Contacts of the helix formed by residues 156 - 174 (chain A) in PDB entry 3L6B
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 GLU 156 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ALA* 4.9 1.6 - - + -
150A MET 4.7 9.4 - - - +
151A VAL* 4.7 7.0 - - + -
152A HIS* 3.7 34.5 + - + +
154A ASN 3.6 0.8 - - - -
155A GLN* 1.3 75.3 - - - +
157A PRO* 1.4 87.3 - - - +
158A ALA* 3.6 20.1 + - + +
159A VAL* 2.9 27.1 + - + +
160A ILE* 2.9 13.4 + - - +
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Residues in contact with PRO 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ASP* 3.8 33.7 - - + +
7A ILE* 3.4 17.5 - - + +
155A GLN 3.4 8.9 - - - +
156A GLU* 1.4 97.2 - - - +
158A ALA* 1.3 56.0 + - - +
160A ILE* 3.2 5.9 + - + -
161A ALA* 2.9 28.3 + - - +
247A ASN* 4.7 4.5 - - - +
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Residues in contact with ALA 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A GLY 4.4 1.3 - - - -
62A ASN* 2.9 35.3 + - - +
63A ALA* 3.7 25.6 - - + -
66A SER* 4.0 15.5 - - - +
156A GLU* 3.2 13.3 + - + +
157A PRO* 1.3 78.6 - - - +
159A VAL* 1.3 61.8 + - - +
161A ALA* 4.6 1.1 - - - -
162A GLY* 3.1 9.2 + - - -
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Residues in contact with VAL 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A GLY* 3.5 23.6 - - - +
63A ALA* 3.9 2.9 - - + -
87A HIS* 4.2 7.0 - - + -
151A VAL* 3.8 22.0 - - + -
152A HIS 3.4 18.2 - - - +
153A PRO 3.5 21.8 - - - +
154A ASN* 4.5 3.4 - - - +
156A GLU* 2.9 14.6 + - + +
158A ALA* 1.3 74.7 - - - +
160A ILE* 1.3 65.1 - - - +
162A GLY 3.1 2.6 + - - -
163A GLN* 2.9 51.2 + - + +
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Residues in contact with ILE 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ASP* 5.5 3.1 - - + -
7A ILE* 3.7 23.3 - - + -
154A ASN 3.3 28.5 - - - +
155A GLN* 3.8 18.4 - - - +
156A GLU 2.9 14.1 + - - +
157A PRO* 3.7 9.6 - - + +
159A VAL* 1.3 76.6 - - - +
161A ALA* 1.3 62.2 + - - +
163A GLN* 3.2 5.0 + - - +
164A GLY 3.1 17.5 + - - -
188A GLY* 3.6 13.5 - - - +
191A ALA* 4.2 7.4 - - + -
192A GLY* 3.6 28.0 - - - +
247A ASN* 4.5 10.8 - - + +
248A THR* 3.8 13.5 - - + -
251A ILE* 5.1 3.6 - - + -
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Residues in contact with ALA 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ILE* 4.1 6.2 - - + +
11A ASP* 3.8 38.6 - - + +
12A VAL* 3.7 16.4 - - + +
15A ALA* 3.9 3.4 - - - +
62A ASN* 4.2 7.4 - - - +
157A PRO 2.9 17.6 + - - +
158A ALA* 4.0 4.7 - - - +
160A ILE* 1.3 75.0 - - - +
162A GLY* 1.3 63.5 + - - +
164A GLY 3.3 8.3 + - - -
165A THR* 3.6 13.3 + - - +
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Residues in contact with GLY 162 (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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15A ALA* 4.1 12.1 - - - -
19A ILE* 4.7 1.1 - - - -
58A ARG* 3.3 28.9 - - - +
59A GLY* 4.0 0.2 - - - -
62A ASN* 4.0 2.2 - - - +
158A ALA 3.1 12.8 + - - -
159A VAL 3.1 7.4 + - - -
161A ALA* 1.3 76.8 - - - +
163A GLN* 1.3 58.6 + - - +
165A THR* 2.7 29.1 + - - -
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Residues in contact with GLN 163 (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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55A PHE* 3.4 40.2 - - + +
56A LYS* 3.7 19.4 + - - +
58A ARG* 4.5 4.0 - - - +
59A GLY* 2.9 27.2 + - - -
87A HIS* 5.2 0.6 + - - -
153A PRO 4.2 2.8 + - - -
159A VAL* 2.9 45.0 + - + +
160A ILE* 3.2 3.5 + - - +
162A GLY* 1.3 74.5 - - - +
164A GLY* 1.3 62.3 + - - +
165A THR 3.1 1.4 + - - -
166A ILE* 3.2 26.0 + - - +
188A GLY* 4.1 4.7 - - - -
189A MET* 3.6 32.1 - - + +
192A GLY* 5.0 0.2 - - - -
193A ILE* 4.3 3.9 - - - +
350A PLP 5.3 1.4 + - - -
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Residues in contact with GLY 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A VAL* 3.5 10.3 - - - +
160A ILE 3.1 10.1 + - - -
161A ALA 3.3 5.8 + - - -
162A GLY 3.2 1.0 - - - -
163A GLN* 1.3 78.0 - - - +
165A THR* 1.3 55.1 + - - +
166A ILE 3.0 1.1 - - - -
167A ALA* 3.0 29.2 + - - +
168A LEU 3.8 1.2 + - - -
192A GLY* 3.4 31.8 - - - -
193A ILE* 3.7 1.6 - - - -
196A THR* 3.6 5.5 + - - -
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Residues in contact with THR 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A VAL* 3.5 29.8 - - + +
15A ALA* 4.0 4.7 - - + -
16A HIS* 3.5 34.9 + - + +
19A ILE* 3.7 7.1 - - + +
