Contacts of the helix formed by residues 140 - 156 (chain K) 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 ALA 140 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135K ASN* 5.6 3.6 - - + -
137K ILE* 3.0 25.7 + - + +
138K VAL 3.3 1.8 - - - -
139K GLY* 1.3 77.6 - - - +
141K GLN* 1.3 62.6 + - - +
142K VAL 3.0 1.4 + - - -
143K PRO* 3.2 11.3 - - - +
144K LEU* 3.6 14.0 + - - +
174K GLN* 3.3 13.1 - - - +
91L ASP* 3.8 21.3 - - - +
92L GLN* 3.7 15.0 + - - +
96L SER* 4.5 7.6 - - - +
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Residues in contact with GLN 141 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86K ILE* 3.7 16.2 - - + +
87K THR* 3.7 11.4 - - - +
88K ALA* 3.4 28.4 - - - +
135K ASN* 3.6 31.0 - - - +
137K ILE 3.7 4.9 + - - +
139K GLY* 3.1 14.5 + - - +
140K ALA* 1.3 86.3 + - - +
142K VAL* 1.3 60.1 + - + +
143K PRO 3.5 0.2 - - - -
144K LEU* 3.6 5.2 - - - +
145K GLY 3.0 24.1 + - - -
163K THR* 3.6 6.8 - - + +
164K LEU 3.4 25.9 + - - +
165K TYR* 3.7 15.0 - - - +
166K GLY 5.2 0.4 - - - +
169K ALA* 5.3 0.8 - - - +
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Residues in contact with VAL 142 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139K GLY 3.1 6.7 + - - +
140K ALA 3.0 2.0 + - - -
141K GLN* 1.3 80.3 - - + +
143K PRO* 1.3 73.6 - - + +
145K GLY 3.4 0.2 + - - -
146K ALA* 3.1 19.6 + - - +
163K THR* 3.4 12.2 - - + +
164K LEU 4.9 0.2 - - - +
165K TYR* 3.5 35.2 - - + -
175K ILE* 3.6 31.6 - - + -
178K ALA* 3.8 13.2 - - + -
191K PHE* 3.7 27.8 - - + -
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Residues in contact with PRO 143 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139K GLY 3.4 9.2 - - - +
140K ALA 3.2 9.4 - - - +
142K VAL* 1.3 94.4 - - + +
144K LEU* 1.3 62.2 + - - +
146K ALA* 3.1 9.4 + - + +
147K GLY 2.9 17.5 + - - -
174K GLN* 3.3 40.6 - - + +
178K ALA* 4.4 5.6 - - + -
61L GLY* 3.6 28.3 - - - +
64L GLY* 3.4 17.5 - - - +
65L ILE* 3.5 5.2 - - + -
92L GLN* 4.1 2.2 - - - +
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Residues in contact with LEU 144 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86K ILE* 3.8 13.7 - - + -
135K ASN* 4.0 20.2 - - - +
140K ALA 3.6 13.2 - - - +
141K GLN* 3.4 9.6 + - - +
142K VAL 3.2 0.8 - - - -
143K PRO* 1.3 78.9 - - - +
145K GLY* 1.3 51.2 + - - +
147K GLY 2.9 2.8 + - - -
148K ILE* 2.8 34.7 + - + +
64L GLY* 3.4 19.5 + - - +
67L VAL* 3.8 22.0 - - + -
68L GLY* 3.2 12.8 - - - +
71L MET* 3.9 26.5 - - + -
92L GLN* 3.9 20.4 - - - +
96L SER* 3.9 13.5 - - - +
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Residues in contact with GLY 145 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86K ILE* 4.0 12.9 - - - +
141K GLN 3.0 14.3 + - - -
142K VAL 3.8 0.4 - - - -
144K LEU* 1.3 73.1 - - - +
146K ALA* 1.3 60.2 + - - +
147K GLY 3.0 1.3 - - - -
148K ILE* 3.2 5.1 + - - +
149K ALA* 2.8 27.8 + - - +
161K CYS* 3.6 8.0 - - - -
163K THR* 3.2 23.5 + - - -
189K CYS* 4.6 0.2 - - - -
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Residues in contact with ALA 146 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142K VAL 3.1 13.3 + - - +
143K PRO* 3.1 9.8 + - + +
145K GLY* 1.3 74.9 - - - +
147K GLY* 1.3 58.0 + - - +
149K ALA* 3.3 9.8 - - - +
150K LEU* 2.8 22.7 + - - +
163K THR* 3.9 1.4 + - - -
178K ALA* 4.5 11.2 - - + -
182K ALA* 4.7 2.9 - - + -
187K LEU* 3.7 18.3 - - + +
189K CYS* 4.2 5.8 - - - -
191K PHE* 4.5 11.9 - - + -
65L ILE* 4.0 19.0 - - + +
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Residues in contact with GLY 147 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143K PRO 2.9 7.3 + - - -
144K LEU 2.9 7.1 + - - -
146K ALA* 1.3 76.0 - - - +
148K ILE* 1.3 58.8 + - - +
150K LEU* 3.1 4.5 + - - +
151K ALA 2.9 22.7 + - - -
65L ILE* 3.1 35.2 - - - +
69L ALA* 3.3 17.5 - - - -
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Residues in contact with ILE 148 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84K HIS* 3.6 37.5 - - + +
