Contacts of the helix formed by residues 119 - 132 (chain B) in PDB entry 1EJI
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 119 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A TYR* 4.0 12.1 + - - -
305A HIS* 3.4 22.4 + - - -
117B PRO* 3.1 2.2 - - - +
118B TYR* 1.3 81.2 + - - +
120B GLY* 1.3 62.5 + - - +
122B PRO* 3.2 17.0 - - - +
123B ALA* 3.2 21.5 + - - +
256B HIS* 4.2 7.6 - - - -
263B ARG* 5.1 0.7 + - - -
264B ALA 3.7 10.5 + - - -
265B GLY* 3.8 9.7 - - - -
501B PLG 2.7 22.8 + - - -
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Residues in contact with GLY 120 (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 SER* 1.3 68.0 + - - +
121B SER* 1.3 64.6 + - - -
123B ALA* 3.0 18.1 + - - +
124B ASN* 3.2 14.2 + - - +
253B THR 4.8 2.5 - - - -
254B THR* 3.5 25.5 - - - +
264B ALA 4.1 0.4 + - - -
265B GLY* 4.8 0.4 - - - -
501B PLG 2.8 31.7 + - - -
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Residues in contact with SER 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A LEU 3.8 19.5 - - - -
301A GLN* 4.1 1.1 - - - -
302A GLY* 3.6 13.4 + - - -
120B GLY* 1.3 70.7 - - - +
122B PRO* 1.3 71.8 - - - +
124B ASN* 3.2 7.4 + - - +
125B PHE* 3.0 23.7 + - - +
148B HIS* 4.3 1.4 - - - -
150B THR* 3.4 30.7 - - - +
501B PLG 3.2 27.3 + - - -
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Residues in contact with PRO 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A TYR* 4.0 24.7 - - + -
300A LEU 5.6 2.7 - - - +
301A GLN* 5.8 0.7 - - + -
117B PRO* 4.7 1.1 - - - -
118B TYR* 4.3 5.2 - - + +
119B SER* 3.2 34.5 - - - +
120B GLY 3.7 0.2 - - - +
121B SER* 1.3 96.3 - - - +
123B ALA* 1.3 62.6 + - - +
125B PHE* 3.4 5.8 + - + +
126B ALA* 2.9 24.9 + - - +
300B LEU* 5.5 0.7 - - - +
301B GLN* 4.2 17.3 - - + +
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Residues in contact with ALA 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B PRO* 3.8 19.7 - - + +
119B SER 3.2 10.3 + - - +
120B GLY* 3.0 12.9 + - - +
122B PRO* 1.3 77.6 - - - +
124B ASN* 1.3 63.9 + - - +
126B ALA* 3.2 16.2 - - - +
127B VAL* 3.2 8.7 + - - +
252B THR* 4.4 8.3 - - - -
253B THR 4.9 1.6 - - - +
265B GLY* 4.7 0.4 - - - -
266B MSE 4.2 12.8 - - - +
267B ILE* 3.3 27.6 - - + +
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Residues in contact with ASN 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 GLY 3.2 6.9 + - - +
121B SER* 3.2 8.0 + - - +
123B ALA* 1.3 75.4 - - - +
125B PHE* 1.3 68.3 + - - +
127B VAL* 2.8 16.2 + - - +
128B TYR* 3.0 41.3 + - + +
150B THR* 3.0 26.2 + - - +
151B HIS* 4.4 0.4 - - - -
226B MSE 3.6 6.3 - - - +
228B ASP* 2.7 24.5 + - - +
252B THR* 2.7 32.8 + - - -
501B PLG 3.8 10.5 - - - -
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Residues in contact with PHE 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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125A PHE* 4.3 12.8 - + - -
166A PHE* 3.8 23.8 - + - -
300A LEU* 4.9 5.4 - - + -
121B SER 3.0 12.7 + - - +
122B PRO* 3.9 6.3 - - + +
124B ASN* 1.3 78.3 - - - +
126B ALA* 1.3 57.7 + - - +
128B TYR* 3.3 12.4 + + - +
129B THR* 2.8 50.9 + - - -
150B THR* 6.0 0.2 - - - -
162B ALA* 4.0 22.7 - - + -
163B THR* 4.8 5.6 - - - -
166B PHE* 3.7 32.5 - + - -
167B PHE* 3.9 18.2 - + - -
300B LEU* 3.8 21.1 - - + -
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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
