Contacts of the strand formed by residues 192 - 203 (chain F) in PDB entry 4GDF
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 HIS 192 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131F LYS 6.1 1.6 - - - -
134F ASP* 4.4 7.7 + - - -
135F PRO* 4.0 29.1 - - + +
162F TYR* 4.1 8.9 + - + -
163F THR 3.2 9.9 - - - +
164F THR* 3.9 17.9 - - + +
165F LYS* 4.7 3.7 + - - +
188F ASN* 3.5 2.4 - - - +
189F SER 2.6 39.2 + - - +
190F TYR 2.9 20.9 + - - -
191F ASN* 1.3 92.9 + - + +
193F ASN* 1.3 66.6 + - - +
220F PHE* 3.5 24.5 - + + -
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Residues in contact with ASN 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162F TYR* 3.1 22.5 - - - -
163F THR 3.1 14.6 + - - +
164F THR 3.9 6.3 - - - +
165F LYS* 3.4 26.1 - - - +
168F ALA* 3.3 21.8 - - + -
186F ARG* 2.5 37.9 + - + -
187F HIS 3.0 16.0 + - - -
188F ASN* 3.7 5.3 + - - -
192F HIS* 1.3 81.3 + - - +
194F ILE* 1.3 65.2 + - - +
244F ILE* 3.3 15.0 - - - +
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Residues in contact with ILE 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138F PHE* 3.9 27.1 - - + -
139F PRO* 4.1 5.6 - - + -
142F LEU* 4.2 12.1 - - + -
160F ALA* 5.0 1.1 - - + -
161F ILE 3.3 9.2 - - - +
162F TYR* 3.3 19.7 - - + -
168F ALA* 5.6 0.2 - - - -
185F SER 3.7 0.9 - - - +
186F ARG* 3.4 4.3 - - - -
187F HIS* 2.8 43.0 + - + +
189F SER* 3.5 27.4 - - - +
193F ASN* 1.3 83.6 - - - +
195F LEU* 1.3 70.0 + - - +
232F MET* 4.9 3.8 - - + -
236F LEU* 4.1 27.1 - - + -
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Residues in contact with LEU 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159F PHE 3.8 0.5 - - - +
160F ALA* 3.0 8.8 - - - +
161F ILE* 2.8 48.8 + - + +
163F THR* 6.1 0.4 - - + +
168F ALA* 3.5 21.1 - - + +
171F LEU* 3.4 39.9 - - + +
172F TYR* 3.7 34.3 - - + +
175F ILE* 4.6 7.4 - - + -
184F ILE* 4.3 7.9 - - + -
185F SER 3.6 14.4 - - - +
186F ARG* 3.9 11.2 - - + -
194F ILE* 1.3 74.4 - - - +
196F PHE* 1.3 59.4 + - - +
197F PHE* 4.2 9.6 - - + -
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Residues in contact with PHE 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158F CYS* 3.6 26.7 - - - -
159F PHE 3.6 7.9 - - - -
160F ALA* 5.1 1.6 - - + -
183F PHE* 4.0 18.8 - + - -
184F ILE* 3.3 1.0 - - - +
185F SER* 2.8 43.6 + - - +
194F ILE* 4.0 0.4 + - + -
195F LEU* 1.3 74.3 - - - +
197F PHE* 1.3 66.8 + - - +
198F LEU* 3.6 20.2 - - + -
226F VAL* 4.2 1.8 - - + -
229F GLU 3.7 14.6 - - - -
232F MET* 3.3 42.8 - - + -
233F TYR* 4.1 10.3 - + + -
236F LEU* 3.9 21.1 - - + -
252F LEU* 3.8 17.7 - - + -
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Residues in contact with PHE 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157F ALA 3.9 0.2 - - - +
158F CYS* 3.6 3.5 - - - -
159F PHE* 3.1 71.8 + + + -
161F ILE* 4.2 22.9 - - + -
175F ILE* 3.9 27.4 - - + -
179F TYR* 5.2 0.4 - + - -
