Contacts of the helix formed by residues 163 - 181 (chain A) in PDB entry 3V9G
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 ALA 163 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A LEU* 5.4 0.9 - - - -
140A ARG* 3.6 34.3 - - + +
143A ILE* 4.9 1.8 - - + -
144A LEU* 3.9 11.7 - - + -
158A ALA 3.6 3.0 + - - -
159A GLU* 3.4 16.4 - - - +
161A ASP 3.1 1.0 + - - -
162A ALA* 1.3 78.9 - - - +
164A ALA* 1.3 62.3 + - - +
165A GLU 3.4 0.8 + - - -
166A LEU 3.5 0.9 + - - -
167A ILE* 2.9 45.9 + - + +
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Residues in contact with ALA 164 (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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35A GLU* 4.2 23.1 - - + +
37A VAL* 4.1 25.8 - - + -
140A ARG* 5.2 2.5 - - - +
159A GLU 3.0 16.2 + - - +
160A ILE* 3.8 8.1 - - + +
163A ALA* 1.3 76.9 - - + +
165A GLU* 1.3 58.0 + - - +
167A ILE* 3.8 0.7 - - - +
168A ASP* 2.9 39.3 + - - +
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Residues in contact with GLU 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A ILE 3.2 16.8 + - - +
161A ASP* 3.5 5.2 + - - +
163A ALA 3.5 0.2 - - - -
164A ALA* 1.3 78.0 - - - +
166A LEU* 1.3 58.0 + - - +
168A ASP* 3.3 6.2 + - - +
169A PHE* 2.8 59.9 + - + -
212A PHE* 3.6 26.5 - - - +
214A ALA* 3.5 13.3 - - + +
215A ILE* 5.2 4.2 - - - +
513A SER* 4.2 23.0 + - - +
515A VAL* 4.1 13.2 - - + +
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Residues in contact with LEU 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A LEU* 3.6 25.4 - - + -
161A ASP 3.3 4.2 + - - +
162A ALA 3.6 22.9 - - - +
164A ALA 3.5 0.2 - - - -
165A GLU* 1.3 75.0 - - - +
167A ILE* 1.3 64.4 + - - +
169A PHE* 3.5 4.4 + - + +
170A PHE* 3.2 44.5 + - + -
213A THR* 4.7 2.9 - - + +
214A ALA* 3.5 38.5 - - + +
217A GLY* 3.9 11.0 - - - -
245A VAL* 3.6 32.8 - - + -
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Residues in contact with ILE 167 (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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35A GLU* 3.7 22.0 - - + +
132A ALA* 3.7 21.7 - - + +
135A LEU* 3.7 18.2 - - + +
136A SER* 3.6 28.9 - - - +
140A ARG* 4.2 0.7 - - - +
163A ALA* 2.9 42.5 + - + +
164A ALA 3.8 1.8 - - - +
166A LEU* 1.3 71.2 - - - +
168A ASP* 1.3 57.8 + - - +
170A PHE* 3.3 3.2 + - - +
171A ARG* 3.0 66.7 + - - +
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Residues in contact with ASP 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ALA 4.0 2.4 - - - +
34A ASN* 3.0 30.3 + - - +
35A GLU* 2.8 31.1 + - - +
164A ALA* 2.9 31.2 + - - +
165A GLU* 3.3 3.4 + - - +
167A ILE* 1.3 73.0 - - - +
169A PHE* 1.3 61.1 + - - +
171A ARG* 4.5 2.2 + - - +
172A PHE* 2.8 43.2 + - + +
514A ILE* 4.6 5.0 - - - +
515A VAL* 3.6 24.7 + - + +
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Residues in contact with PHE 169 (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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165A GLU* 2.8 52.9 + - + +
166A LEU* 3.6 6.7 - - + +
167A ILE 3.4 0.2 - - - -
168A ASP* 1.3 72.1 - - - +
170A PHE* 1.3 67.4 + - + +
172A PHE* 5.1 0.2 - - - -
173A ASN* 3.0 35.8 + - - +
214A ALA* 4.0 15.3 - - + -
215A ILE* 5.1 7.6 - - + -