86K ILE* 4.5 5.8 - - + -
132K TYR* 3.4 48.9 - - + +
144K LEU* 2.8 21.3 + - + +
145K GLY* 3.4 14.1 - - - +
147K GLY* 1.3 76.0 - - - +
149K ALA* 1.3 57.5 + - - +
151K ALA* 3.0 9.2 + - - +
152K CYS* 2.8 25.9 + - - -
161K CYS* 3.8 11.7 - - + -
68L GLY* 3.6 18.1 - - - +
71L MET* 5.3 1.3 - - + -
72L ALA* 4.5 5.8 - - + -
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Residues in contact with ALA 149 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145K GLY 2.8 11.0 + - - +
146K ALA* 3.3 10.1 - - - +
148K ILE* 1.3 72.2 - - - +
150K LEU* 1.3 65.8 + - - +
152K CYS* 3.2 10.1 + - - +
153K LYS* 3.1 18.2 + - - +
161K CYS* 4.0 9.2 - - + +
187K LEU* 4.1 8.5 - - + -
188K PRO* 3.4 13.9 - - - +
189K CYS* 3.4 37.0 - - + -
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Residues in contact with LEU 150 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146K ALA 2.8 14.3 + - - +
147K GLY* 3.1 11.8 + - - +
149K ALA* 1.3 76.6 - - - +
151K ALA* 1.3 64.2 + - - +
153K LYS* 3.4 11.7 + - + +
154K TYR* 3.0 32.8 + - + +
185K TRP* 4.7 9.4 - - + -
187K LEU* 3.7 26.7 - - + +
24L PHE* 4.0 20.6 - - + -
26L LEU* 5.5 0.4 - - + -
53L ILE* 3.7 31.6 - - + -
65L ILE* 4.3 17.9 - - + -
69L ALA* 4.9 2.9 - - + -
74L LEU* 5.6 0.2 - - + -
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Residues in contact with ALA 151 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147K GLY 2.9 12.1 + - - +
148K ILE 3.0 9.2 + - - +
150K LEU* 1.3 78.1 - - - +
152K CYS* 1.3 63.1 + - - +
154K TYR* 3.2 1.6 + - - +
155K ASN* 2.9 32.6 + - - +
69L ALA* 4.3 4.0 - - - +
72L ALA* 3.7 26.9 - - + -
74L LEU* 3.7 30.2 - - + +
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Residues in contact with CYS 152 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84K HIS* 3.4 34.5 - - - -
148K ILE* 2.8 21.1 + - - -
149K ALA* 3.2 13.9 + - - +
151K ALA* 1.3 74.6 - - - +
153K LYS* 1.3 63.1 + - - +
155K ASN* 3.2 4.5 + - - +
156K GLY* 3.2 18.9 + - - -
157K LYS* 4.0 6.1 + - - +
158K ASP 5.1 0.9 + - - -
159K GLU* 3.3 39.9 + - - +
160K VAL 4.2 7.4 - - - -
188K PRO* 3.9 5.6 - - + -
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Residues in contact with LYS 153 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149K ALA 3.1 3.7 + - - +
150K LEU* 3.8 14.2 - - + +
152K CYS* 1.3 79.0 - - - +
154K TYR* 1.3 63.4 + - - +
156K GLY* 3.2 14.4 + - - -
185K TRP* 2.8 40.5 + - - +
186K LYS* 3.7 14.1 - - - +
187K LEU* 4.4 7.1 - - + +
188K PRO* 3.8 19.8 - - + +
50L LYS* 5.4 1.2 - - - -
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Residues in contact with TYR 154 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150K LEU* 3.0 29.2 + - + +
151K ALA 3.4 6.1 - - - +
153K LYS* 1.3 79.3 - - - +
155K ASN* 1.3 72.3 + - - +
156K GLY 3.5 0.2 + - - -
21L GLU* 2.6 33.5 + - + -
22L LYS* 3.9 8.3 - - + -
23L VAL 4.1 1.6 + - - -
24L PHE* 4.2 18.3 - + + +
50L LYS* 3.1 65.1 + - + +
51L ARG* 3.2 20.1 + - - -
53L ILE* 6.0 0.2 - - + -
74L LEU* 3.5 29.8 - - + -
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Residues in contact with ASN 155 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151K ALA* 2.9 25.2 + - - +
152K CYS 3.2 2.4 + - - +
154K TYR* 1.3 91.6 - - - +
156K GLY* 1.3 68.6 + - - +
157K LYS* 3.4 26.1 - - + +
159K GLU* 5.0 8.0 + - - +
22L LYS* 4.9 9.8 - - - +
72L ALA 5.0 6.3 + - - -
74L LEU* 3.9 18.0 - - - +
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Residues in contact with GLY 156 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152K CYS 3.2 6.9 + - - -
153K LYS 3.2 13.2 + - - -
154K TYR 3.3 0.8 + - - -
155K ASN* 1.3 80.9 - - - +
157K LYS* 1.3 65.0 + - - +
158K ASP* 3.5 3.1 - - - -
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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
------------------------------------------------------------
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