181F VAL* 3.9 17.7 - - + -
183F PHE 3.2 8.1 - - - +
184F ILE* 3.3 24.5 - - + -
195F LEU* 4.2 11.0 - - + -
196F PHE* 1.3 85.0 - - - +
198F LEU* 1.3 64.1 - - - +
199F THR* 4.0 11.2 - - + -
208F ILE* 4.0 23.6 - - + -
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Residues in contact with LEU 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157F ALA* 3.2 9.2 - - + +
158F CYS* 3.5 33.4 - - + -
181F VAL* 3.1 8.1 - - - +
182F THR* 2.8 48.7 + - + +
183F PHE* 2.7 12.6 + - + +
196F PHE* 3.6 21.1 - - + -
197F PHE* 1.3 73.1 - - - +
199F THR* 1.3 58.5 + - - +
229F GLU* 4.6 5.4 - - + +
252F LEU* 3.6 28.9 - - + -
256F ASP 5.5 0.4 - - - +
257F PHE* 3.7 23.6 - - - +
258F ASN* 5.8 0.2 - - - -
259F PRO* 5.9 2.5 - - + -
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Residues in contact with THR 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157F ALA* 2.9 36.6 + - - +
159F PHE* 3.7 7.9 - - + -
179F TYR* 3.9 24.9 - - + -
181F VAL* 4.1 2.2 - - + +
182F THR* 4.2 3.4 - - - +
197F PHE* 4.0 25.6 - - + -
198F LEU* 1.3 77.7 - - - +
200F PRO* 1.3 65.5 - - - +
201F HIS 2.9 29.9 + - - -
203F HIS* 4.0 12.6 - - + -
208F ILE* 5.3 0.2 - - + -
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Residues in contact with PRO 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157F ALA* 5.3 0.7 - - - -
179F TYR 3.4 14.6 - - - +
180F SER* 3.2 34.3 - - - +
181F VAL* 3.8 4.5 - - - -
182F THR* 3.7 19.3 - - + -
199F THR* 1.3 81.5 - - - +
201F HIS* 1.3 78.1 + - + +
261F GLU* 3.1 30.4 - - - +
262F ALA 4.9 0.4 + - - +
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Residues in contact with HIS 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156F LEU 4.4 0.2 - - - -
157F ALA* 4.4 1.8 - - - -
199F THR* 2.9 22.9 + - - -
200F PRO* 1.3 104.1 + - + +
202F ARG* 1.3 63.5 + - - +
203F HIS* 3.2 21.9 + - + +
261F GLU* 3.0 31.3 - - + +
262F ALA 3.5 24.1 + - - -
264F GLU* 3.5 41.7 + - + +
265F THR 5.6 0.2 - - - -
17G C 6.1 0.7 - - - +
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Residues in contact with ARG 202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155F THR* 3.4 23.2 + - - +
156F LEU* 3.0 22.4 - - - +
157F ALA* 4.2 5.4 - - + +
201F HIS* 1.3 72.1 - - - +
203F HIS* 1.3 76.9 + - - +
261F GLU* 3.8 25.0 + - - +
16G G 3.9 14.4 - - - +
17G C 3.4 39.5 + - - +
18G T 3.1 48.1 + - - +
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Residues in contact with HIS 203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155F THR* 3.8 6.3 - - - -
156F LEU 2.9 16.6 + - - -
159F PHE* 3.0 27.4 - + + -
179F TYR* 3.3 38.0 + + - +
199F THR* 3.9 18.6 - - + -
201F HIS* 3.2 32.6 + - + +
202F ARG* 1.3 80.5 + - - +
204F ARG* 1.3 61.6 + - - +
205F VAL 3.6 0.3 + - - -
207F ALA* 4.8 1.8 - - + -
208F ILE* 3.9 16.8 - - + -
16G G 2.6 33.2 + - - +
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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