218A ASN* 3.5 49.8 - - + +
515A VAL* 3.8 19.0 - - + +
532A PRO* 4.0 10.1 - - + -
533A GLY* 3.6 28.7 - - - -
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Residues in contact with PHE 170 (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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128A PHE* 3.5 55.6 - + + +
129A LEU* 4.6 0.3 - - - +
131A ALA* 4.0 12.6 - - + -
132A ALA* 4.0 9.4 - - + -
135A LEU* 4.2 18.8 - - + -
166A LEU* 3.2 28.6 + - + +
167A ILE 3.7 7.2 - - - +
168A ASP 3.3 0.2 - - - -
169A PHE* 1.3 81.1 - - + +
171A ARG* 1.3 62.3 + - - +
173A ASN* 4.3 1.8 - - - +
174A ALA* 3.3 23.6 + - - +
217A GLY* 3.8 23.6 - - - -
218A ASN* 4.9 2.0 - - - -
221A GLY* 4.7 2.7 - - - -
225A LEU* 5.7 0.3 - - - +
245A VAL* 4.7 4.9 - - + -
248A ILE* 6.0 0.4 - - + -
249A LEU* 4.0 36.3 - - + -
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Residues in contact with ARG 171 (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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32A VAL* 3.8 25.2 - - + +
33A ALA 4.3 15.8 + - - +
34A ASN 5.2 0.2 - - - -
35A GLU* 3.0 32.3 + - - +
129A LEU* 4.0 18.4 + - + +
132A ALA* 3.8 16.5 + - + +
133A ASP* 2.9 27.9 + - - -
136A SER* 3.9 15.2 + - - -
167A ILE* 3.0 37.0 + - - +
168A ASP* 4.1 2.9 + - - +
170A PHE* 1.3 75.9 - - - +
172A PHE* 1.3 66.8 + - + +
174A ALA* 3.2 4.2 + - - +
175A LYS* 3.0 26.9 + - - +
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Residues in contact with PHE 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A VAL* 3.9 23.8 - - + -
33A ALA 4.0 18.4 - - - -
34A ASN* 3.6 42.6 - - - -
168A ASP* 2.8 37.8 + - + +
169A PHE* 4.6 0.4 - - - +
171A ARG* 1.3 77.6 - - + +
173A ASN* 1.3 57.1 + - - +
175A LYS* 3.2 10.4 + - + +
176A TYR* 3.0 61.2 + + + -
515A VAL* 3.7 18.8 - - + -
516A GLY* 4.1 8.7 - - - -
186B ILE* 3.8 25.8 - - + -
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Residues in contact with ASN 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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169A PHE* 3.0 25.7 + - - +
170A PHE* 4.5 1.6 - - - +
172A PHE* 1.3 77.9 - - - +
174A ALA* 1.3 57.1 + - - +
176A TYR* 3.8 19.3 - - - +
177A ALA* 3.0 22.9 + - - +
218A ASN* 2.9 30.5 + - - -
222A ALA* 3.9 9.0 - - + +
225A LEU* 3.3 24.0 - - + +
533A GLY* 5.1 6.9 - - - +
534A GLY 4.3 6.5 + - - -
537A TYR* 4.6 7.6 - - - -
538A ILE* 3.9 21.6 - - + +
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Residues in contact with ALA 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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30A LEU* 4.3 4.3 - - + -
125A ALA* 3.8 27.1 - - + +
128A PHE* 5.1 1.1 - - + -
129A LEU* 4.1 18.4 - - + -
170A PHE 3.3 19.1 + - - +
171A ARG 3.2 5.1 + - - +
172A PHE 3.2 0.4 - - - -
173A ASN* 1.3 77.2 - - - +
175A LYS* 1.3 65.6 + - - +
177A ALA* 4.0 0.7 - - - +
178A VAL* 3.1 29.8 + - - +
225A LEU* 4.0 11.3 - - + +
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Residues in contact with LYS 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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29A SER* 4.8 1.4 + - - -
30A LEU* 3.3 37.7 + - + +
31A LYS* 5.3 0.4 - - - +
32A VAL* 3.5 27.4 - - + +
171A ARG 3.0 14.3 + - - +
