Contacts of the strand formed by residues 183 - 192 (chain A) in PDB entry 4GFU
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 GLU 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A TRP* 3.5 21.0 + - + -
179A THR* 3.3 5.2 - - - +
180A PHE 3.0 36.2 + - - +
181A GLN 3.1 4.4 - - - +
182A LYS* 1.3 80.3 - - - +
184A SER* 1.3 68.4 - - - +
185A ARG* 3.3 29.1 + - - +
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Residues in contact with SER 184 (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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177A LYS* 3.1 24.7 + - - -
178A VAL 3.4 3.8 - - - -
179A THR* 3.0 23.5 + - - +
182A LYS 4.2 0.9 + - - -
183A GLU* 1.3 78.6 - - - +
185A ARG* 1.3 68.2 + - - +
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Residues in contact with ARG 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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119A VAL 4.5 0.4 + - - -
120A TRP* 2.8 73.4 + - + +
123A GLY* 3.9 17.0 - - - -
124A VAL 5.8 2.7 + - - -
177A LYS* 3.5 6.4 - - - +
178A VAL* 2.9 43.5 + - + +
183A GLU* 3.3 25.9 + - - +
184A SER* 1.3 79.8 - - - +
186A SER* 1.3 66.3 + - - +
187A VAL* 5.0 3.4 - - + -
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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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124A VAL 4.8 0.3 - - - +
125A LYS* 4.5 12.1 - - - +
162A ILE* 5.9 1.9 - - - +
175A THR* 5.0 6.0 - - - +
176A LEU 3.4 8.2 + - - -
177A LYS* 5.4 2.1 - - - +
185A ARG* 1.3 76.5 - - - +
187A VAL* 1.3 66.7 + - - +
188A TYR* 4.5 25.1 - - - -
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Residues in contact with VAL 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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116A TRP* 4.6 6.5 - - + -
119A VAL* 4.1 14.8 - - + -
124A VAL 3.7 17.0 - - - +
125A LYS 3.6 8.5 - - - +
127A ILE* 3.8 32.1 - - + -
175A THR* 4.0 0.2 - - - -
176A LEU* 2.8 46.8 + - + +
178A VAL* 3.8 24.0 - - + -
185A ARG* 4.0 4.4 + - + -
186A SER* 1.3 80.3 - - - +
188A TYR* 1.3 71.1 + - - +
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Residues in contact with TYR 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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125A LYS* 2.9 23.1 + - + +
126A VAL* 3.4 7.0 - - + -
127A ILE* 2.8 34.7 + - - +
163A LYS* 4.8 4.0 - - - -
173A LEU* 4.2 5.8 - - + -
174A ARG 3.5 3.6 - - - +
175A THR* 3.5 40.6 - - + +
186A SER* 4.5 19.6 + - - -
187A VAL* 1.3 77.6 - - - +
189A GLN* 1.3 55.0 + - - +
190A LEU* 5.8 0.2 - - + -
217A LEU* 3.9 59.8 - - + +
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Residues in contact with GLN 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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127A ILE* 3.4 16.8 - - + +
129A MET* 3.4 17.6 - - + +
144A TYR* 3.0 31.5 + - + +
145A TRP* 3.3 25.5 - - - -
172A MET 3.5 1.0 - - - +
173A LEU* 3.4 3.8 - - - +
174A ARG* 2.7 80.4 + - + +
176A LEU* 4.4 15.7 - - + -
187A VAL 4.1 0.6 + - - -
188A TYR* 1.3 75.0 - - - +
190A LEU* 1.3 65.9 - - - +
191A GLN* 4.1 5.2 + - - +
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Residues in contact with LEU 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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126A VAL* 4.4 9.6 - - + -
127A ILE 2.9 9.6 + - - +
128A LEU* 3.5 2.1 - - + -
129A MET* 2.8 32.6 + - - +
167A LEU* 4.7 3.6 - - + -
171A ILE* 3.9 14.1 - - + -
172A MET 3.2 7.6 - - - +
173A LEU* 3.4 39.3 - - + -
189A GLN* 1.3 73.6 - - - +
191A GLN* 1.3 55.1 + - - +
210A MET* 3.2 43.6 - - + +
213A GLU* 4.2 15.7 - - + -
214A ALA* 3.8 24.2 - - + +
217A LEU* 4.5 2.9 - - + -
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Residues in contact with GLN 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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129A MET* 3.3 26.4 - - + +
131A CYS 3.1 26.3 + - - +
132A ARG* 3.8 9.9 - - - +
133A GLU* 4.6 3.4 + - - +
145A TRP* 4.0 8.5 - - - -
170A ASP 3.5 0.5 - - - +
171A ILE* 3.3 6.9 - - - +
172A MET* 3.0 32.2 + - + +
174A ARG* 2.9 34.6 + - - +
189A GLN* 4.1 6.7 - - - +
190A LEU* 1.3 72.8 - - - +
192A TYR* 1.3 62.2 + - - +
193A MET* 3.3 34.2 + - + +
210A MET* 4.3 1.6 - - - -
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Residues in contact with TYR 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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129A MET 2.8 15.6 + - - +
130A ALA* 3.7 22.4 - - - +
131A CYS 3.7 13.9 - - - +
170A ASP* 3.4 11.8 + - + -
171A ILE* 3.6 21.1 - - + -
191A GLN* 1.3 71.0 - - - +
193A MET* 1.3 63.4 + - - +
194A SER* 3.4 34.5 + - - -
195A TRP* 3.6 21.0 + + + -
201A PRO* 3.3 14.1 - - + +
202A SER* 4.2 0.2 - - - -
203A SER* 2.9 42.3 + - - -
206A HIS* 3.9 8.7 - - + -
207A MET* 3.7 26.0 - - + -
210A MET* 3.9 19.4 - - + +
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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