Contacts of the helix formed by residues 147 - 165 (chain A) in PDB entry 5GQQ
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 SER 147 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A TRP* 3.8 2.2 - - - -
59A ASP* 3.2 18.6 - - - -
145A PHE 3.9 1.7 + - - -
146A SER* 1.3 77.2 - - - +
148A ALA* 1.3 60.4 + - - +
149A GLN* 3.5 7.0 + - - +
150A LYS* 3.0 26.1 + - - +
151A ASN* 2.8 36.6 + - - -
38D ASP* 6.1 0.7 - - - -
40D SER* 5.8 0.3 - - - -
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Residues in contact with ALA 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ASP* 6.0 0.2 - - - +
58A TRP* 3.8 29.5 - - + +
59A ASP* 3.1 21.4 + - - +
147A SER* 1.3 73.7 - - - +
149A GLN* 1.3 64.6 + - - +
151A ASN* 3.7 6.1 - - - +
152A GLN* 3.0 24.8 + - - +
174A TYR* 5.7 0.5 + - - -
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Residues in contact with GLN 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A SER* 3.3 6.6 + - - +
148A ALA* 1.3 78.3 - - - +
150A LYS* 1.3 63.9 + - - +
152A GLN* 3.2 28.9 + - - +
153A GLU* 3.1 46.0 + - - +
50C GLN* 3.7 25.0 - - - +
38D ASP* 3.6 24.5 - - - +
40D SER* 5.6 0.4 - - - -
44D SER* 4.9 6.5 - - - -
204D CL 3.8 9.2 - - + +
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Residues in contact with LYS 150 (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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142A PHE* 3.9 28.7 - - + -
143A ASP* 2.7 34.7 + - - +
144A GLY* 4.9 1.0 - - - -
145A PHE 3.7 15.9 + - - +
147A SER* 3.0 22.7 + - - +
149A GLN* 1.3 77.4 - - - +
151A ASN* 1.3 65.1 + - - +
153A GLU* 3.3 10.4 + - - +
154A GLN* 3.0 32.0 + - + +
39D ARG 4.1 7.4 + - - +
40D SER* 3.3 42.6 + - - +
41D GLY* 5.4 0.4 - - - -
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Residues in contact with ASN 151 (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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58A TRP* 3.5 30.5 - - - +
142A PHE* 3.6 22.4 - - - -
146A SER* 4.0 4.0 + - - -
147A SER 2.8 32.8 + - - +
148A ALA* 3.7 5.5 - - - +
150A LYS* 1.3 72.4 - - - +
152A GLN* 1.3 58.5 + - - +
154A GLN* 3.8 1.2 - - - -
155A LEU* 2.8 33.2 + - - +
174A TYR* 4.8 10.9 + - + +
176A THR* 3.4 30.0 - - + +
191A GLU 5.2 0.2 - - - +
192A VAL* 3.8 17.2 - - + +
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Residues in contact with GLN 152 (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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148A ALA 3.0 18.2 + - - +
149A GLN* 3.4 27.8 + - - +
150A LYS 3.2 0.2 - - - -
151A ASN* 1.3 77.8 - - - +
153A GLU* 1.3 60.3 + - - +
155A LEU* 3.5 7.6 - - - +
156A LEU* 3.0 43.4 + - + +
174A TYR* 5.8 2.7 - - - +
49C GLN* 6.3 0.2 - - - -
57C TRP 4.7 6.1 - - - +
59C PRO* 3.8 36.9 - - + +
77D LYS 5.7 0.4 + - - -
78D ALA* 5.6 4.9 - - - +
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Residues in contact with GLU 153 (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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149A GLN* 3.1 30.9 + - - +
150A LYS* 3.3 5.0 + - - +
152A GLN* 1.3 77.8 - - + +
154A GLN* 1.3 57.3 + - - +
156A LEU* 3.5 2.7 + - - +
157A THR* 2.7 36.7 + - - -
40D SER* 2.6 34.4 + - - +
42D VAL* 3.4 37.6 - - + +
44D SER* 4.2 6.9 - - - -
77D LYS* 3.6 22.7 - - + +
78D ALA 5.6 1.0 - - - +
204D CL 3.0 24.3 - - - +
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Residues in contact with GLN 154 (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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140A ARG* 2.6 49.6 + - - +
142A PHE* 3.8 43.8 - - + +
150A LYS* 3.0 23.9 + - + +
151A ASN 4.1 2.0 - - - +
153A GLU* 1.3 77.8 + - - +
155A LEU* 1.3 58.6 + - - +
157A THR* 3.2 5.2 + - - +
158A LEU* 2.8 26.5 + - - +
192A VAL* 4.0 8.3 - - + -
40D SER 4.6 8.9 + - - -
42D VAL* 4.1 23.6 - - - +
77D LYS* 5.7 0.2 - - - +
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Residues in contact with LEU 155 (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 ASN 2.8 23.9 + - - +
152A GLN* 3.5 8.3 - - + +
154A GLN* 1.3 72.4 - - - +
156A LEU* 1.3 59.4 + - + +
158A LEU* 3.1 5.7 + - + +
159A ALA* 2.8 29.6 + - - +
174A TYR* 3.6 46.2 - - + -
192A VAL* 3.8 22.8 - - + +
193A TRP 4.4 2.7 - - - +
194A LEU* 3.6 32.7 - - + +
57C TRP* 3.6 34.9 - - + +
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Residues in contact with LEU 156 (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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152A GLN* 3.0 30.8 + - + +
153A GLU 3.8 3.4 - - - +
155A LEU* 1.3 81.4 - - + +
157A THR* 1.3 61.6 + - - +
159A ALA* 3.4 5.3 + - + +
