Contacts of the helix formed by residues 130 - 147 (chain B) in PDB entry 3IH9
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 130 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B GLU 3.5 3.1 + - - -
129B ALA* 1.3 74.5 - - - +
131B ARG* 1.3 65.1 + - - +
132B LYS* 3.8 7.4 + - - +
133B GLU* 2.9 46.8 + - - +
134B ARG* 3.1 14.3 + - - +
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Residues in contact with ARG 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B HIS* 5.1 2.3 - - - -
129B ALA 4.0 0.4 + - - -
130B SER* 1.3 74.3 - - - +
132B LYS* 1.3 68.2 + - - +
134B ARG* 3.3 8.2 + - - +
135B LEU* 3.2 22.4 + - + +
157B TYR* 4.4 6.9 + - - -
185B GLU 5.0 1.6 + - - -
186B GLU* 3.9 51.0 + - + +
189B ALA* 4.3 26.2 - - - +
190B GLY* 5.6 6.8 - - - +
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Residues in contact with LYS 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B SER* 3.2 7.9 + - - +
131B ARG* 1.3 87.6 - - + +
133B GLU* 1.3 60.6 + - + +
135B LEU* 4.0 15.9 - - + +
136B ASP* 3.0 60.7 + - - +
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Residues in contact with GLU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B VAL* 3.6 19.5 - - + +
128B GLU 4.4 1.2 - - - +
129B ALA* 3.3 11.8 - - - +
130B SER* 2.9 43.2 + - - +
132B LYS* 1.3 78.5 - - + +
134B ARG* 1.3 59.4 + - - +
136B ASP* 3.5 8.0 + - - +
137B ARG* 3.0 26.3 + - - +
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Residues in contact with ARG 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ARG* 5.1 0.6 - - - +
121B HIS* 3.4 36.6 - - + -
122B GLN* 3.0 36.0 + - - +
124B LEU* 3.5 17.9 - - + +
125B VAL* 3.7 24.6 - - + +
126B GLY 2.7 27.7 + - - -
127B PRO* 3.3 14.5 + - - +
129B ALA* 3.4 20.6 + - + +
130B SER 3.1 9.5 + - - +
131B ARG* 3.3 7.2 + - - +
133B GLU* 1.3 75.5 - - - +
135B LEU* 1.3 59.3 + - - +
137B ARG* 3.3 1.0 + - - +
138B ALA* 3.0 23.9 + - - +
182B ASP* 2.7 27.1 + - - -
186B GLU* 3.9 8.1 + - - -
187B ILE* 4.6 4.1 - - - +
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B HIS* 4.3 9.5 - - + +
131B ARG* 3.2 17.7 + - + +
132B LYS* 4.1 15.9 - - + +
133B GLU 3.4 0.2 - - - -
134B ARG* 1.3 75.9 - - - +
136B ASP* 1.3 67.3 + - - +
138B ALA* 3.4 3.4 + - + -
139B VAL* 2.9 51.1 + - + +
152B VAL* 4.7 4.9 - - + -
154B TRP* 4.4 22.0 - - + -
190B GLY* 4.2 9.2 - - - +
193B ALA* 3.7 29.4 - - + -
194B GLN* 4.1 13.0 - - - +
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Residues in contact with ASP 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B LYS* 3.0 53.1 + - - +
133B GLU* 3.7 7.6 - - - +
135B LEU* 1.3 82.3 - - - +
137B ARG* 1.3 59.2 + - - +
139B VAL* 3.3 6.3 + - - +
140B GLU* 2.8 30.6 + - - +
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Residues in contact with ARG 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B ALA* 3.6 23.3 + - + +
76B VAL* 4.2 13.1 - - - +
77B ASP* 2.6 38.8 + - - +
124B LEU* 3.7 27.4 - - + +
125B VAL* 3.7 13.0 - - + -
133B GLU 3.0 17.7 + - - +
134B ARG 3.6 4.9 - - - +
136B ASP* 1.3 74.4 - - - +
138B ALA* 1.3 65.9 + - - +
140B GLU* 3.1 28.6 + - - -
141B ILE* 3.0 42.8 + - - +
144B LEU* 5.2 3.2 - - - +
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Residues in contact with ALA 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B THR* 4.1 14.7 - - + +
121B HIS* 4.4 2.5 - - - +
124B LEU* 3.7 18.1 - - + +
134B ARG 3.0 15.9 + - - +
135B LEU* 3.6 10.3 - - + +
137B ARG* 1.3 76.7 - - - +
139B VAL* 1.3 64.4 + - + +
141B ILE* 3.1 23.9 - - - +
142B MET* 3.5 15.0 + - - +
194B GLN* 4.3 17.3 - - + +
197B VAL* 5.7 0.9 - - + -
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Residues in contact with VAL 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B LEU* 2.9 37.6 + - + +
