Contacts of the strand formed by residues 197 - 204 (chain F) in PDB entry 3Q3G
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 SER 197 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155F LYS 4.4 0.4 - - - -
156F ILE* 3.5 5.2 - - - +
157F ASP* 2.7 50.5 + - - +
158F GLY 5.1 2.2 - - - -
196F ASN* 1.3 74.8 - - - +
198F TYR* 1.3 61.2 + - - +
199F THR* 4.4 5.5 - - - +
214F SER* 3.3 20.1 + - - -
215F PHE 3.5 4.4 + - - -
216F ASN* 3.5 20.5 + - - +
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Residues in contact with TYR 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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123F ILE* 3.7 7.3 - - + +
138F VAL* 4.4 8.7 - - + -
154F TRP* 5.1 1.1 - + + -
155F LYS 3.4 2.9 - - - -
156F ILE* 3.7 34.8 - - + -
185F LEU* 4.2 11.0 - - + -
187F LEU* 4.3 9.5 - - + +
191F GLU 3.8 0.2 + - - -
192F TYR* 2.6 59.2 + + - -
195F HIS* 3.5 28.7 + - + +
196F ASN 3.4 17.7 - - - -
197F SER* 1.3 71.6 - - - +
199F THR* 1.3 58.6 + - - +
214F SER* 2.8 19.6 + - - -
215F PHE* 3.0 52.0 + + + -
217F ARG* 4.5 1.1 - - + -
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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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123F ILE* 4.0 1.3 - - - +
153F LYS 3.8 0.3 - - - +
154F TRP* 3.3 11.7 - - - -
155F LYS* 2.7 67.5 + - + +
158F GLY* 5.0 8.7 - - - +
197F SER* 4.4 7.4 - - - +
198F TYR* 1.3 78.3 - - - +
200F CYS* 1.3 62.4 + - - +
201F GLU* 4.1 3.2 + - - +
212F VAL* 3.3 24.4 - - + +
213F LYS 3.4 7.6 - - - -
214F SER* 3.5 18.8 - - - +
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Residues in contact with CYS 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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121F VAL* 4.0 10.5 - - - +
123F ILE* 4.0 13.8 - - - +
140F CYS* 2.0 53.6 - - + -
152F VAL* 5.0 5.6 - - + -
153F LYS 3.3 5.8 - - - +
154F TRP* 3.9 16.2 - - + -
199F THR* 1.3 74.8 - - - +
201F GLU* 1.3 60.5 + - - +
202F ALA 4.0 0.6 + - - -
211F ILE 3.7 3.3 - - - +
212F VAL* 3.8 0.2 - - - -
213F LYS* 3.0 36.0 + - - +
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Residues in contact with GLU 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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151F ASN 3.5 0.9 - - - +
152F VAL* 3.3 7.2 - - - +
153F LYS* 2.7 71.1 + - + +
155F LYS* 3.4 32.3 - - + +
199F THR* 4.1 4.9 + - - +
200F CYS* 1.3 73.1 - - - +
202F ALA* 1.3 60.4 + - - +
203F THR* 4.0 3.1 + - - +
210F PRO* 3.3 29.9 - - + +
211F ILE 3.5 2.2 - - - -
212F VAL* 3.6 24.9 - - + +
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Residues in contact with ALA 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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119F PRO* 4.6 9.0 - - + -
121F VAL* 3.8 26.2 - - + -
142F LEU* 3.8 22.9 - - + -
150F ILE* 5.0 1.1 - - + -
151F ASN 3.4 4.0 - - - -
200F CYS 4.0 0.4 + - - -
201F GLU* 1.3 70.6 - - - +
203F THR* 1.3 63.0 + - - +
204F HIS* 4.0 2.2 + - - +
210F PRO* 3.3 5.0 - - - +
211F ILE* 2.7 47.6 + - + +
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Residues in contact with THR 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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150F ILE* 3.6 5.0 - - - +
151F ASN* 2.7 53.1 + - - +
153F LYS* 5.5 8.1 - - - +
201F GLU* 4.4 6.9 + - - +
202F ALA* 1.3 72.1 - - - +
204F HIS* 1.3 63.8 + - - +
207F SER 5.6 3.8 - - - +
208F THR 5.6 3.8 - - - +
210F PRO* 4.1 20.1 - - + +
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Residues in contact with HIS 204 (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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117F ALA 3.2 14.5 + - - -
119F PRO* 4.0 13.1 - - + +
145F PHE* 3.6 5.8 - + + -
146F TYR 2.9 26.4 + - - -
147F PRO* 2.9 29.3 + - + +
149F ASP 3.2 25.1 - - - -
150F ILE* 3.7 24.0 - - + -
202F ALA 4.0 2.9 + - - +
203F THR* 1.3 76.5 - - - +
205F LYS* 1.4 58.3 - - - +
206F THR* 2.8 34.8 + - + +
207F SER* 2.8 31.1 + - - +
210F PRO* 5.8 0.8 - - - +
211F ILE* 5.9 1.6 - - + -
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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