160A SER* 3.1 18.4 + - - -
163A ARG* 5.1 2.0 + - - +
57C TRP* 3.9 25.6 - - + +
58C THR* 4.5 8.3 - - + +
59C PRO* 4.1 35.4 - - + -
75D GLU 3.6 10.3 - - - +
76D ASN* 3.8 16.5 - - - +
77D LYS* 3.7 30.1 - - - +
78D ALA* 4.6 2.9 - - + +
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Residues in contact with THR 157 (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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140A ARG* 3.6 33.0 - - - +
153A GLU 2.7 22.2 + - - -
154A GLN* 3.5 10.6 + - - -
155A LEU 3.1 0.2 - - - -
156A LEU* 1.3 74.5 - - - +
158A LEU* 1.3 65.3 + - - +
160A SER* 3.1 18.6 + - - -
161A ILE* 3.4 15.7 + - + +
75D GLU* 3.5 29.8 - - + +
77D LYS* 3.4 20.6 - - - +
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Residues in contact with LEU 158 (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 SER 5.1 0.9 - - - +
38A TYR* 3.7 29.4 - - + -
138A PHE* 3.4 28.5 - - + +
140A ARG* 3.5 25.9 - - + +
154A GLN 2.8 13.7 + - - +
155A LEU* 3.2 10.1 - - + +
157A THR* 1.3 75.3 - - - +
159A ALA* 1.3 63.1 + - - +
161A ILE* 3.1 10.1 + - + +
162A LEU* 2.9 43.5 + - + +
192A VAL* 4.2 8.7 - - + +
193A TRP 4.8 0.4 - - - -
194A LEU* 3.6 25.6 - - + +
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Residues in contact with ALA 159 (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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155A LEU 2.8 15.9 + - - +
156A LEU* 3.6 7.2 - - + +
157A THR 3.2 0.2 - - - -
158A LEU* 1.3 78.8 - - - +
160A SER* 1.3 61.8 + - - +
162A LEU* 3.3 3.8 + - - +
163A ARG* 3.0 42.5 + - - +
169A PHE* 4.0 8.4 - - + -
194A LEU* 4.1 9.0 - - + -
57C TRP* 3.6 31.4 - - + -
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Residues in contact with SER 160 (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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156A LEU 3.1 6.0 + - - -
157A THR 3.1 10.6 + - - -
159A ALA* 1.3 75.7 - - - +
161A ILE* 1.3 66.0 + - - +
163A ARG* 3.4 14.3 + - - +
164A GLU* 3.2 25.1 + - - +
74D ARG 5.3 0.9 - - - -
75D GLU* 3.1 45.4 + - - +
76D ASN* 4.7 9.0 - - - -
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Residues in contact with ILE 161 (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 SER* 4.1 22.7 - - - +
38A TYR* 3.8 29.2 - - + -
140A ARG* 3.8 24.2 - - - +
157A THR* 3.4 22.2 - - + +
158A LEU* 3.1 9.1 + - + +
160A SER* 1.3 79.7 + - - +
162A LEU* 1.3 63.9 + - - +
164A GLU* 3.5 9.0 + - - +
165A ASP* 3.1 27.5 + - - +
75D GLU* 5.7 4.0 - - + +
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Residues in contact with LEU 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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38A TYR* 3.5 42.2 - - + -
138A PHE* 3.8 29.8 - - + -
158A LEU* 2.9 28.9 + - + +
159A ALA 3.7 5.6 - - - +
160A SER 3.3 0.2 - - - -
161A ILE* 1.3 76.2 - - - +
163A ARG* 1.3 61.7 + - - +
165A ASP* 3.2 3.3 + - - -
166A GLY 3.0 4.3 + - - -
167A LYS* 2.8 37.9 + - + +
169A PHE* 3.7 17.5 - - + -
194A LEU* 3.6 31.4 - - + -
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Residues in contact with ARG 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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156A LEU* 5.1 2.2 + - - +
159A ALA* 3.0 34.6 + - - +
160A SER* 3.8 12.1 - - - +
161A ILE 3.3 0.2 - - - -
162A LEU* 1.3 75.5 - - - +
164A GLU* 1.3 59.2 + - - +
166A GLY* 2.9 18.8 + - - +
167A LYS 4.7 5.4 - - - +
169A PHE* 3.9 19.4 - - + -
171A GLU* 3.5 28.1 + - - -
57C TRP* 4.0 16.6 - - - -
58C THR* 4.9 4.6 + - - -
140C ARG 5.2 3.6 + - - -
141C GLN* 3.5 26.1 + - - +
142C GLY* 5.5 3.4 - - - +
143C ARG* 4.5 6.3 - - - +
76D ASN* 5.5 6.9 - - - +
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Residues in contact with GLU 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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160A SER 3.2 15.8 + - - +
161A ILE* 3.9 6.9 - - - +
163A ARG* 1.3 79.0 - - - +
165A ASP* 1.3 66.0 + - - +
166A GLY 3.2 1.3 + - - -
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Residues in contact with ASP 165 (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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34A GLN* 4.9 4.7 + - - -
37A SER* 5.1 0.5 + - - -
38A TYR* 3.3 39.1 + - - +
161A ILE* 3.1 22.9 + - - +
162A LEU 3.7 4.0 - - - +
163A ARG 3.2 0.4 - - - -
164A GLU* 1.3 84.2 - - - +
166A GLY* 1.3 61.6 + - - +
167A LYS* 3.2 13.1 + - + +
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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
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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