Contacts of the helix formed by residues 134 - 151 (chain B) in PDB entry 1H4R
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 PRO 134 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A GLU* 3.3 33.7 - - + +
132B TYR* 3.6 30.5 - - + +
133B CYS* 1.3 89.9 - - - +
135B PRO* 1.3 73.6 - - + +
136B GLU 3.5 0.2 - - - -
137B ALA* 3.5 8.1 + - + -
138B SER* 2.9 24.1 + - - -
172B ARG* 4.0 0.9 - - - +
173B VAL* 4.4 0.2 - - - -
214B LEU* 3.9 17.9 - - + -
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Residues in contact with PRO 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A GLU* 3.3 14.1 - - + +
132B TYR* 4.8 2.7 - - - +
133B CYS 3.9 0.2 - - - -
134B PRO* 1.3 85.0 - - + +
136B GLU* 1.3 60.8 + - - +
138B SER* 2.7 24.7 + - - +
139B VAL* 3.1 13.9 + - - +
173B VAL* 3.9 18.1 - - + +
176B LEU* 3.9 26.7 - - + -
177B TYR* 3.6 39.5 - - + +
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Residues in contact with GLU 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A ARG* 4.2 3.0 + - - -
190A ALA* 3.5 30.6 - - + +
191A TRP* 3.6 43.6 + - + +
194A GLU* 2.8 26.3 + - - +
135B PRO* 1.3 71.2 - - - +
137B ALA* 1.3 64.8 + - - +
139B VAL* 3.2 6.5 + - - +
140B LEU 3.1 18.0 + - - -
177B TYR* 2.7 28.2 + - - +
187B ARG* 2.6 44.4 + - - -
191B TRP* 5.0 0.3 + - - -
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Residues in contact with ALA 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A TRP* 3.7 12.9 - - + -
194A GLU* 3.2 12.5 + - - +
133B CYS* 3.9 14.1 - - - -
134B PRO* 3.7 17.5 - - + +
136B GLU* 1.3 79.3 - - - +
138B SER* 1.3 56.2 + - - +
140B LEU* 3.3 4.2 + - - +
141B LEU* 2.9 33.3 + - - +
210B ILE* 4.8 11.8 - - + +
214B LEU* 4.6 8.3 - - + -
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Residues in contact with SER 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ILE* 5.6 1.3 - - - -
133B CYS* 3.6 13.9 - - - -
134B PRO 2.9 15.3 + - - -
135B PRO 2.7 16.7 + - - -
137B ALA* 1.3 76.6 - - - +
139B VAL* 1.3 57.8 + - - +
141B LEU* 3.7 5.1 - - - +
142B ALA* 3.0 28.2 + - - +
168B LEU 4.6 1.2 - - - +
169B LEU* 3.7 9.4 - - - +
170B PRO* 3.8 24.6 - - - +
173B VAL* 3.5 24.2 - - - +
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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
----------------------------------------------------------
135B PRO 3.1 15.7 + - - +
136B GLU* 3.2 6.7 + - - +
138B SER* 1.3 79.3 - - - +
140B LEU* 1.3 64.7 + - - +
142B ALA* 3.3 7.3 + - - +
143B SER* 3.0 21.7 + - - -
169B LEU* 4.4 7.4 - - + -
177B TYR* 5.6 0.7 - - + -
184B TRP* 4.3 24.7 - - + -
187B ARG* 3.5 57.9 - - + +
188B ILE* 3.8 8.8 - - + +
191B TRP* 4.0 9.6 - - + -
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Residues in contact with LEU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A LEU* 4.9 7.9 - - + -
191A TRP* 4.1 20.6 - - + -
136B GLU 3.1 12.6 + - - +
137B ALA 3.6 6.5 - - - +
139B VAL* 1.3 76.2 - - - +
141B LEU* 1.3 61.4 + - - +
143B SER* 2.5 26.0 + - - +
144B TYR* 3.4 23.6 + - + +
191B TRP* 3.5 49.3 - - + +
195B HIS* 4.5 1.1 - - + -
210B ILE* 3.6 31.9 - - + -
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Residues in contact with LEU 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ILE* 4.4 11.0 - - + -
133B CYS* 3.6 30.3 - - - -
137B ALA* 2.9 16.7 + - + +
138B SER* 3.7 5.8 - - - +
140B LEU* 1.3 76.1 - - - +
142B ALA* 1.3 62.9 + - - +
144B TYR* 3.0 14.6 + - - -
145B ALA 3.0 9.7 + - - -
207B TYR* 3.3 70.7 - - + +
210B ILE* 3.5 26.5 - - + -
211B ALA* 3.9 3.6 - - + +
214B LEU* 4.5 10.5 - - + -
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Residues in contact with ALA 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B SER 3.0 18.0 + - - +
139B VAL 3.3 5.4 + - - +
141B LEU* 1.3 74.7 - - - +
143B SER* 1.3 58.3 + - - +
145B ALA* 3.1 9.3 + - - +
146B VAL* 2.9 33.3 + - - +
168B LEU* 3.5 32.5 - - + +
169B LEU* 3.6 13.2 - - + -
188B ILE* 4.1 11.9 - - + -
207B TYR* 5.2 0.4 - - - -
