Contacts of the helix formed by residues 154 - 168 (chain B) in PDB entry 4R0C
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 154 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B PHE* 3.1 18.6 - - - -
152B GLY 3.8 0.6 - - - +
153B ARG* 1.3 76.3 - - + +
155B PRO* 1.3 74.8 - - + +
157B ALA* 3.1 10.7 + - + +
229B GLU* 3.0 30.7 - - + +
232B LEU* 3.6 34.5 - - + +
233B ALA* 3.6 37.7 - - + +
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Residues in contact with PRO 155 (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 GLY* 3.6 21.5 - - - +
148B PHE* 4.0 4.5 - - + -
149B GLN* 3.6 37.5 - - + +
153B ARG 3.3 5.1 - - - +
154B PRO* 1.3 83.0 - - + +
156B ILE* 1.3 56.8 + - + +
158B GLY* 2.6 25.6 + - - -
159B ILE* 3.0 12.0 + - - +
232B LEU* 6.0 0.2 - - + -
452B TYR* 3.3 35.2 - - + -
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Residues in contact with ILE 156 (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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154B PRO* 3.4 0.6 - - - +
155B PRO* 1.3 73.1 - - + +
157B ALA* 1.3 60.8 + - - +
159B ILE* 3.7 10.8 - - + -
160B ALA* 3.0 27.2 + - - +
228B THR* 4.4 0.8 - - + +
232B LEU* 4.5 21.1 - - + -
449B ALA* 4.1 37.5 - - + +
452B TYR* 4.6 11.0 - - + -
453B GLN* 3.9 28.0 - - + +
456B THR* 5.4 4.0 - - + -
464B LEU* 3.6 30.7 - - + -
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Residues in contact with ALA 157 (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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148B PHE* 3.8 13.7 - - + -
154B PRO* 3.1 23.1 + - + +
155B PRO 3.0 0.4 - - - -
156B ILE* 1.3 78.5 - - - +
158B GLY* 1.3 57.8 + - - +
160B ALA* 4.0 1.2 - - - +
161B THR* 3.1 31.7 + - - +
224B THR* 4.4 6.1 + - + +
228B THR* 4.0 12.7 - - + +
229B GLU* 4.0 32.3 - - + +
232B LEU* 4.8 1.9 - - + +
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Residues in contact with GLY 158 (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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144B ALA* 3.1 27.7 - - - +
145B GLY 4.3 0.2 - - - -
148B PHE* 3.5 25.7 - - - -
155B PRO 2.6 15.6 + - - -
157B ALA* 1.3 75.3 - - - +
159B ILE* 1.3 56.0 + - - -
161B THR* 3.1 22.7 - - - +
162B ALA* 3.1 6.4 + - - +
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Residues in contact with ILE 159 (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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141B ILE* 3.6 27.7 - - + +
142B PRO* 5.5 1.3 - - + +
145B GLY* 4.1 2.9 - - - -
155B PRO 3.0 13.4 + - - +
156B ILE* 4.0 10.3 - - + +
157B ALA 3.3 0.2 - - - -
158B GLY* 1.3 75.8 - - - +
160B ALA* 1.3 58.6 + - - +
162B ALA* 3.6 4.4 - - - +
163B PHE* 2.7 34.5 + - - +
445B VAL* 4.5 17.9 - - + +
448B PHE* 4.0 15.5 - - + +
449B ALA* 4.3 22.7 - - + -
452B TYR* 3.4 39.5 - - + -
461B LEU* 5.4 1.1 - - + -
464B LEU* 5.1 4.5 - - + -
465B MET* 5.0 5.6 - - + -
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Residues in contact with ALA 160 (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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156B ILE 3.0 17.5 + - - +
157B ALA 4.0 0.2 - - - +
159B ILE* 1.3 76.1 - - - +
161B THR* 1.3 64.5 + - - +
162B ALA 3.1 0.5 + - - -
163B PHE* 3.1 1.0 + - - +
164B ALA* 3.1 29.5 + - - +
228B THR* 3.9 4.3 - - + -
464B LEU* 3.8 14.6 - - + -
465B MET* 3.4 22.2 - - + +
468B TYR* 3.7 29.8 - - + +
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Residues in contact with THR 161 (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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119B VAL* 3.8 21.6 + - + +
122B VAL* 3.5 21.6 - - + +
123B ALA* 4.1 2.3 - - - +
148B PHE* 4.9 5.6 - - + -
157B ALA 3.1 16.6 + - - +