136B ASP* 3.8 6.7 - - - +
138B ALA* 1.3 78.8 - - + +
140B GLU* 1.3 52.2 + - - +
142B MET* 3.7 3.6 + - - +
143B SER* 2.7 40.0 + - - +
149B ARG* 5.6 3.8 - - - +
150B LEU* 3.5 31.3 - - + +
152B VAL* 4.2 18.8 - - + -
194B GLN* 5.8 0.2 - - - -
197B VAL* 4.3 15.9 - - + -
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Residues in contact with GLU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ASP 2.8 18.0 + - - +
137B ARG* 3.1 34.8 + - - +
138B ALA 3.2 0.4 - - - -
139B VAL* 1.3 74.7 - - - +
141B ILE* 1.3 64.9 + - - +
142B MET 3.1 1.6 - - - -
143B SER* 3.0 6.2 + - - -
144B LEU* 2.8 55.7 + - + +
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Residues in contact with ILE 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B PHE* 3.6 36.8 - - + +
70B THR* 4.6 2.2 - - + +
72B ALA* 5.1 0.4 - - + -
73B ALA* 3.9 17.9 - - + +
137B ARG* 3.0 32.2 + - - +
138B ALA* 3.1 18.8 - - - +
140B GLU* 1.3 78.5 + - - +
142B MET* 1.3 65.1 - - + +
144B LEU* 3.7 9.8 + - + +
145B LEU* 3.4 35.8 + - + +
224B MET* 5.3 2.5 - - + +
225B LEU* 3.8 29.2 - - + -
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Residues in contact with MET 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ILE* 3.1 55.0 - - + -
66B SER* 3.7 17.9 - - - +
69B PHE* 3.9 19.7 - - + -
70B THR* 5.5 2.0 - - - -
138B ALA 3.5 17.0 + - - +
139B VAL 4.1 3.4 - - - +
140B GLU 3.1 0.8 - - - -
141B ILE* 1.3 80.7 - - - +
143B SER* 1.3 58.8 + - - +
145B LEU* 3.5 1.1 + - - -
146B ALA* 2.9 32.4 + - - +
150B LEU* 3.5 12.7 - - + +
194B GLN* 4.7 4.5 - - - +
197B VAL* 3.6 26.7 - - + -
199B VAL* 4.5 1.1 - - + -
207B MET* 3.5 21.3 - - + +
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Residues in contact with SER 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B VAL* 2.7 26.5 + - - +
140B GLU* 3.0 9.0 + - - -
142B MET* 1.3 73.8 - - - +
144B LEU* 1.3 65.8 + - - +
147B GLY* 2.8 25.8 + - - -
148B ARG 3.2 25.4 + - - -
149B ARG* 3.8 10.8 + - - -
150B LEU* 3.1 27.1 + - - +
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Residues in contact with LEU 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B ARG* 5.2 4.0 - - - +
140B GLU* 2.8 47.1 + - + +
141B ILE* 4.0 12.6 - - + +
143B SER* 1.3 82.0 - - - +
145B LEU* 1.3 64.6 + - + +
147B GLY* 3.5 7.2 + - - -
217B HIS* 3.8 12.0 - - - -
224B MET* 4.0 19.3 - - + +
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Residues in contact with LEU 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B PHE* 3.4 36.1 - - + -
72B ALA* 6.0 0.2 - - + -
141B ILE* 3.4 27.4 + - + +
142B MET* 4.1 1.6 - - - +
143B SER 3.3 0.4 - - - -
144B LEU* 1.3 74.2 - - + +
146B ALA* 1.3 58.0 + - - +
147B GLY 3.0 5.2 - - - -
206B VAL* 3.8 6.4 - - - +
207B MET* 3.9 17.7 - - + +
210B CYS* 3.7 27.4 - - + -
211B LEU* 4.9 1.1 - - + -
217B HIS* 3.0 22.5 + - - -
224B MET* 3.3 35.4 - - + -
225B LEU* 4.5 22.0 - - + -
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Residues in contact with ALA 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B MET 2.9 19.8 + - - +
143B SER 3.9 3.1 - - - +
145B LEU* 1.3 78.1 - - - +
147B GLY* 1.3 59.5 + - - +
148B ARG* 3.2 8.3 + - - +
150B LEU* 4.0 16.4 - - + -
203B ASP* 3.9 27.2 - - + +
206B VAL* 4.6 11.4 - - - +
207B MET* 3.6 22.4 - - + +
217B HIS* 4.4 0.9 - - - -
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Residues in contact with GLY 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B SER 2.8 10.3 + - - -
144B LEU 4.0 7.9 - - - -
145B LEU 3.0 3.6 - - - -
146B ALA* 1.3 77.7 - - - +
148B ARG* 1.3 59.9 + - - +
217B HIS* 4.2 11.9 - - - -
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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