----------------------------------------------------------
117B PRO* 5.6 0.9 - - + -
122B PRO 2.9 15.2 + - - +
123B ALA* 3.2 12.1 - - - +
124B ASN 3.0 0.2 - - - -
125B PHE* 1.3 78.1 - - - +
127B VAL* 1.3 56.7 + - - +
129B THR* 3.4 2.8 + - - -
130B ALA* 3.0 28.1 + - - +
267B ILE* 3.9 14.4 - - + -
292B ILE* 5.3 1.9 - - + +
295B ALA* 3.5 4.7 - - - +
296B VAL* 4.1 19.5 - - + +
300B LEU* 3.6 21.9 - - + +
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Residues in contact with VAL 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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123B ALA 3.5 13.2 - - - +
124B ASN 2.8 7.7 + - - +
126B ALA* 1.3 74.3 - - - +
128B TYR* 1.3 66.2 + - - +
130B ALA* 3.0 5.1 + - - +
131B LEU* 2.8 48.1 + - + +
197B LEU* 4.2 7.4 - - + -
226B MSE 3.9 22.0 - - - -
250B VAL* 4.2 10.1 - - + -
252B THR* 3.7 22.7 - - + -
267B ILE* 3.7 22.4 - - + -
292B ILE* 4.7 5.8 - - + -
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Residues in contact with TYR 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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124B ASN* 3.0 35.7 + - + +
125B PHE* 3.8 10.5 - + - +
127B VAL* 1.3 74.7 - - - +
129B THR* 1.3 59.4 + - - +
132B VAL* 2.7 33.7 + - - +
133B GLU 3.1 8.3 + - - -
138B ILE* 3.8 18.8 - - + -
150B THR* 2.8 32.2 + - - -
151B HIS* 4.1 1.2 - - - -
163B THR* 3.5 24.5 - - + -
167B PHE* 3.5 24.9 - + + -
197B LEU* 4.3 12.6 - - + -
199B ILE* 3.4 29.4 - - + +
226B MSE 3.7 22.7 - - + +
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Residues in contact with THR 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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162A ALA* 5.6 0.9 - - + -
165A ILE* 4.8 16.4 - - + -
166A PHE* 3.7 19.7 - - + -
125B PHE* 2.8 47.7 + - - -
126B ALA 3.5 5.4 - - - -
128B TYR* 1.3 79.0 - - - +
130B ALA* 1.3 61.0 - - - +
133B GLU* 4.0 16.0 + - - +
134B PRO* 5.6 0.7 - - - +
167B PHE* 3.8 7.8 - - - -
295B ALA* 4.2 9.9 - - + -
299B GLY* 6.3 0.9 - - - -
300B LEU* 3.7 18.3 - - + +
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Residues in contact with ALA 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 17.5 + - - +
127B VAL 3.6 3.1 - - - +
129B THR* 1.3 78.7 - - - +
131B LEU* 1.3 61.1 + - + +
133B GLU* 4.7 9.0 - - - +
291B LEU* 3.5 51.6 - - + +
292B ILE* 3.7 15.3 - - + +
295B ALA* 3.6 8.7 - - + -
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Residues in contact with LEU 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 VAL* 2.8 38.8 + - + +
130B ALA* 1.3 83.2 - - + +
132B VAL* 1.3 60.2 + - - +
133B GLU* 4.5 4.6 - - - +
196B LYS* 3.5 20.1 + - - +
197B LEU* 4.5 10.1 - - + -
224B TYR* 4.0 35.3 - - + -
250B VAL* 4.1 13.0 - - + -
288B LEU* 3.5 35.2 - - + -
291B LEU* 3.9 24.7 - - + -
292B ILE* 4.5 7.0 - - + -
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Residues in contact with VAL 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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128B TYR* 2.7 23.8 + - - +
131B LEU* 1.3 76.2 - - - +
133B GLU* 1.3 74.6 + - - +
136B GLY* 3.3 38.3 - - - +
137B ARG 4.0 4.5 - - - +
138B ILE* 3.8 18.2 - - + -
167B PHE* 3.8 8.7 - - + -
196B LYS* 3.2 24.0 + - + +
197B LEU* 3.8 38.1 - - + -
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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