Contacts of the strand formed by residues 139 - 151 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138I ALA* 1.3 79.3 - - - +
140I VAL* 1.3 64.0 - - - +
141I TYR* 3.7 7.9 - - - -
205I HIS* 3.9 7.3 - - - -
206I LEU 2.9 28.9 + - - +
239I ARG* 4.2 10.5 - - - -
241I THR* 4.5 6.3 - - - -
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Residues in contact with VAL 140 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92G PHE* 3.6 35.4 - - + -
119G SER* 4.8 8.1 - - - +
139I GLY* 1.3 75.4 - - - +
141I TYR* 1.3 62.9 + - - +
203I LEU* 4.4 20.9 - - + -
204I LEU 3.4 14.8 - - - +
205I HIS* 4.6 15.5 - - + -
239I ARG* 4.5 0.9 - - - +
240I VAL* 3.0 28.6 + - + +
241I THR* 3.3 25.6 + - - +
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Residues in contact with TYR 141 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91I MET* 3.9 13.8 - - + -
124I LEU* 5.4 1.3 - - + -
135I VAL* 3.7 16.1 - - + +
137I LYS 2.4 30.6 + - - -
138I ALA 3.8 0.2 - - - -
139I GLY 3.7 20.6 - - - -
140I VAL* 1.3 73.0 - - - +
142I TYR* 1.3 58.0 - - - +
143I VAL* 3.8 2.8 + - + -
203I LEU* 3.7 5.5 - - - -
204I LEU* 2.8 35.6 + - - +
206I LEU* 3.5 33.0 - - + -
237I LEU* 3.4 34.8 - - + -
238I PHE 3.5 2.0 - - - -
239I ARG* 2.8 57.0 + - + -
240I VAL* 4.4 0.4 - - - +
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Residues in contact with TYR 142 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142G TYR* 3.8 16.7 + + - -
144G PHE* 3.7 26.7 - + - -
199G PHE* 3.5 26.7 - - - -
238G PHE* 3.8 18.8 - + - -
141I TYR* 1.3 71.6 - - - +
143I VAL* 1.3 60.8 + - - +
144I PHE* 3.7 28.4 - + + -
199I PHE* 4.5 6.2 - + - -
201I GLY* 4.5 6.9 - - - -
202I ARG 4.1 11.9 - - - -
203I LEU* 4.1 16.6 - - + -
236I GLY 3.9 0.3 - - - +
237I LEU* 3.4 5.2 - - - +
238I PHE* 2.9 72.7 + + + -
240I VAL* 4.4 3.4 - - + +
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Residues in contact with VAL 143 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141I TYR* 4.5 11.2 - - + +
142I TYR* 1.3 78.3 - - - +
144I PHE* 1.3 62.1 + - - +
165I LEU* 4.0 10.5 - - + -
179I LEU* 3.6 19.7 - - + +
201I GLY* 3.2 18.4 - - - -
202I ARG 3.2 13.0 + - - +
204I LEU* 3.9 26.2 - - + -
206I LEU* 4.5 2.9 - - + -
212I LEU* 4.5 9.2 - - + -
235I LEU* 3.7 26.9 - - + -
236I GLY 3.5 4.9 - - - +
237I LEU* 3.9 22.7 - - + -
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Residues in contact with PHE 144 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93I ALA 5.3 0.4 - - - -
94I GLN* 3.5 20.9 - - - -
142I TYR* 3.7 26.7 - + + -
143I VAL* 1.3 74.8 - - - +
145I PHE* 1.3 75.0 + - - +
146I GLN* 4.9 8.5 - - + -
179I LEU* 4.2 0.2 - - - -
199I PHE* 3.6 34.1 - + + -
200I GLN 3.1 6.5 - - - +
201I GLY* 4.2 1.3 - - - -
234I VAL* 4.5 9.0 - - + -
235I LEU* 3.7 2.1 - - - +
236I GLY* 3.2 56.9 + - - -
237I LEU 3.9 4.0 - - - -
238I PHE* 4.2 20.0 - + - -
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Residues in contact with PHE 145 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109I TRP* 5.9 1.1 - + - -
144I PHE* 1.3 83.0 - - - +
146I GLN* 1.3 63.5 + - - +
163I LEU* 3.6 50.3 - - + -
164I ALA 4.0 4.0 - - - -
165I LEU* 3.5 33.2 - - + -
179I LEU* 3.6 20.9 - - + -
180I ALA 4.9 0.4 - - - -
