Contacts of the strand formed by residues 202 - 209 (chain F) in PDB entry 3WBR
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 GLN 202 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101D MET* 3.4 8.5 - - - +
200D VAL* 3.8 9.1 - - - +
201D PRO* 2.8 28.0 - - - +
202D GLN* 3.3 1.7 - - - +
100F GLY 3.4 1.2 - - - +
101F MET* 3.2 7.9 - - - -
102F GLN 2.9 28.5 + - - +
107F SER* 4.2 3.6 + - - -
139F SER* 2.8 36.3 + - - +
141F PHE* 3.6 31.6 - - + +
182F ILE* 3.4 23.3 - - + +
196F ILE* 5.1 2.0 - - + -
200F VAL* 3.5 4.7 + - + +
201F PRO* 1.3 87.8 - - - +
203F LYS* 1.3 72.8 + - - +
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Residues in contact with LYS 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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99D THR 4.6 5.1 + - - -
101D MET* 4.0 12.4 - - - +
203D LYS* 4.2 25.9 - - - +
98F SER 3.5 8.3 - - - +
99F THR* 3.4 36.0 + - - +
100F GLY 3.5 6.1 - - - -
101F MET* 3.9 9.9 - - + +
135F LYS* 3.7 15.7 - - - +
137F ASN* 4.9 1.0 + - - +
138F SER* 3.1 35.3 + - - +
139F SER 3.2 13.3 + - - +
140F TYR* 3.1 18.3 - - + -
141F PHE* 2.8 22.7 + - - +
202F GLN* 1.3 79.8 - - - +
204F SER* 1.3 61.2 + - - +
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Residues in contact with SER 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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97F ILE* 3.6 1.9 - - - -
98F SER* 2.7 53.5 + - - +
100F GLY 4.3 2.5 + - - -
107F SER* 3.7 25.1 + - - -
110F ASN* 4.9 1.9 + - - -
118F LEU* 3.7 21.4 - - - +
140F TYR* 3.8 4.3 - - - -
141F PHE* 4.0 7.4 - - - +
203F LYS* 1.3 80.4 - - - +
205F ILE* 1.3 64.7 + - - +
206F CYS* 4.8 3.6 - - - -
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Residues in contact with ILE 205 (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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95F TYR* 4.7 7.6 - - + -
96F PHE 3.5 3.6 - - - +
97F ILE* 3.8 18.8 - - + -
111F CYS* 4.4 0.2 - - - -
118F LEU* 3.4 9.7 - - - +
119F VAL* 2.8 54.3 + - + +
130F ILE* 3.9 18.6 - - + -
134F LEU* 3.6 29.8 - - + -
140F TYR* 3.7 20.9 - - + -
141F PHE 3.7 7.0 + - - +
183F ILE* 3.9 13.7 - - + -
204F SER* 1.3 80.3 - - - +
206F CYS* 1.3 69.1 + - - +
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Residues in contact with CYS 206 (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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87F TRP* 4.2 20.4 - - + -
95F TYR* 3.4 7.8 - - - +
96F PHE* 2.7 48.3 + - + +
98F SER* 4.9 5.4 - - - -
110F ASN* 4.9 3.6 - - - -
111F CYS* 2.0 53.6 - - + -
114F MET* 5.5 1.8 - - - -
116F ALA* 4.3 1.1 - - + -
117F ASP 3.2 5.2 - - - +
119F VAL 4.4 0.4 - - - -
204F SER* 4.8 6.1 - - - -
205F ILE* 1.3 79.0 - - - +
207F LYS* 1.3 61.8 + - - +
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Residues in contact with LYS 207 (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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93F SER* 3.6 23.1 + - - -
94F CYS 3.4 6.1 - - - +
95F TYR* 3.7 15.5 - - + -
116F ALA* 3.4 1.7 - - - +
117F ASP* 2.7 35.4 + - + +
118F LEU 4.9 0.4 - - - +
119F VAL* 3.9 20.0 - - + -
120F VAL* 3.0 27.3 + - + +
122F ASN* 3.2 21.0 - - - +
126F GLU* 2.6 29.9 + - - +
206F CYS* 1.3 76.0 - - - +
208F MET* 1.3 66.4 + - - +
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Residues in contact with MET 208 (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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84F PRO* 4.4 21.3 - - + -
87F TRP* 3.9 21.8 - - + -
93F SER* 3.4 5.3 - - - -
94F CYS* 2.6 62.3 + - + +
114F MET 3.5 25.6 - - - +
115F GLY* 3.4 19.1 - - - +
116F ALA* 3.8 5.2 - - + +
207F LYS* 1.3 80.0 - - - +
209F LYS* 1.3 71.5 + - - +
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Residues in contact with LYS 209 (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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92F SER* 3.1 38.9 + - - +
93F SER* 4.4 7.5 + - - +
94F CYS* 4.7 0.4 - - - -
208F MET* 1.3 85.9 - - - +
210F LYS* 1.3 68.1 + - - +
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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