Contacts of the strand formed by residues 139 - 151 (chain E) in PDB entry 6A3V
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 GLY 139 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138E ALA* 1.3 80.5 - - - +
140E VAL* 1.3 63.7 + - - -
141E TYR* 4.1 7.6 - - - -
205E HIS* 3.2 14.5 + - - -
206E LEU 2.9 26.0 + - - -
239E ARG* 3.9 9.9 - - - -
241E THR* 4.2 9.6 - - - -
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Residues in contact with VAL 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A PHE* 3.5 42.4 - - + -
119A SER* 4.9 7.0 - - - +
139E GLY* 1.3 76.7 - - - +
141E TYR* 1.3 63.6 + - - +
203E LEU* 4.1 19.7 - - + -
204E LEU 3.2 12.6 - - - +
205E HIS* 3.8 20.2 - - + +
239E ARG* 4.1 1.1 - - - +
240E VAL* 2.8 33.3 + - + +
241E THR* 3.2 19.2 + - - +
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Residues in contact with TYR 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E MET* 4.4 15.4 - - + -
124E LEU* 5.5 1.8 - - + -
135E VAL* 3.7 21.5 - - + +
137E LYS 2.5 25.8 + - - -
138E ALA 3.4 8.0 + - - -
139E GLY 4.1 12.3 - - - -
140E VAL* 1.3 75.2 - - - +
142E TYR* 1.3 61.1 + - - +
143E VAL* 3.7 5.1 + - + -
203E LEU* 3.5 1.4 - - - -
204E LEU* 2.8 36.0 + - - +
206E LEU* 3.6 30.7 - - + -
237E LEU* 3.4 36.6 - - + -
238E PHE 3.3 7.4 - - - +
239E ARG* 3.4 47.2 + - + -
240E VAL* 4.4 2.9 - - - -
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Residues in contact with TYR 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A TYR* 3.8 15.8 + + - -
144A PHE* 3.7 25.6 - + - -
199A PHE* 3.2 30.0 - - - -
238A PHE* 4.2 6.1 - + + -
142C TYR* 3.9 23.7 + + - -
141E TYR* 1.3 70.3 - - - +
143E VAL* 1.3 59.4 + - - +
144E PHE* 3.9 19.4 + + + -
199E PHE* 4.7 0.5 - - - -
201E GLY* 4.1 7.5 - - - -
202E ARG* 3.9 17.5 - - - -
203E LEU* 3.8 23.6 - - + -
237E LEU* 3.4 4.3 - - - -
238E PHE* 2.8 71.9 + + + -
240E VAL* 4.1 2.9 - - + +
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Residues in contact with VAL 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E TYR* 4.2 10.3 - - + +
142E TYR* 1.3 76.7 - - - +
144E PHE* 1.3 61.8 + - - +
165E LEU* 3.7 19.5 - - + -
179E LEU* 3.4 10.7 - - + +
201E GLY* 3.2 2.3 - - - -
202E ARG 3.1 29.4 + - - +
204E LEU* 4.0 26.2 - - + -
206E LEU* 4.8 1.6 - - + -
212E LEU* 4.5 7.2 - - + -
235E LEU* 3.6 27.1 - - + -
236E GLY 3.6 5.8 - - - +
237E LEU* 3.8 26.9 - - + -
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Residues in contact with PHE 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C TYR* 3.7 21.5 - + - -
201C GLY 3.4 22.7 - - - -
202C ARG* 3.6 16.6 - - + -
203C LEU* 3.9 6.5 - - + -
94E GLN* 3.4 17.0 - - - -
142E TYR* 3.9 17.9 - + + -
143E VAL* 1.3 73.7 - - - +
145E PHE* 1.3 66.6 + - - +
146E GLN* 5.2 0.4 - - - -
179E LEU* 4.5 2.2 - - - -
199E PHE* 3.7 18.2 - + + -
200E GLN 3.2 12.6 - - - +
201E GLY* 4.1 4.9 - - - -
234E VAL* 4.1 6.5 - - + -
235E LEU* 3.6 11.1 - - - +
236E GLY* 3.3 57.3 + - - -
237E LEU 3.9 3.6 - - - -
238E PHE* 4.5 9.2 - + - -
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Residues in contact with PHE 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109E TRP* 4.9 2.0 - + - -
144E PHE* 1.3 77.9 - - - +
146E GLN* 1.3 63.7 + - - +
147E LEU 4.3 0.2 - - - -
163E LEU* 4.2 20.6 - - + -
164E ALA 4.3 1.1 - - - -
165E LEU* 3.5 30.5 - - + -
