Contacts of the helix formed by residues 170 - 187 (chain A) in PDB entry 4EY7
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 170 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A GLY 3.9 4.4 + - - -
158A PHE* 3.9 16.5 + - - +
168A PRO 5.3 0.2 + - - -
169A GLY* 1.3 72.8 + - - +
171A VAL* 1.3 64.3 + - - +
172A GLY 3.2 3.1 - - - -
173A LEU* 2.9 30.0 + - + +
174A LEU* 3.1 14.9 + - + +
300A VAL 5.7 0.2 + - - -
301A PRO* 3.1 12.0 - - - +
302A VAL* 2.8 51.4 + - - +
304A ASP* 4.1 9.5 + - - -
307A PHE* 3.8 27.1 - - + +
308A LEU* 5.0 1.6 - - - +
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Residues in contact with VAL 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PHE* 3.5 17.3 - - - +
48A LEU 3.5 10.3 - - - +
49A PRO* 3.4 36.1 - - + -
152A ARG* 3.7 16.7 + - - +
156A PHE 3.5 20.9 - - - +
157A GLY 3.1 16.9 + - - +
159A LEU 6.0 1.6 - - - +
168A PRO* 4.3 4.0 - - + -
169A GLY* 3.8 13.5 - - - +
170A ASN* 1.3 77.1 - - - +
172A GLY* 1.3 56.7 + - - +
174A LEU* 3.1 11.4 + - + +
175A ASP* 2.8 33.2 + - - +
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Residues in contact with GLY 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A TYR* 3.5 10.4 - - - +
152A ARG 3.6 23.8 - - - -
157A GLY* 2.9 12.0 + - - -
158A PHE* 3.7 10.5 - - - -
171A VAL* 1.3 77.0 - - - +
173A LEU* 1.3 61.5 + - - +
175A ASP* 3.3 15.3 - - - +
176A GLN* 3.2 18.9 + - - +
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Residues in contact with LEU 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A PHE* 4.9 0.7 - - + -
158A PHE* 3.7 12.8 - - + -
170A ASN* 2.9 21.9 + - - +
172A GLY* 1.3 77.2 - - - +
174A LEU* 1.3 57.5 + - - +
176A GLN* 3.1 29.7 + - - +
177A ARG* 3.0 21.8 + - - +
208A SER* 4.0 17.3 - - - +
211A MET* 3.8 31.6 - - + -
212A HIS* 3.7 13.7 - - - +
301A PRO* 3.9 17.0 - - + -
307A PHE* 3.8 36.8 - - + -
308A LEU* 5.5 0.9 - - + -
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Residues in contact with LEU 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A PRO* 4.0 30.5 - - + -
50A PRO* 3.6 14.8 - - + +
168A PRO* 6.3 0.4 - - + -
169A GLY 5.2 2.9 - - - +
170A ASN* 3.1 17.8 + - + +
171A VAL* 3.1 13.9 + - + +
173A LEU* 1.3 74.7 - - - +
175A ASP* 1.3 59.1 + - - +
177A ARG* 3.7 34.5 - - - +
178A LEU* 2.8 31.5 + - - +
307A PHE* 3.9 16.8 - - + -
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Residues in contact with ASP 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A PHE* 3.3 18.2 - - + -
50A PRO* 3.4 15.7 - - - +
97A LEU* 3.5 15.6 - - + +
151A TYR* 3.7 14.8 - - + -
152A ARG* 2.8 66.6 + - - +
171A VAL 2.8 17.4 + - - +
172A GLY* 3.3 9.4 - - - +
174A LEU* 1.3 71.3 - - - +
176A GLN* 1.3 62.6 + - - +
178A LEU* 3.5 0.5 + - - +
179A ALA* 3.1 17.5 + - - +
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Residues in contact with GLN 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A ILE* 3.6 14.3 - - + +
123A PHE* 5.0 1.0 - - - -
149A MET* 4.4 14.4 - - + +
151A TYR* 3.5 47.0 - - + -
158A PHE* 5.4 0.4 - - - -
172A GLY 3.2 10.9 + - - +
173A LEU* 3.1 16.5 + - - +
175A ASP* 1.3 74.9 - - - +
177A ARG* 1.3 58.5 + - - +
179A ALA* 3.2 7.8 + - - +
180A LEU* 2.9 34.6 + - + +
208A SER* 3.1 33.4 + - - -
212A HIS* 2.7 32.8 + - - +
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Residues in contact with ARG 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A LEU 3.0 13.1 + - - +
174A LEU* 3.2 28.5 + - + +
176A GLN* 1.3 72.9 - - - +
178A LEU* 1.3 62.7 + - - +
180A LEU* 3.1 8.6 + - - +
181A GLN* 2.8 46.4 + - - +
212A HIS* 4.0 6.5 - - + -
215A SER* 2.8 29.1 + - - -
217A PRO* 3.4 33.2 - - - +
218A SER* 2.9 28.6 + - - +
221A LEU* 3.8 15.5 - - + -
307A PHE* 3.2 22.1 - - - +
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Residues in contact with LEU 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A PHE* 3.5 31.0 - - + +
38A ALA* 3.6 20.2 - - + -
50A PRO* 3.8 21.8 - - + +
51A GLU 4.0 10.5 - - - +
52A PRO* 4.3 20.6 - - + -
174A LEU 2.8 16.8 + - - +
175A ASP 3.8 4.0 - - - +
177A ARG* 1.3 77.9 - - - +
179A ALA* 1.3 57.3 + - - +
