Contacts of the helix formed by residues 149 - 163 (chain T) in PDB entry 3EXG
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 149 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5T VAL* 4.1 3.8 - - - -
148T TRP* 1.3 109.7 - - + +
150T SER* 1.3 66.9 + - - +
151T GLU* 3.3 14.8 + - - +
152T ASP* 3.0 24.5 + - - +
153T ALA* 3.0 20.8 + - - +
180T PHE* 3.5 37.8 - - + -
199T LYS* 5.2 4.3 - - - +
201T GLU* 3.9 8.7 + - - -
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Residues in contact with SER 150 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3T VAL* 2.7 31.2 + - - -
4T THR 3.4 12.0 - - - -
5T VAL* 3.4 8.2 + - - +
8T ALA* 3.4 14.8 - - - +
149T ASN* 1.3 74.9 - - - +
151T GLU* 1.3 67.3 + - - +
153T ALA* 3.0 1.3 + - - -
154T LYS* 2.9 20.8 + - - +
180T PHE* 3.6 19.2 - - - -
182T PHE* 3.7 23.1 - - - -
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Residues in contact with GLU 151 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149T ASN* 3.4 12.6 + - - +
150T SER* 1.3 81.5 - - - +
152T ASP* 1.3 64.0 + - - +
154T LYS 3.4 0.3 + - - -
155T GLY 3.2 15.8 + - - -
180T PHE* 5.6 0.4 - - - +
181T GLU 4.5 3.8 - - - +
182T PHE* 3.9 10.8 - - + -
183T PRO* 3.3 30.9 - - + +
186T ALA* 4.2 10.8 - - + -
191T PHE* 3.4 32.5 - - + -
193T ILE* 3.4 5.2 - - + +
199T LYS* 4.3 21.4 + - - -
239T ARG* 5.0 5.1 + - - +
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Residues in contact with ASP 152 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147T PRO* 3.8 0.2 - - + -
148T TRP* 2.8 29.4 + - - +
149T ASN* 3.0 29.9 + - - +
151T GLU* 1.3 74.5 - - - +
153T ALA* 1.3 68.2 + - - +
154T LYS 3.1 0.3 + - - -
156T LEU* 2.9 37.9 + - + +
193T ILE* 3.7 7.4 - - - -
199T LYS* 4.6 4.5 - - - +
201T GLU* 4.7 0.2 - - - +
237T ASN* 3.1 20.6 + - - +
239T ARG* 3.0 34.4 + - - -
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Residues in contact with ALA 153 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5T VAL* 3.7 22.4 - - + -
8T ALA* 4.4 2.0 - - + -
9T ILE* 3.6 29.3 - - + +
147T PRO* 3.7 19.7 - - + -
149T ASN 3.0 5.1 + - - +
150T SER 3.6 6.1 - - - +
152T ASP* 1.3 80.9 - - - +
154T LYS* 1.3 62.4 + - - +
156T LEU* 4.8 0.9 - - - -
157T ILE* 3.2 25.8 + - - +
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Residues in contact with LYS 154 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8T ALA* 3.9 26.2 - - + +
11T GLN* 2.8 32.7 + - - +
12T GLY 4.2 2.0 - - - +
15T GLU* 3.0 29.2 + - - -
150T SER 2.9 15.0 + - - +
151T GLU 4.1 2.5 - - - +
152T ASP 3.1 0.2 + - - -
153T ALA* 1.3 75.7 - - - +
155T GLY* 1.3 60.5 + - - +
157T ILE* 3.0 25.0 - - - +
158T LYS* 3.2 21.9 - - + +
182T PHE* 3.6 11.7 - - + -
186T ALA 3.1 19.4 + - - +
187T GLN 3.4 2.0 + - - -
188T SER 2.8 27.8 + - - -
191T PHE* 4.1 5.6 - - + -
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Residues in contact with GLY 155 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151T GLU 3.2 7.7 + - - -
152T ASP 3.8 1.1 - - - -
154T LYS* 1.3 75.5 - - - +
156T LEU* 1.3 64.6 + - - +
158T LYS* 3.0 2.9 + - - +
159T SER* 2.9 26.5 + - - -
191T PHE* 3.8 21.0 - - - -
193T ILE* 3.6 25.6 + - - -
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Residues in contact with LEU 156 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145T VAL* 3.8 37.8 - - + +
147T PRO* 3.8 28.9 - - + -
152T ASP* 2.9 36.8 + - + +
153T ALA* 4.5 2.0 - - - +
155T GLY* 1.3 70.2 - - - -
157T ILE* 1.3 62.7 + - - +
159T SER* 3.2 2.7 + - - -
160T ALA* 3.0 24.9 + - - +
169T VAL* 5.5 2.7 - - + -
193T ILE* 4.0 28.9 - - + +