179E LEU* 3.5 36.8 - - + -
181E LEU* 3.9 25.8 - - + -
199E PHE* 3.1 24.1 - - - -
200E GLN* 2.6 22.7 + - + +
214E VAL* 3.5 45.1 - - + -
234E VAL 3.7 8.7 - - - -
235E LEU* 4.0 14.6 - - + -
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Residues in contact with GLN 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200C GLN* 3.2 25.5 - - - +
201C GLY 2.8 23.2 - - - +
202C ARG* 3.1 40.1 - - - +
144E PHE* 5.3 0.4 - - + -
145E PHE* 1.3 71.9 - - - +
147E LEU* 1.3 61.2 + - - +
163E LEU* 4.6 3.4 - - - +
197E PHE* 4.2 9.2 - - + -
198E GLY 3.9 2.2 - - - -
199E PHE* 3.5 21.5 - - + -
232E ALA* 3.7 18.7 + - - +
233E THR* 3.2 8.3 - - - +
234E VAL* 2.8 50.2 + - + +
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Residues in contact with LEU 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145E PHE 4.3 0.2 - - - -
146E GLN* 1.3 74.1 - - - +
148E GLU* 1.3 61.3 + - - +
149E LEU* 3.6 13.5 - - + -
161E VAL* 4.1 17.7 - - + +
163E LEU* 3.6 42.2 - - + -
181E LEU* 3.8 16.4 - - + +
183E VAL* 3.8 23.0 - - + +
196E ALA 4.0 0.2 - - - +
197E PHE* 3.3 5.8 - - - -
198E GLY 3.0 34.2 + - - -
216E LEU* 5.0 1.6 - - + -
228E LEU* 3.7 29.4 - - + -
233E THR* 3.9 11.2 - - + -
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Residues in contact with GLU 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180C ALA* 5.0 9.6 - - - +
182C THR* 5.8 0.5 + - - -
200C GLN* 4.7 8.1 + - - -
147E LEU* 1.3 75.7 - - - +
149E LEU* 1.3 64.1 + - - +
195E SER* 5.1 10.2 + - - -
196E ALA 3.2 10.5 - - - +
197E PHE* 4.1 22.1 - - + +
228E LEU* 3.7 4.9 - - - -
229E THR* 2.7 45.1 + - - +
232E ALA* 3.2 35.9 + - + +
233E THR* 4.0 6.5 + - - -
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Residues in contact with LEU 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E LEU* 3.9 19.5 - - + -
147E LEU* 3.6 33.9 - - + -
148E GLU* 1.3 81.7 - - - +
150E ARG* 1.3 59.3 + - - +
161E VAL* 3.7 26.9 - - + -
183E VAL* 4.2 16.4 - - + -
185E LEU* 3.8 12.8 - - + -
195E SER* 3.4 5.7 - - - -
196E ALA* 2.6 38.4 + - + +
226E TRP* 3.9 19.0 - - + -
227E GLN 3.6 8.7 - - - +
228E LEU* 3.8 8.7 - - + -
229E THR* 3.4 7.9 + - - -
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Residues in contact with ARG 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149E LEU* 1.3 75.7 - - - +
151E ARG* 1.3 64.0 + - - +
152E VAL* 3.5 16.1 + - + +
194E ASN 3.4 10.3 - - - +
195E SER* 5.3 3.1 - - - +
226E TRP* 3.4 7.8 - - - -
227E GLN* 3.1 45.9 + - - +
228E LEU 5.1 1.6 + - - -
229E THR* 3.8 26.9 - - - +
230E GLN* 4.0 19.3 - - - +
66F ARG* 3.7 28.3 - - - +
72F PHE* 3.8 8.3 - - - -
100F SER* 2.8 43.6 + - - +
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Residues in contact with ARG 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150E ARG* 1.3 74.9 + - - +
152E VAL* 1.3 57.5 + - - +
153E VAL 3.3 24.0 - - - +
154E ALA* 4.4 2.7 - - - +
155E GLY 4.0 12.1 - - - +
156E GLU 3.2 21.1 + - - +
157E GLY 3.2 15.6 + - - -
186E PRO 3.0 20.6 + - - -
187E PRO 3.8 9.5 + - - -
188E ALA* 3.9 16.4 - - - +
192E ALA* 4.4 4.8 - - - +
193E ARG 3.0 25.3 + - - +
194E ASN* 3.3 31.7 + - - +
225E ALA 3.1 15.3 - - - +
226E TRP* 3.4 25.0 - - + +
100F SER* 4.2 1.9 + - - +
101F MET* 3.0 24.4 - - - +
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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