181I LEU* 3.8 22.7 - - + -
199I PHE* 3.1 23.4 - - - -
200I GLN* 2.5 26.1 + - + +
214I VAL* 3.8 18.2 - - + -
234I VAL 3.8 0.9 - - - -
235I LEU* 3.6 26.9 - - + -
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Residues in contact with GLN 146 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144I PHE* 4.9 9.7 - - + -
145I PHE* 1.3 81.0 - - - +
147I LEU* 1.3 61.0 + - - +
163I LEU* 4.0 5.0 - - - +
181I LEU* 4.9 0.2 - - - -
197I PHE* 5.0 12.3 - - + -
198I GLY 3.8 4.9 - - - +
199I PHE* 3.7 24.5 - - + -
232I ALA* 3.4 20.9 - - - +
233I THR* 3.3 11.9 - - - +
234I VAL* 3.0 45.4 + - + +
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Residues in contact with LEU 147 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146I GLN* 1.3 73.4 - - - +
148I GLU* 1.3 60.0 + - - +
149I LEU* 3.7 9.4 - - + -
161I VAL* 3.8 31.6 - - + +
163I LEU* 3.7 34.1 - - + +
181I LEU* 4.5 7.4 - - + +
183I VAL* 3.7 25.6 - - + +
197I PHE* 3.1 6.9 - - - -
198I GLY 2.9 33.4 + - - +
216I LEU* 4.7 2.2 - - + -
228I LEU* 3.6 27.4 - - + -
233I THR* 3.7 20.0 - - + +
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Residues in contact with GLU 148 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146I GLN 4.3 0.4 - - - -
147I LEU* 1.3 74.9 - - - +
149I LEU* 1.3 63.4 + - - +
195I SER* 5.7 5.7 + - - -
196I ALA 3.4 15.3 - - - +
197I PHE* 4.2 20.4 - - + -
228I LEU* 3.7 3.5 - - - +
229I THR* 2.8 43.8 + - - +
232I ALA* 3.5 31.3 + - + +
233I THR* 3.7 10.7 + - - -
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Residues in contact with LEU 149 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102I LEU* 4.1 18.4 - - + -
147I LEU* 3.7 26.9 - - + -
148I GLU* 1.3 83.6 - - - +
150I ARG* 1.3 62.1 + - - +
161I VAL* 3.7 28.9 - - + -
183I VAL* 3.8 24.9 - - + -
185I LEU* 3.8 12.8 - - + -
195I SER* 3.5 5.5 - - - -
196I ALA* 3.0 31.0 + - + +
226I TRP* 3.6 21.1 - - + -
227I GLN 3.7 8.7 - - - +
228I LEU* 3.9 9.0 - - + -
229I THR* 3.5 5.1 + - - -
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Residues in contact with ARG 150 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100I VAL* 6.2 0.4 - - - +
149I LEU* 1.3 73.2 - - - +
151I ARG* 1.3 61.2 + - - +
152I VAL* 3.6 12.3 + - + +
194I ASN 3.4 10.3 - - - +
195I SER* 5.4 2.2 - - - +
226I TRP* 3.2 15.7 - - - -
227I GLN* 3.3 33.5 + - - +
228I LEU 5.1 1.6 + - - -
229I THR* 3.6 26.2 - - - +
230I GLN* 5.3 9.2 - - - +
66J ARG* 3.7 16.7 - - - +
72J PHE* 3.3 37.2 - - - -
99J CYS 3.6 2.4 + - - -
100J SER* 3.1 39.6 + - - +
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Residues in contact with ARG 151 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150I ARG* 1.3 71.9 - - - +
152I VAL* 1.3 60.2 + - - +
153I VAL 3.2 24.7 - - - +
154I ALA* 4.1 11.9 - - - +
155I GLY 4.2 4.3 - - - +
156I GLU 2.8 28.8 + - - +
157I GLY 3.5 7.7 + - - -
186I PRO* 2.8 24.0 + - - +
187I PRO 3.7 14.0 + - - -
188I ALA* 4.8 4.2 - - - +
192I ALA* 5.2 3.0 - - - +
193I ARG 3.0 21.6 + - - +
194I ASN* 3.2 37.2 + - - +
225I ALA 3.2 11.4 - - - +
226I TRP* 3.3 28.5 - - + +
100J SER 3.0 16.5 - - - +
101J MET* 3.2 13.8 - - - +
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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