 2.0 - - + -
262B PHE* 3.6 36.8 - - + -
271B ILE* 3.7 30.5 - - + -
144C LEU* 4.5 2.2 - - + -
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Residues in contact with TYR 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ARG* 3.2 28.6 + - + -
123B GLU* 3.6 11.2 + - + +
124B GLN 3.4 0.2 - - - -
125B LEU* 1.3 79.1 - - + +
127B GLN* 1.3 63.3 + - + +
129B ILE* 3.3 4.9 + - + +
130B PHE* 3.1 60.4 + + + -
221B LEU* 4.1 16.4 + - + -
222B THR* 4.3 2.6 - - - +
223B LEU* 3.7 35.9 + - + -
225B PHE* 3.8 29.8 - + - -
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Residues in contact with GLN 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B LEU* 3.6 23.4 - - + +
123B GLU* 3.2 25.5 + - + +
124B GLN* 4.4 4.8 - - - +
126B TYR* 1.3 78.3 - - + +
128B ALA* 1.3 61.1 + - - +
129B ILE 3.4 0.2 - - - -
130B PHE* 4.1 6.9 - - + +
131B HIS* 3.3 25.6 + - - +
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Residues in contact with ALA 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B PHE 4.9 2.8 - - - +
107B LEU* 4.4 18.8 + - + +
119B ALA* 5.4 0.7 - - + -
124B GLN 3.2 19.3 + - - +
125B LEU* 3.9 3.6 - - - +
126B TYR 3.2 0.8 - - - -
127B GLN* 1.3 78.5 - - - +
129B ILE* 1.3 62.6 + - - +
131B HIS* 4.3 1.4 - - - +
132B ALA* 3.4 20.6 + - - +
262B PHE* 3.7 27.6 - - + -
273B ILE* 4.4 12.3 - - + -
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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
----------------------------------------------------------
125B LEU* 3.2 25.1 - - + +
126B TYR* 3.3 7.9 + - + +
128B ALA* 1.3 75.9 - - - +
130B PHE* 1.3 79.3 + - + +
132B ALA* 3.2 14.1 + - - +
133B VAL* 3.2 14.6 + - + +
165B LEU* 4.2 27.8 - - + -
221B LEU* 5.0 4.5 - - + -
223B LEU* 4.1 30.1 - - + -
231B VAL* 4.5 16.8 - - + -
233B ILE* 4.6 8.5 - - + +
262B PHE* 4.0 24.0 - - + -
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Residues in contact with PHE 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B TYR* 3.1 54.6 + + + +
127B GLN* 4.6 5.8 - - + +
129B ILE* 1.3 89.6 - - + +
131B HIS* 1.3 58.4 + - - +
133B VAL* 3.2 6.9 + - + +
134B ASP* 3.0 42.2 + - - +
218B TYR* 4.5 21.8 - + - -
219B LYS* 4.4 40.8 - - + +
221B LEU* 4.7 10.5 - - + -
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Residues in contact with HIS 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B LEU 4.2 9.6 + - - -
105B PHE 4.6 2.9 - - - -
106B LEU 4.3 5.1 + - - -
107B LEU* 3.6 48.4 - - + +
127B GLN 3.3 19.0 + - - +
128B ALA 4.3 2.5 - - - +
129B ILE 3.3 0.2 - - - -
130B PHE* 1.3 79.5 - - - +
132B ALA* 1.3 60.2 + - - +
134B ASP* 4.0 8.1 - - - +
135B GLN* 3.4 48.8 + - + +
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Residues in contact with ALA 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B PHE* 3.7 31.4 - - - +
128B ALA 3.4 13.5 + - - +
129B ILE 3.2 11.0 + - - +
131B HIS* 1.3 80.5 - - - +
133B VAL* 1.3 60.7 + - - +
136B TYR* 3.8 16.3 + - - +
163B LEU* 5.2 1.0 - - - +
233B ILE* 4.3 15.6 - - + +
235B PHE* 5.8 2.8 - - - -
260B ILE* 4.3 20.4 - - + +
262B PHE* 5.5 1.1 - - + -
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Residues in contact with VAL 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ILE* 3.4 15.7 - - + +
130B PHE* 3.2 7.5 + - + +
132B ALA* 1.3 76.6 - - - +
134B ASP* 1.3 60.3 + - - +
136B TYR* 3.0 6.1 + - - +
137B LEU* 3.0 32.8 + - + +
163B LEU* 4.0 26.5 - - + -
165B LEU* 3.9 26.9 - - + -
195B VAL* 5.0 6.1 - - + -
218B TYR* 3.6 37.7 - - + +
233B ILE* 4.8 7.0 - - + -
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Residues in contact with ASP 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B PHE* 3.0 31.1 + - - +
131B HIS* 4.2 8.2 + - - +
132B ALA 3.5 0.2 - - - -
133B VAL* 1.3 76.2 - - - +
135B GLN* 1.3 66.0 + - + +
137B LEU* 3.2 9.8 + - - +
138B ALA* 3.1 23.9 + - - +
218B TYR* 3.0 26.0 + - - -
219B LYS* 4.3 12.2 + - - -
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Residues in contact with GLN 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A THR* 5.6 3.4 - - - +
104B LEU* 3.3 42.1 + - + +
105B PHE* 4.0 11.4 - - + -
131B HIS* 3.4 37.0 + - + +
132B ALA 4.6 0.2 - - - +
133B VAL 3.3 0.6 - - - -
134B ASP* 1.3 78.6 - - + +
136B TYR* 1.3 63.1 + - - +
138B ALA* 3.3 6.0 + - - +
139B LEU* 3.2 29.7 + - + +
142B VAL* 3.8 29.4 - - - +
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Residues in contact with TYR 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B PHE* 4.2 10.7 - + + -
132B ALA 3.8 12.1 + - - +
133B VAL 3.0 10.9 + - - +
135B GLN* 1.3 80.4 - - - +
137B LEU* 1.3 68.5 + - + +
138B ALA 3.3 0.7 + - - -
139B LEU* 3.7 6.9 + - + +
149B TYR* 2.8 63.1 + + - +
150B VAL* 5.3 1.4 + - - +
162B GLY* 4.0 17.0 + - - -
163B LEU* 3.5 41.1 - - + -
195B VAL* 5.1 1.6 - - + -
196B ASP 5.3 0.2 - - - -
197B PRO* 4.1 19.6 - - + +
235B PHE* 3.7 41.6 - + + +
236B ARG 5.0 3.0 + - - -
237B LEU* 4.8 6.1 - - + -
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Residues in contact with LEU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B VAL* 3.0 22.3 + - + +
134B ASP* 3.2 8.9 + - - +
136B TYR* 1.3 84.6 - - + +
138B ALA* 1.3 58.5 + - - +
139B LEU 3.6 0.6 + - - -
140B PRO* 5.2 1.6 - - - +
149B TYR* 4.2 6.6 + - - -
195B VAL* 4.3 20.0 - - + -
196B ASP 4.3 3.8 - - - +
197B PRO* 4.4 4.0 - - + -
198B PRO* 3.9 36.7 - - + +
216B SER 5.9 0.4 - - - +
218B TYR* 3.4 36.8 - - + +
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Residues in contact with ALA 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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134B ASP 3.1 16.0 + - - +
135B GLN* 3.3 8.0 + - - +
136B TYR 3.2 0.4 - - - -
137B LEU* 1.3 80.5 - - + +
139B LEU* 1.3 61.6 + - - +
140B PRO* 3.6 3.8 - - - -
141B ASP* 3.4 19.7 + - + +
142B VAL* 3.3 28.3 + - + +
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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