158B GLY* 3.1 27.1 - - - +
160B ALA* 1.3 79.1 - - - +
162B ALA* 1.3 58.0 + - - +
165B ALA* 3.4 22.3 + - - +
220B VAL* 3.8 16.9 - - - +
224B THR* 3.3 30.1 + - + -
468B TYR* 4.0 1.0 + - - -
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Residues in contact with ALA 162 (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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122B VAL* 3.9 9.2 - - + -
126B GLY* 5.5 0.9 - - - -
140B LEU* 4.1 7.4 - - + +
141B ILE* 3.9 28.7 - - + +
144B ALA* 3.9 9.6 - - + -
158B GLY 3.1 20.9 + - - +
159B ILE 3.6 3.8 - - - +
160B ALA 3.1 0.4 - - - -
161B THR* 1.3 76.5 - - - +
163B PHE* 1.3 64.6 + - - +
165B ALA* 3.5 2.6 + - - +
166B VAL* 3.0 30.6 + - + +
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Residues in contact with PHE 163 (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 TYR* 4.1 3.8 - + - -
141B ILE* 4.0 10.9 - - + +
159B ILE 2.7 20.5 + - - +
160B ALA 3.1 3.1 + - - +
162B ALA* 1.3 71.8 - - - +
164B ALA* 1.3 55.9 + - - +
166B VAL* 3.8 0.2 - - - -
167B SER* 2.7 52.2 + - - -
434B ILE* 3.6 28.0 - - + -
439B MET* 3.5 24.7 - - + -
442B PHE* 4.1 17.7 - + - -
445B VAL* 3.6 42.6 - - + -
461B LEU* 4.5 4.9 - - + -
465B MET* 3.5 33.2 - - + -
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Residues in contact with ALA 164 (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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160B ALA 3.1 13.3 + - - +
163B PHE* 1.3 78.5 - - - +
165B ALA* 1.3 59.6 + - - +
168B GLY* 2.8 25.6 + - - -
169B GLY 2.9 8.5 + - - -
216B VAL* 5.2 0.2 - - - +
220B VAL* 4.0 11.9 - - + -
434B ILE* 3.6 17.5 - - + +
465B MET* 4.4 1.0 - - - -
468B TYR* 3.8 40.2 - - + -
472B LEU* 4.7 3.7 - - + +
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Residues in contact with ALA 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ALA* 3.2 36.6 - - + +
126B GLY* 3.6 8.1 - - - -
127B VAL* 3.1 32.3 - - + +
161B THR 3.4 20.1 + - - +
162B ALA 3.5 1.7 + - - +
163B PHE 3.3 0.4 - - - -
164B ALA* 1.3 78.6 - - - +
166B VAL* 1.3 59.7 + - - +
169B GLY* 3.5 9.6 - - - +
216B VAL* 4.6 5.6 - - - -
220B VAL* 4.4 4.7 - - + +
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Residues in contact with VAL 166 (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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126B GLY* 3.2 31.1 - - - +
127B VAL* 5.5 0.3 - - - -
129B SER* 3.2 16.4 + - - +
130B SER* 5.6 2.3 - - - -
136B GLY* 3.2 30.3 - - - +
137B TYR* 3.7 33.9 + - + -
140B LEU* 4.4 3.4 - - + -
141B ILE* 5.2 1.1 - - + -
162B ALA* 3.0 18.4 + - + +
163B PHE* 3.9 2.5 - - - +
165B ALA* 1.3 76.3 - - - +
167B SER* 1.3 63.7 + - - +
170B PHE* 3.4 23.9 + - - +
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Residues in contact with SER 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B TYR* 3.4 24.2 + - - -
163B PHE* 2.7 38.2 + - - -
166B VAL* 1.3 70.6 - - - +
168B GLY* 1.3 61.2 + - - +
169B GLY 3.3 1.6 - - - -
170B PHE* 3.3 8.5 - - - +
430B SER 3.6 0.2 - - - +
433B ASN* 2.8 54.2 + - - +
434B ILE* 3.7 4.3 - - - -
439B MET* 3.5 6.6 - - - +
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Residues in contact with GLY 168 (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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164B ALA 2.8 13.7 + - - -
167B SER* 1.3 75.8 - - - +
169B GLY* 1.3 56.3 + - - +
170B PHE 3.3 1.8 - - - -
430B SER* 3.1 35.1 - - - -
431B SER 3.7 2.9 + - - -
434B ILE* 3.5 14.3 - - - +
472B LEU* 3.9 16.5 - - - +
476B TRP* 3.2 11.6 - - - -
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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
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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