181A GLN* 3.2 24.6 + - + +
182A TRP* 2.8 27.7 + - + +
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Residues in contact with ALA 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A PHE* 4.0 9.3 - - + -
99A LEU* 3.9 11.9 - - + +
147A VAL* 6.2 0.4 - - + -
149A MET* 3.8 37.7 - - + -
175A ASP 3.1 13.8 + - - +
176A GLN 3.5 7.9 - - - +
178A LEU* 1.3 78.1 - - - +
180A LEU* 1.3 57.6 + - - +
182A TRP* 3.1 10.9 + - - +
183A VAL* 2.9 32.1 + - + +
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Residues in contact with LEU 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A VAL* 3.8 25.4 - - + -
118A ILE* 5.5 2.5 - - + -
149A MET* 4.7 5.2 - - + -
176A GLN* 2.9 18.9 + - + +
177A ARG* 3.1 8.7 + - - +
179A ALA* 1.3 76.2 - - - +
181A GLN* 1.3 61.9 + - - +
183A VAL* 3.2 7.9 + - + +
184A GLN* 3.0 25.8 + - - +
197A VAL* 5.1 1.6 - - + -
199A LEU* 3.6 42.4 - - + -
212A HIS* 4.4 24.7 - - + +
218A SER* 5.3 0.4 - - - -
221A LEU* 3.8 34.2 - - + +
222A PHE* 4.6 3.8 - - + -
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Residues in contact with GLN 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A ARG* 2.8 37.4 + - - +
178A LEU* 3.4 29.8 - - + +
180A LEU* 1.3 72.1 - - - +
182A TRP* 1.3 66.5 + - - +
184A GLN* 3.3 9.1 + - - +
185A GLU* 3.1 35.4 + - - +
217A PRO 5.2 2.4 + - - -
221A LEU* 3.7 20.3 - - + +
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Residues in contact with TRP 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A VAL* 4.0 16.9 - - + +
35A ILE* 3.8 23.5 - - + +
36A PRO 4.4 9.9 + - - -
37A PHE* 3.9 21.3 - - + +
56A TRP* 5.9 1.0 - - - -
99A LEU* 3.6 35.2 - - + -
101A VAL* 4.0 10.3 - - + -
147A VAL* 5.6 0.4 - - + -
178A LEU* 2.8 19.0 + - + +
179A ALA* 3.1 14.8 + - - +
181A GLN* 1.3 72.2 - - - +
183A VAL* 1.3 72.2 + - + +
185A GLU* 3.2 2.8 + - - -
186A ASN* 2.8 71.7 + - + +
187A VAL* 4.9 3.1 - - + -
190A PHE* 3.6 29.2 - + - -
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Residues in contact with VAL 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A VAL* 4.5 7.0 - - + -
116A VAL* 4.7 10.5 - - + -
147A VAL* 3.9 33.2 - - + -
179A ALA 2.9 18.5 + - - +
180A LEU* 3.4 12.6 - - + +
181A GLN 3.2 0.2 - - - -
182A TRP* 1.3 87.9 - - + +
184A GLN* 1.3 65.5 + - - +
187A VAL* 2.9 53.0 + - + +
197A VAL* 4.1 24.0 - - + -
221A LEU 5.9 0.2 - - - +
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Residues in contact with GLN 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A LEU 3.0 16.6 + - - +
181A GLN* 3.5 9.9 - - - +
183A VAL* 1.3 77.0 - - - +
185A GLU* 1.3 64.5 + - + +
187A VAL 4.8 0.5 + - - -
188A ALA* 5.7 0.9 + - - +
194A PRO* 2.9 53.4 + - - +
197A VAL* 3.9 10.5 - - - +
220A GLY 4.7 5.1 - - - +
221A LEU* 3.5 45.6 + - + -
223A HIS* 4.7 1.4 - - - -
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Residues in contact with GLU 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ARG* 3.1 60.5 + - - +
181A GLN* 3.1 24.2 + - - +
182A TRP* 5.4 0.8 - - - -
184A GLN* 1.3 81.0 - - + +
186A ASN* 1.3 72.4 + - - +
188A ALA* 5.5 2.3 - - - +
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Residues in contact with ASN 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A VAL* 3.4 10.3 - - + +
13A ARG* 3.0 41.5 + - - +
182A TRP* 2.8 69.7 + - + +
185A GLU* 1.3 90.3 + - - +
187A VAL* 1.3 66.0 + - - +
188A ALA* 3.2 3.6 - - - -
189A ALA* 3.1 17.8 + - - +
190A PHE* 3.3 12.9 - - - -
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Residues in contact with VAL 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A VAL* 5.2 1.3 - - + -
114A VAL* 4.0 20.0 - - + -
145A VAL* 4.0 19.3 - - + -
147A VAL* 4.3 10.3 - - + -
182A TRP* 4.3 3.8 + - + -
183A VAL* 2.9 45.1 + - + +
184A GLN 4.8 0.4 + - - -
186A ASN* 1.3 78.8 - - - +
188A ALA* 1.3 60.0 + - - +
190A PHE* 2.9 28.0 + - + +
192A GLY* 3.0 20.0 + - - +
194A PRO* 3.8 30.1 - - + -
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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
------------------------------------------------------------
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