194T PRO 5.1 1.6 - - - +
195T ILE* 5.0 6.9 - - + +
239T ARG* 4.2 21.1 - - + +
240T THR* 4.5 6.1 - - - +
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Residues in contact with ILE 157 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9T ILE* 4.3 12.3 - - + +
12T GLY* 3.8 24.2 - - - -
13T MET* 4.3 17.3 - - + +
77T ILE* 5.4 1.3 - - + -
113T VAL* 4.9 7.6 - - + -
115T ARG* 3.8 32.5 - - + -
153T ALA 3.2 16.0 + - - +
154T LYS* 3.0 18.4 - - - +
156T LEU* 1.3 78.3 - - - +
158T LYS* 1.3 67.4 + - - +
160T ALA* 3.4 3.3 + - - +
161T ILE* 3.2 29.8 + - + +
169T VAL* 4.7 16.9 - - + +
171T GLU* 4.2 9.6 - - - +
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Residues in contact with LYS 158 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12T GLY* 3.7 16.6 - - - -
15T GLU* 3.5 17.3 + - - +
16T GLU* 2.8 40.4 + - + +
154T LYS* 3.2 39.5 - - + +
155T GLY 3.0 5.2 + - - +
156T LEU 3.0 1.0 - - - -
157T ILE* 1.3 77.5 - - + +
159T SER* 1.3 66.6 + - - +
160T ALA 3.0 1.8 - - - -
161T ILE* 3.4 3.6 + - - +
162T ARG* 3.2 28.2 + - - +
189T LYS 3.4 18.6 + - - -
191T PHE* 2.8 35.7 - - - +
192T LEU* 3.7 13.9 - - + -
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Residues in contact with SER 159 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155T GLY 2.9 11.9 + - - -
156T LEU 4.1 2.9 - - - -
158T LYS* 1.3 78.3 - - - +
160T ALA* 1.3 53.0 + - - +
162T ARG* 3.5 5.4 - - - +
163T ASP* 2.6 36.6 + - - +
192T LEU* 3.7 14.8 - - - +
193T ILE 3.1 35.9 + - - -
194T PRO* 4.8 1.2 - - - +
195T ILE* 4.5 15.7 - - - -
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Residues in contact with ALA 160 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113T VAL* 3.5 19.3 - - + +
145T VAL* 5.9 0.2 - - + -
156T LEU 3.0 16.9 + - - +
157T ILE* 3.5 7.0 - - - +
158T LYS 3.0 0.2 - - - -
159T SER* 1.3 76.3 - - - +
161T ILE* 1.3 67.0 + - - +
162T ARG 3.3 0.3 + - - -
163T ASP* 3.3 11.7 + - - +
167T VAL* 3.6 36.5 - - + +
169T VAL* 4.1 7.6 - - + -
195T ILE* 4.7 2.9 - - + +
1006T K 3.0 13.3 - - - -
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Residues in contact with ILE 161 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12T GLY 4.9 0.2 - - - +
13T MET* 4.5 6.7 - - - -
16T GLU* 3.7 38.4 - - + +
19T ARG* 6.1 0.4 - - - +
23T VAL* 3.8 29.4 - - + -
75T ARG* 3.5 15.5 + - + +
77T ILE* 3.5 30.7 - - + -
113T VAL* 3.8 15.7 - - + -
157T ILE* 3.2 27.0 + - + +
158T LYS 3.8 6.7 - - - +
160T ALA* 1.3 76.0 - - - +
162T ARG* 1.3 60.3 + - + +
163T ASP 3.4 0.5 - - - +
1006T K 2.8 18.0 - - - -
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Residues in contact with ARG 162 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16T GLU* 2.5 51.7 + - - +
19T ARG* 3.3 49.4 - - - +
75T ARG* 3.3 13.6 + - - +
158T LYS* 3.2 16.6 + - - +
159T SER* 3.8 6.3 - - - +
160T ALA 3.2 0.4 - - - -
161T ILE* 1.3 77.6 - - + +
163T ASP* 1.3 65.7 + - - +
164T ASN* 3.5 7.6 + - - -
189T LYS 4.8 4.0 + - - -
190T ASP* 5.0 10.9 + - - +
192T LEU* 3.6 34.3 - - + +
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Residues in contact with ASP 163 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343S ASP* 4.9 2.8 - - - +
75T ARG* 3.3 2.3 + - - -
143T LYS* 2.7 36.0 + - - +
159T SER 2.6 20.9 + - - +
160T ALA* 3.3 7.8 + - - +
162T ARG* 1.3 72.5 - - - +
164T ASN* 1.3 75.0 + - - +
165T ASN* 2.8 28.0 + - - +
167T VAL* 3.7 18.2 - - + -
195T ILE* 3.5 11.0 - - + +
1006T K 2.7 27.2 - - - -
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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