Contacts of the strand formed by residues 135 - 141 (chain X) in PDB entry 3FEW
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 PHE 135 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131X SER* 3.2 3.5 - - - -
132X ILE 2.8 42.8 + - - +
133X ASP* 3.2 19.3 - - + -
134X GLY* 1.3 72.5 - - - +
136X LYS* 1.3 60.7 + - - +
137X TYR* 3.6 22.8 - - + +
152X ARG* 4.2 16.6 - - - -
154X GLY 3.7 5.2 - - - +
155X VAL* 4.2 9.2 - - + -
156X ARG* 3.7 43.5 - - + -
186X PHE* 3.6 42.0 - + - -
193X ARG* 3.3 36.3 - - - -
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Residues in contact with LYS 136 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130X VAL 3.7 3.8 - - - +
131X SER* 4.1 24.1 + - - -
134X GLY* 3.7 11.8 + - - +
135X PHE* 1.3 74.1 - - - +
137X TYR* 1.3 58.8 + - - +
152X ARG* 3.6 2.9 - - - +
153X THR* 2.7 50.3 + - + -
154X GLY* 3.0 23.3 + - - +
155X VAL 5.1 2.7 - - - +
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Residues in contact with TYR 137 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128X ILE 3.7 0.7 - - - +
129X ASP* 3.4 4.4 - - - +
130X VAL* 2.9 38.5 + - + +
132X ILE* 4.2 11.2 - - + -
135X PHE* 3.6 33.1 - - + +
136X LYS* 1.3 73.7 - - - +
138X ARG* 1.3 58.9 + - - +
139X VAL* 4.0 0.9 - - + -
150X ILE* 3.9 28.7 - - + -
151X LEU 3.3 5.4 - - - +
152X ARG* 3.7 28.5 - - + -
153X THR* 4.1 4.2 - - - +
190X GLU* 2.9 38.1 + - - -
193X ARG* 2.9 36.8 + - + +
194X GLN* 4.2 7.9 - - + -
197X ALA* 4.0 17.7 - - + -
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Residues in contact with ARG 138 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127X GLU* 3.5 49.5 + - + +
128X ILE 3.5 4.7 - - - +
129X ASP* 3.5 31.6 + - - +
137X TYR* 1.3 74.0 - - - +
139X VAL* 1.3 60.5 + - - +
140X THR* 4.1 3.4 + - - +
150X ILE* 3.4 2.0 - - - -
151X LEU* 2.7 64.7 + - + +
153X THR* 4.5 15.3 + - - -
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Residues in contact with VAL 139 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126X ARG 3.3 3.5 - - - +
127X GLU* 3.4 2.0 - - - -
128X ILE* 2.8 39.3 + - - +
130X VAL* 4.4 6.5 - - + -
137X TYR* 4.6 0.9 - - + -
138X ARG* 1.3 73.4 - - - +
140X THR* 1.3 71.3 + - - +
141X LEU* 4.2 2.9 - - + -
147X ALA* 3.9 18.6 - - + -
149X GLY 3.4 12.8 - - - +
150X ILE* 3.8 25.6 - - + -
197X ALA* 3.9 25.4 - - + +
198X LYS* 4.2 4.9 - - + +
201X ALA* 3.7 23.8 - - + -
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Residues in contact with THR 140 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126X ARG* 3.3 12.3 - - + +
127X GLU* 4.3 19.1 + - + +
138X ARG* 4.9 4.0 + - - +
139X VAL* 1.3 72.7 - - - +
141X LEU* 1.3 69.6 + - - +
147X ALA* 3.5 4.7 - - - -
148X ILE* 3.0 35.0 + - + -
149X GLY* 3.1 24.3 + - - +
150X ILE* 4.9 0.7 + - - -
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Residues in contact with LEU 141 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125X PRO 4.8 0.7 - - - +
126X ARG* 2.7 38.5 + - - +
128X ILE* 3.8 18.4 - - + -
139X VAL* 4.2 10.1 - - + +
140X THR* 1.3 80.2 - - - +
142X ASN* 1.3 66.2 + - - +
145X GLY* 3.7 17.0 - - - +
146X ARG 3.2 2.7 - - - +
147X ALA* 3.5 31.0 - - + +
148X ILE* 4.2 4.7 - - - +
201X ALA* 3.7 22.4 - - + +
202X GLU* 4.1 7.9 - - + -
205X TRP* 3.7 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