58A ARG* 2.9 20.5 + - - -
161A ALA 3.6 8.7 - - - +
162A GLY 2.7 21.9 + - - +
164A GLY* 1.3 73.5 - - - +
166A ILE* 1.3 66.0 + - - +
168A LEU* 3.1 16.5 + - - +
169A GLU* 3.3 14.9 + - - +
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Residues in contact with ILE 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LYS* 4.1 24.6 - - + -
47A GLU* 4.3 6.5 - - + -
55A PHE* 3.8 22.0 - - + -
58A ARG* 3.5 27.8 - - - +
163A GLN 3.2 17.2 + - - +
165A THR* 1.3 78.7 + - - +
167A ALA* 1.3 58.2 + - - +
169A GLU* 3.2 6.1 + - - +
170A VAL* 2.9 30.9 + - + +
180A LEU* 5.5 0.2 - - + -
189A MET* 3.7 34.1 - - + -
193A ILE* 4.2 13.7 - - + -
311A VAL* 4.2 10.3 - - + -
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Residues in contact with ALA 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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164A GLY 3.0 12.4 + - - +
166A ILE* 1.3 76.7 - - - +
168A LEU* 1.3 66.4 + - - +
170A VAL* 4.3 7.0 - - - +
171A LEU* 2.9 30.4 + - - +
180A LEU* 4.3 4.7 - - + -
193A ILE* 4.1 15.4 - - + +
196A THR* 3.7 22.0 - - + -
197A VAL* 3.9 22.7 - - + -
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Residues in contact with LEU 168 (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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9A PHE* 3.6 31.9 - - + -
12A VAL* 3.9 23.3 - - + +
13A GLU* 4.1 11.0 - - + -
16A HIS* 3.6 42.6 - - + +
165A THR* 3.1 9.2 + - - +
167A ALA* 1.3 78.1 - - - +
169A GLU* 1.3 61.5 + - - +
171A LEU* 4.2 5.1 - - - +
172A ASN* 3.4 20.6 + - - +
196A THR* 3.7 13.7 - - + -
200A LEU* 3.7 12.1 - - + -
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Residues in contact with GLU 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A HIS* 2.9 30.1 + - + +
23A ILE* 3.8 7.4 - - - +
24A HIS 4.7 0.3 - - - +
25A LEU* 3.5 28.4 - - + +
45A LYS* 2.8 36.7 + - - +
58A ARG* 2.8 40.1 + - - -
165A THR 3.3 2.0 + - - +
166A ILE 3.2 6.0 + - - +
167A ALA 3.2 0.2 - - - -
168A LEU* 1.3 75.2 - - - +
170A VAL* 1.3 60.1 + - - +
172A ASN* 3.1 7.2 + - - +
173A GLN* 2.8 37.5 + - - +
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Residues in contact with VAL 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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28A VAL* 5.3 1.1 - - + -
45A LYS* 3.8 30.7 - - + -
166A ILE* 2.9 26.8 + - + +
167A ALA 3.3 3.5 + - - +
169A GLU* 1.3 76.2 - - - +
171A LEU* 1.3 58.7 + - - +
173A GLN* 4.2 5.4 - - - -
174A VAL* 2.8 35.7 + - + +
177A VAL* 4.6 5.2 - - + -
180A LEU* 4.0 28.0 - - + -
309A CYS* 3.7 36.8 - - + -
311A VAL* 5.5 0.7 - - + -
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Residues in contact with LEU 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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167A ALA* 2.9 24.3 + - + +
168A LEU* 4.2 4.0 - - - +
170A VAL* 1.3 77.2 - - + +
172A ASN* 1.3 59.7 + - - +
174A VAL 4.3 2.9 - - - -
175A PRO* 3.5 22.8 - - - +
177A VAL* 3.6 24.0 - - + -
180A LEU* 5.0 4.3 - - + -
196A THR* 4.8 0.7 - - + +
197A VAL* 4.4 22.2 - - + +
200A LEU* 3.8 37.9 - - + -
201A LYS* 5.0 10.3 - - + +
204A VAL* 4.4 20.2 - - + -
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Residues in contact with ASN 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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25A LEU* 5.9 5.7 - - - +
168A LEU 3.4 12.1 + - - +
169A GLU* 3.1 10.1 + - - +
171A LEU* 1.3 80.1 - - - +
173A GLN* 1.3 71.9 + - - +
174A VAL 3.6 0.3 + - - -
175A PRO* 3.9 11.5 - - - +
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Residues in contact with GLN 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 3.7 22.3 - - + +
26A THR 3.0 23.8 + - - -
27A PRO* 4.2 5.1 - - - +
28A VAL* 3.6 27.3 - - + +
45A LYS* 2.8 26.9 + - - +
169A GLU* 2.8 25.1 + - - +
170A VAL* 3.9 2.4 + - - +
172A ASN* 1.3 82.9 - - - +
174A VAL* 1.3 62.0 + - - +
175A PRO* 3.5 7.1 - - - +
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Residues in contact with VAL 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A VAL* 3.9 33.7 - - + -
43A PHE* 3.9 42.8 - - + -
170A VAL* 2.8 24.6 + - + +
171A LEU 3.8 1.3 - - - +
173A GLN* 1.3 82.4 - - - +
175A PRO* 1.3 67.2 - - + +
176A LEU* 3.1 3.4 - - + +
177A VAL* 2.9 45.0 + - + +
307A ASN* 5.1 0.2 - - + -
309A CYS* 4.8 1.8 - - - -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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