Contacts of the helix formed by residues 148 - 166 (chain I) in PDB entry 3MQT
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 THR 148 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146I ASP 4.7 4.7 - - - +
147I ALA* 1.3 76.4 - - - +
149I LEU* 1.3 60.0 + - - +
150I SER* 3.6 9.9 + - - -
151I GLU* 3.1 37.4 + - - +
152I ILE* 2.8 32.3 + - - +
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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
----------------------------------------------------------
148I THR* 1.3 72.2 - - - +
150I SER* 1.3 57.5 + - - +
152I ILE* 3.2 15.3 + - + +
153I VAL* 2.8 34.9 + - - +
175I ILE* 5.9 2.0 - - + -
176I ILE 5.9 2.0 - - - +
178I ASN* 5.1 9.5 + - + +
181I VAL* 3.6 35.9 - - + -
185I GLU* 3.7 32.3 - - + +
186I ILE* 4.5 9.2 - - + -
189I TYR* 3.8 38.6 - - + -
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Residues in contact with SER 150 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148I THR* 3.2 9.9 + - - -
149I LEU* 1.3 77.9 - - - +
151I GLU* 1.3 58.6 + - - +
153I VAL* 3.2 10.3 + - - +
154I GLU* 3.0 34.8 + - - +
192I GLU* 5.5 3.6 - - - -
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Residues in contact with GLU 151 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143I VAL* 4.5 4.2 - - + +
144I ALA* 6.1 0.2 - - - +
146I ASP 4.5 1.9 - - - +
147I ALA* 3.5 15.0 - - + +
148I THR* 3.1 39.6 + - - +
150I SER* 1.3 78.3 - - - +
152I ILE* 1.3 60.8 + - - +
154I GLU* 3.5 9.9 + - - +
155I ALA* 3.2 21.5 + - - +
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Residues in contact with ILE 152 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141I PRO* 4.3 8.5 - - + -
143I VAL* 4.3 16.8 - - + -
147I ALA* 3.9 24.7 - - + +
148I THR 2.8 24.7 + - - +
149I LEU* 3.5 17.0 - - + +
151I GLU* 1.3 74.9 - - - +
153I VAL* 1.3 66.3 + - - +
155I ALA* 3.1 4.3 + - - +
156I TYR* 2.9 35.1 + - + -
176I ILE* 4.0 30.3 - - + -
178I ASN* 5.7 2.9 - - - +
189I TYR* 3.5 26.9 - - + +
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Residues in contact with VAL 153 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149I LEU 2.8 18.5 + - - +
150I SER* 3.2 9.4 + - - +
152I ILE* 1.3 76.3 - - - +
154I GLU* 1.3 63.9 + - - +
156I TYR* 3.1 17.6 + - - +
157I LYS* 3.2 25.5 + - + +
189I TYR* 3.7 26.7 - - + +
192I GLU* 3.2 39.9 - - + +
193I LEU* 4.1 18.6 - - + +
196I VAL* 4.7 7.9 - - + -
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Residues in contact with GLU 154 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150I SER* 3.0 22.5 + - - +
151I GLU* 3.7 11.2 - - - +
152I ILE 3.3 0.2 - - - -
153I VAL* 1.3 79.5 - - - +
155I ALA* 1.3 59.7 + - - +
157I LYS* 2.6 51.6 + - - +
158I PRO* 3.3 11.6 - - - +
192I GLU* 5.1 1.4 - - - +
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Residues in contact with ALA 155 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141I PRO* 3.7 13.2 - - + +
142I SER 4.3 5.6 - - - +
143I VAL* 3.7 30.3 - - + -
151I GLU 3.2 7.8 + - - +
152I ILE 3.1 6.5 + - - +
154I GLU* 1.3 75.3 - - - +
156I TYR* 1.3 62.0 + - - +
158I PRO* 3.2 18.8 - - - +
159I LEU* 4.1 12.0 + - - +
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Residues in contact with TYR 156 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139I LEU* 2.8 49.3 + - + -
141I PRO* 3.3 28.2 - - + +
152I ILE* 2.9 26.2 + - + -
153I VAL 3.1 9.1 + - - +
155I ALA* 1.3 77.7 - - - +
157I LYS* 1.3 64.7 + - - +
159I LEU* 3.2 9.7 + - + +
160I ILE* 2.8 38.7 + - + +
173I VAL* 3.8 20.2 - - + -
174I CYS* 2.9 23.0 + - - +
176I ILE* 5.6 0.8 - - + +
189I TYR* 3.5 22.2 - - - -
193I LEU* 4.1 19.7 - - + -
196I VAL* 6.0 0.4 - - + -
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Residues in contact with LYS 157 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153I VAL* 3.2 24.4 + - - +
154I GLU* 2.6 41.6 + - - +
155I ALA 3.2 0.2 - - - -
156I TYR* 1.3 75.8 - - - +
158I PRO* 1.3 67.8 - - + +
160I ILE* 3.3 2.6 + - - +
161I ALA* 2.9 29.2 + - - +
192I GLU* 4.6 5.5 + - - -
196I VAL* 4.4 32.5 - - + +
200Q ASP* 4.0 28.8 + - - -