172A PHE* 3.5 11.9 - - + +
174A ALA* 1.3 77.8 - - - +
176A TYR* 1.3 82.7 + - + +
178A VAL* 3.5 0.9 + - - +
179A GLU* 2.8 65.4 + - - +
186B ILE* 6.4 1.1 - - - -
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Residues in contact with TYR 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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172A PHE* 3.0 49.6 + + + +
173A ASN* 3.8 14.8 - - - +
175A LYS* 1.3 95.6 - - + +
177A ALA* 1.3 58.6 + - - +
179A GLU* 3.8 6.3 - - - +
180A LEU* 3.0 28.9 + - - +
516A GLY* 3.9 7.6 - - - -
533A GLY 3.8 14.2 + - - -
534A GLY* 3.3 30.5 - - - -
535A PRO* 3.7 35.4 - - + +
538A ILE* 3.7 16.6 - - + +
186B ILE* 6.0 0.2 - - - +
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Residues in contact with ALA 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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121A ILE* 3.6 24.0 - - + +
173A ASN 3.0 18.4 + - - +
174A ALA 4.0 2.9 - - - +
175A LYS 3.3 0.2 - - - -
176A TYR* 1.3 74.7 - - - +
178A VAL* 1.3 64.0 + - - +
180A LEU* 3.4 14.9 + - - +
181A GLU* 3.6 13.3 + - - +
225A LEU* 3.9 5.6 - - + -
226A MET* 3.6 28.7 - - + +
538A ILE* 3.7 9.4 - - - +
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Residues in contact with VAL 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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28A SER* 4.0 28.6 + - - +
29A SER 4.7 4.3 - - - +
30A LEU* 5.0 4.0 - - + -
121A ILE* 4.5 17.3 - - + -
122A ALA* 4.8 2.7 - - + -
125A ALA* 4.1 15.7 - - + -
174A ALA 3.1 18.7 + - - +
175A LYS* 3.8 4.7 - - - +
177A ALA* 1.3 78.3 - - - +
179A GLU* 1.3 62.7 + - + +
181A GLU* 3.5 18.0 + - - +
182A GLY 4.2 1.6 + - - -
24C TRP* 3.8 41.3 - - + -
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Residues in contact with GLU 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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28A SER 3.9 16.2 - - - +
29A SER* 2.8 16.0 + - - -
30A LEU 2.8 27.6 + - - +
175A LYS* 2.8 49.0 + - - +
176A TYR* 4.1 7.3 - - + +
178A VAL* 1.3 76.7 - - + +
180A LEU* 1.3 63.2 + - - +
182A GLY* 3.3 14.0 + - - +
183A GLN* 3.9 9.4 + - - +
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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
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176A TYR 3.0 18.7 + - - +
177A ALA 3.5 7.2 - - - +
178A VAL 3.2 0.4 - - - -
179A GLU* 1.3 74.4 - - - +
181A GLU* 1.3 64.5 + - - +
182A GLY 3.0 2.2 - - - -
183A GLN* 2.9 33.7 + - - +
197A TYR* 3.3 39.6 - - + -
226A MET* 4.0 24.0 - - + -
538A ILE* 4.2 5.8 - - + -
539A LEU* 3.8 22.9 - - + -
542A THR* 4.6 1.6 - - + -
536B HIS* 3.6 31.2 - - + +
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Residues in contact with GLU 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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121A ILE* 3.4 37.8 - - + +
124A ARG* 5.9 0.3 + - - -
177A ALA 3.6 7.9 + - - +
178A VAL 3.5 9.2 - - - +
179A GLU 3.2 0.2 - - - -
180A LEU* 1.3 77.1 - - - +
182A GLY* 1.3 57.6 + - - +
184A GLN* 3.0 31.4 + - - +
195A THR 5.0 2.6 - - - +
196A VAL* 5.8 0.7 - - - -
197A TYR* 3.8 33.5 + - - +
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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