Contacts of the helix formed by residues 184 - 193 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A ALA* 3.2 6.2 + - - +
127A LEU* 3.7 14.8 - - + +
149A VAL* 3.8 26.2 - - + -
169A LEU* 3.6 36.1 - - + -
170A VAL* 4.1 2.7 - - + -
182A LEU* 3.0 16.9 + - + +
183A GLU* 1.3 74.5 - - - +
185A SER* 1.3 64.0 + - - +
186A SER* 3.3 3.6 - - - -
187A ALA* 3.3 13.5 + - + +
188A VAL* 3.7 9.7 + - - +
203A LEU* 4.7 0.9 - - + -
231A PHE* 3.5 32.1 - - + -
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Residues in contact with SER 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ILE* 5.0 0.6 - - - +
123A THR 4.0 6.8 + - - -
124A ARG* 3.3 18.1 - - - +
125A ALA* 2.9 34.5 + - - +
183A GLU* 3.4 13.4 + - - +
184A VAL* 1.3 76.3 - - - +
186A SER* 1.3 64.2 + - - +
188A VAL* 3.2 5.0 + - - +
189A LYS* 3.1 37.2 + - - +
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Residues in contact with SER 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A LEU* 4.6 9.3 - - - +
184A VAL* 3.3 0.6 - - - -
185A SER* 1.3 79.5 - - - +
187A ALA* 1.3 62.4 + - - +
189A LYS* 3.4 11.5 + - - +
190A ARG* 3.0 48.7 + - - +
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Residues in contact with ALA 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ASP* 3.6 31.4 - - + +
169A LEU* 3.8 22.3 - - + +
184A VAL* 3.3 11.1 + - + +
185A SER 3.3 0.8 - - - -
186A SER* 1.3 78.7 - - - +
188A VAL* 1.3 63.1 + - + +
190A ARG* 3.2 8.0 + - - +
191A TRP* 3.1 41.9 + - + -
203A LEU* 4.9 1.1 - - + -
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Residues in contact with VAL 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A ILE* 3.9 33.7 - - + -
116A ILE* 5.2 0.2 - - + -
122A ILE* 3.7 17.7 - - + -
125A ALA* 3.6 18.2 - - + -
184A VAL 4.0 2.7 - - - +
185A SER 3.2 6.8 + - - +
187A ALA* 1.3 72.5 - - - +
189A LYS* 1.3 55.9 + - - +
191A TRP* 2.9 13.9 + - + +
192A VAL* 2.8 37.5 + - + +
231A PHE* 3.4 32.8 - - + -
233A VAL* 4.5 10.3 - - + -
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Residues in contact with LYS 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A GLN* 5.1 6.4 - - - +
122A ILE* 3.6 41.1 + - + -
123A THR* 4.1 17.6 + - - +
185A SER* 3.1 26.3 + - - +
186A SER* 3.6 11.4 - - - +
187A ALA 3.3 0.2 - - - -
188A VAL* 1.3 77.1 - - - +
190A ARG* 1.3 61.2 + - + +
192A VAL* 3.5 4.5 + - - +
193A ARG* 3.2 22.3 + - - +
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Residues in contact with ARG 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ASP* 2.8 36.4 + - - +
153A LEU* 5.0 3.0 - - - +
167A THR* 3.2 27.5 + - - +
169A LEU* 3.6 10.7 - - - +
186A SER* 3.0 33.0 + - - +
187A ALA* 3.2 9.7 + - - +
188A VAL 3.2 0.4 - - - -
189A LYS* 1.3 76.0 - - + +
191A TRP* 1.3 62.7 + - + +
193A ARG* 2.9 26.9 - - - +
194A ALA* 3.6 3.8 + - - +
200A LYS* 3.8 30.2 + - - +
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Residues in contact with TRP 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A PHE* 4.6 2.9 - + - -
114A ILE* 3.6 39.1 - - + +
151A ASP* 3.2 21.1 + - - -
187A ALA* 3.1 25.7 + - + -
188A VAL* 2.9 19.1 + - + +
190A ARG* 1.3 78.1 - - - +
192A VAL* 1.3 65.1 + - + +
194A ALA* 3.5 16.6 + - - +
200A LYS* 3.6 16.9 - - + +
201A ASN* 3.3 49.8 - - + +
202A LYS* 3.2 31.2 - - - +
203A LEU* 3.7 28.0 - - + -
231A PHE* 3.8 14.8 - + - -
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Residues in contact with VAL 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A ILE* 5.5 1.8 - - + -
116A ILE* 4.1 40.7 - - + +
117A PRO 5.1 4.5 - - - +
118A ARG* 5.6 6.6 - - + +
120A GLU 5.3 6.7 - - - +
122A ILE* 3.7 24.9 - - + -
188A VAL* 2.8 23.3 + - + +
189A LYS* 3.7 7.9 - - - +
190A ARG 3.3 0.2 - - - -
191A TRP* 1.3 79.0 - - + +
193A ARG* 1.3 59.6 + - + +
194A ALA* 3.0 8.1 + - - +
238A ARG* 5.6 6.3 - - - +
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Residues in contact with ARG 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A LYS 3.2 11.5 + - - +
190A ARG* 2.9 14.5 - - - +
192A VAL* 1.3 77.3 - - + +
194A ALA* 1.3 64.9 + - - +
195A ASP* 3.1 34.0 + - - +
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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