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Residues in contact with PRO 158 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154I GLU 3.3 8.7 - - - +
155I ALA* 3.2 18.8 - - - +
157I LYS* 1.3 97.7 - - + +
159I LEU* 1.3 56.5 + - + +
161I ALA* 3.4 6.8 + - + +
162I LYS* 3.0 28.2 + - - +
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Residues in contact with LEU 159 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139I LEU* 4.1 15.0 - - + +
140I TYR 3.7 31.6 - - - +
141I PRO* 3.7 21.1 - - + -
155I ALA 4.2 7.9 - - - +
156I TYR* 3.2 14.5 + - + +
158I PRO* 1.3 77.0 - - + +
160I ILE* 1.3 66.7 + - - +
162I LYS* 3.2 6.8 + - + +
163I ALA* 3.0 22.0 + - - +
339I ASP 4.6 2.7 - - - +
340I PHE* 3.5 45.8 - - + +
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Residues in contact with ILE 160 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139I LEU* 3.7 22.0 - - + -
156I TYR* 2.8 39.4 + - + +
157I LYS 3.8 3.1 - - - +
159I LEU* 1.3 77.5 - - - +
161I ALA* 1.3 60.9 + - - +
163I ALA* 3.3 4.9 + - - +
164I LYS* 3.1 32.0 + - - +
171I VAL* 5.2 0.7 - - + -
173I VAL* 4.8 2.0 - - + -
193I LEU* 4.5 7.6 - - + -
196I VAL* 3.8 41.7 - - + +
197I ILE* 3.8 34.3 - - + -
201I MET* 4.5 4.3 - - + -
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Residues in contact with ALA 161 (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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157I LYS 2.9 17.2 + - - +
158I PRO* 3.8 8.3 - - + +
160I ILE* 1.3 76.1 - - - +
162I LYS* 1.3 60.8 + - - +
164I LYS* 3.4 11.2 + - + +
165I GLU* 2.9 29.0 + - - +
161Q ALA* 5.9 6.7 - - + -
164Q LYS* 6.5 1.1 - - + -
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Residues in contact with LYS 162 (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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158I PRO 3.0 17.1 + - - +
159I LEU* 3.2 5.1 + - + +
161I ALA* 1.3 76.0 - - - +
163I ALA* 1.3 64.4 + - - +
165I GLU* 3.0 8.3 + - + +
166I ARG* 2.9 63.3 + - + +
339I ASP* 3.2 41.4 + - + +
340I PHE* 3.9 7.4 - - + -
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Residues in contact with ALA 163 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139I LEU* 4.6 2.5 - - + -
159I LEU 3.0 13.5 + - - +
160I ILE* 3.6 10.3 - - - +
161I ALA 3.3 0.2 - - - -
162I LYS* 1.3 75.8 - - - +
164I LYS* 1.3 59.9 + - - +
166I ARG* 3.3 3.2 + - - +
167I GLY 3.1 4.3 + - - -
168I ALA* 3.0 31.5 + - + +
171I VAL* 3.7 30.3 - - + -
201I MET* 4.3 4.3 - - + -
340I PHE* 3.5 23.4 - - + -
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Residues in contact with LYS 164 (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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160I ILE* 3.1 23.5 + - + +
161I ALA* 3.6 11.9 - - + +
163I ALA* 1.3 75.9 - - - +
165I GLU* 1.3 64.7 + - - +
167I GLY* 3.1 14.1 + - - +
168I ALA 4.9 0.7 - - - +
196I VAL 3.0 24.5 + - - -
197I ILE 3.0 26.3 + - - -
198I GLY* 4.5 2.4 - - - +
201I MET* 3.9 18.2 - - + -
161Q ALA* 6.3 2.5 - - + -
164Q LYS* 3.8 21.0 - - - +
195Q GLU 5.6 0.4 + - - -
196Q VAL* 4.4 5.9 + - - +
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Residues in contact with GLU 165 (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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161I ALA 2.9 17.9 + - - +
162I LYS* 3.0 9.8 + - - +
164I LYS* 1.3 76.8 - - - +
166I ARG* 1.3 92.3 + - - +
167I GLY 3.7 0.2 + - - -
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Residues in contact with ARG 166 (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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162I LYS* 2.9 54.0 + - + +
163I ALA* 3.8 5.4 - - - +
164I LYS 3.2 0.2 - - - -
165I GLU* 1.3 107.9 + - - +
167I GLY* 1.3 57.7 + - - +
168I ALA* 4.7 0.9 - - + +
339I ASP* 3.0 32.2 + - - +
340I PHE* 4.8 2.5 - - + -
355I LYS* 2.9 42.0 - - - +
356I ILE* 3.7 32.9 - - + +
358I ASP* 3.1 12.9 + - - -
359I GLY 3.0 18.5 + - - -
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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
------------------------------------------------------------
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