Contacts of the helix formed by residues 184 - 193 (chain B) in PDB entry 4YCG
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 VAL 184 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125B ALA* 3.2 10.4 + - - +
127B LEU* 3.7 15.5 - - + +
149B VAL* 3.9 24.5 - - + -
169B LEU* 3.7 34.5 - - + -
170B VAL* 4.2 2.0 - - + -
182B LEU* 2.9 17.6 + - + +
183B GLU* 1.3 76.0 - - - +
185B SER* 1.3 63.1 + - - +
186B SER* 3.3 4.1 + - - -
187B ALA* 3.4 12.2 + - + +
188B VAL* 3.7 7.3 + - - +
203B LEU* 4.9 0.7 - - + -
231B PHE* 3.5 30.5 - - + -
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Residues in contact with SER 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ILE* 4.9 0.3 - - - +
123B THR 4.0 3.1 + - - -
124B ARG* 3.3 9.2 - - - +
125B ALA* 3.0 24.4 + - - +
183B GLU* 2.3 33.9 + - - -
184B VAL* 1.3 75.9 - - - +
186B SER* 1.3 64.4 + - - +
187B ALA 3.3 0.7 + - - -
188B VAL* 3.3 4.5 + - - +
189B LYS* 3.1 44.6 + - - +
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Residues in contact with SER 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B LEU* 4.4 9.6 - - - -
184B VAL* 3.3 0.6 - - - -
185B SER* 1.3 78.9 - - - +
187B ALA* 1.3 62.4 + - - +
189B LYS* 3.4 11.4 + - - +
190B ARG* 3.0 52.0 + - - +
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Residues in contact with ALA 187 (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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151B ASP* 3.4 33.2 - - + +
169B LEU* 3.7 23.2 - - + +
184B VAL* 3.4 9.2 + - + +
185B SER 3.3 1.0 - - - -
186B SER* 1.3 77.4 - - - +
188B VAL* 1.3 58.2 + - + +
190B ARG* 3.2 5.3 + - - +
191B TRP* 2.9 48.3 + - + -
203B LEU* 4.9 0.9 - - + -
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Residues in contact with VAL 188 (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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114B ILE* 3.8 26.5 - - + -
116B ILE* 5.0 0.4 - - + -
122B ILE* 3.6 17.9 - - + -
125B ALA* 3.7 15.9 - - + -
184B VAL 3.7 2.2 + - - +
185B SER 3.3 6.1 + - - +
187B ALA* 1.3 71.9 - - - +
189B LYS* 1.3 60.7 + - - +
191B TRP* 2.9 19.6 + - + +
192B VAL* 2.8 32.4 + - + +
231B PHE* 3.5 35.9 - - + -
233B VAL* 4.5 12.1 - - + -
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Residues in contact with LYS 189 (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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121B GLN* 5.2 5.2 - - - +
122B ILE* 3.6 36.5 + - + -
123B THR* 4.0 23.1 + - - +
185B SER* 3.1 27.1 + - - +
186B SER* 3.5 11.7 - - - +
188B VAL* 1.3 76.9 - - - +
190B ARG* 1.3 61.2 - - + +
192B VAL* 3.5 4.7 + - - +
193B ARG* 3.5 19.6 + - - +
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Residues in contact with ARG 190 (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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151B ASP* 3.1 22.8 + - - +
153B LEU* 5.0 4.0 - - - -
167B THR* 3.6 27.6 + - - +
168B PHE 5.7 1.0 + - - -
169B LEU* 3.9 12.1 - - - +
186B SER* 3.0 31.6 + - - +
187B ALA* 3.4 10.8 - - - +
189B LYS* 1.3 77.1 - - + +
191B TRP* 1.3 60.0 + - - +
193B ARG* 3.0 27.3 - - - +
194B ALA* 3.8 2.4 + - - -
200B LYS* 3.2 31.5 + - - +
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Residues in contact with TRP 191 (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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112B PHE* 4.6 2.7 - + - -
114B ILE* 3.8 26.4 - - + +
151B ASP* 3.1 22.1 + - - -
187B ALA* 2.9 27.8 + - + -
188B VAL* 2.9 19.9 + - + +
190B ARG* 1.3 76.0 - - - +
192B VAL* 1.3 66.4 + - + +
194B ALA* 3.4 18.2 + - - +
200B LYS* 3.5 19.5 - - + +
201B ASN* 3.4 51.3 - - + +
202B LYS* 3.2 30.5 - - - +
203B LEU* 3.6 28.0 - - + -
231B PHE* 3.8 21.8 - + - -
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Residues in contact with VAL 192 (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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114B ILE* 5.6 1.8 - - + -
116B ILE* 4.3 35.7 - - + +
117B PRO 5.3 3.8 - - - +
118B ARG* 5.4 9.7 - - + +
120B GLU 5.5 6.1 - - - +
122B ILE* 3.9 23.6 - - + -
188B VAL* 2.8 23.5 + - + +
189B LYS* 3.8 6.5 - - - +
190B ARG 3.3 0.2 - - - -
191B TRP* 1.3 77.1 - - + +
193B ARG* 1.3 58.7 + - + +
194B ALA* 3.0 8.1 + - - +
238B ARG* 5.9 5.4 - - - +
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Residues in contact with ARG 193 (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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189B LYS 3.5 11.0 + - - +
190B ARG* 3.0 13.8 - - - +
191B TRP 3.4 0.2 - - - -
192B VAL* 1.3 77.8 - - + +
194B ALA* 1.3 63.8 + - - +
195B ASP* 2.9 33.0 + - - +
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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