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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
----------------------------------------------------------
139B VAL 3.0 9.8 + - - -
140B LEU* 2.5 21.4 + - - +
142B ALA* 1.3 76.8 - - - +
144B TYR* 1.3 53.7 + - - +
146B VAL* 3.5 4.3 + - - +
147B GLN* 3.1 21.1 + - - +
188B ILE* 3.7 13.2 - - - +
191B TRP* 3.3 30.4 - - - +
192B TYR* 3.6 12.8 - - - +
195B HIS* 2.8 33.6 + - - -
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Residues in contact with TYR 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B PHE* 5.4 0.2 - - - -
140B LEU* 3.6 29.4 - - + +
141B LEU* 3.0 7.6 + - - +
143B SER* 1.3 77.0 + - - +
145B ALA* 1.3 61.7 + - - +
146B VAL 3.2 0.2 - - - -
147B GLN* 3.2 4.0 + - + +
148B ALA* 2.9 30.9 + - - +
191B TRP* 5.9 0.3 - - - -
195B HIS* 3.4 32.4 - + + -
198B ARG* 4.8 1.6 - - - -
203B ALA* 3.7 28.3 - - + +
206B GLU* 3.5 33.4 + - + +
207B TYR* 4.1 11.9 - - + -
210B ILE* 3.4 31.6 - - + -
1314B SO4 3.3 33.3 + - - -
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Residues in contact with ALA 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B PHE* 4.2 13.1 - - + -
123B LYS* 3.8 30.5 - - + -
141B LEU 3.0 12.0 + - - +
142B ALA* 3.5 12.6 - - - +
144B TYR* 1.3 74.8 - - - +
146B VAL* 1.3 61.8 + - - +
148B ALA* 3.4 3.5 + - - +
149B LYS* 3.1 24.4 + - - +
168B LEU* 4.7 12.3 - - + -
207B TYR* 4.2 3.0 - - + -
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Residues in contact with VAL 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ALA 2.9 20.3 + - - +
143B SER* 3.7 6.5 - - - +
145B ALA* 1.3 73.7 - - - +
147B GLN* 1.3 59.3 + - - +
149B LYS* 3.2 1.0 + - - -
150B TYR* 2.8 48.8 + - + +
163B LEU* 4.1 16.6 - - + -
168B LEU* 3.7 33.9 - - + -
188B ILE* 4.1 9.2 - - + -
192B TYR* 3.6 37.7 - - + -
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Residues in contact with GLN 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 3.1 15.0 + - - +
144B TYR* 3.2 10.1 + - - +
146B VAL* 1.3 74.9 - - - +
148B ALA* 1.3 58.9 + - - +
151B GLY* 2.9 40.6 + - - +
152B ASP* 3.0 25.7 + - - -
153B TYR 4.4 0.3 + - - -
192B TYR* 3.1 31.5 - - + +
195B HIS* 3.4 33.1 + - + +
198B ARG* 2.8 28.9 + - + +
199B ALA 5.1 0.2 - - - +
200B ARG* 4.8 4.9 + - - +
203B ALA* 3.8 17.7 - - + -
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Residues in contact with ALA 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B PHE* 4.4 7.0 - - + -
144B TYR 2.9 16.8 + - - +
145B ALA 3.6 6.5 - - - +
146B VAL 3.2 0.2 - - - -
147B GLN* 1.3 78.0 - - - +
149B LYS* 1.3 61.7 + - - +
151B GLY 4.8 0.3 + - - -
200B ARG* 3.3 36.1 + - - +
203B ALA* 3.8 7.1 - - + +
204B GLU* 3.7 35.4 - - + +
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Residues in contact with LYS 149 (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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145B ALA 3.1 16.2 + - - +
146B VAL* 4.7 0.2 - - - -
148B ALA* 1.3 81.0 - - + +
150B TYR* 1.3 78.1 + - + +
151B GLY 3.6 0.2 - - - -
166B GLU* 2.5 40.7 + - - +
168B LEU* 6.5 0.4 - - + -
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Residues in contact with TYR 150 (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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146B VAL* 2.8 32.8 + - + +
149B LYS* 1.3 97.0 + - + +
151B GLY* 1.3 60.3 + - - +
152B ASP 4.0 3.1 + - - +
158B HIS* 3.7 27.6 + + - +
162B PHE* 3.9 26.5 + + + -
163B LEU* 4.2 11.7 - - + -
166B GLU* 2.4 43.2 + - - +
168B LEU* 6.3 0.2 - - + -
192B TYR* 3.4 16.7 + - + +
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Residues in contact with GLY 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B GLN* 2.9 26.6 + - - +
148B ALA 4.7 0.6 + - - -
149B LYS 3.6 1.4 - - - -
150B TYR* 1.3 78.1 - - - +
152B ASP* 1.3 56.5 + - - -
192B TYR* 2.6 35.2 + - - -
198B ARG 5.5 1.3 - - - -
200B ARG 6.4 0.7 - - - -
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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