Contacts of the strand formed by residues 139 - 149 (chain F) in PDB entry 4PJE
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 LYS 139 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161E MET* 4.0 13.7 - - + -
164E MET* 4.7 12.8 - - - -
166E PHE* 3.7 53.0 - - + -
133F GLU* 3.6 5.1 - - - -
134F ILE* 3.4 24.3 + - - -
137F THR* 3.1 31.1 + - - +
138F GLN* 1.3 82.3 - - - +
140F ALA* 1.3 61.4 + - - +
194F ARG* 3.6 22.4 - - - +
195F VAL 3.5 11.0 - - - +
196F SER* 4.9 1.6 - - - -
197F ALA 3.8 2.2 - - - +
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Residues in contact with ALA 140 (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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129F PRO* 3.6 24.9 - - + -
133F GLU* 3.7 3.4 - - - -
134F ILE* 3.9 8.3 - - + -
139F LYS* 1.3 74.7 - - - +
141F THR* 1.3 61.8 + - - +
142F LEU* 3.9 1.0 + - - +
193F LEU 3.7 0.9 - - - +
194F ARG* 3.4 2.2 - - - -
195F VAL* 2.8 43.0 + - + +
196F SER 4.3 2.5 - - - +
197F ALA* 4.5 0.4 - - - -
200F TRP* 3.6 26.7 - - + -
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Residues in contact with THR 141 (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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121E LEU* 3.4 19.8 - - - +
133E LEU* 3.7 24.5 - - + +
135E THR* 5.3 0.5 + - - -
159E LEU* 4.9 2.9 - - + -
170E SER* 5.8 1.3 - - - +
129F PRO* 3.4 14.6 - - - +
133F GLU* 2.6 35.4 + - - +
140F ALA* 1.3 71.0 - - - +
142F LEU* 1.3 70.2 + - - +
143F VAL* 4.5 2.0 - - + -
192F ARG* 3.8 22.7 - - + -
193F LEU 3.5 7.6 - - - +
194F ARG* 3.1 20.7 + - + +
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Residues in contact with LEU 142 (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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126F VAL* 4.1 20.2 - - + -
127F PHE 3.5 6.5 - - - +
128F GLU* 5.2 0.2 - - - -
129F PRO* 3.9 23.6 - - + -
140F ALA 4.4 5.4 - - - +
141F THR* 1.3 75.6 - - - +
143F VAL* 1.3 60.9 + - - +
158F TRP* 3.8 17.7 - - + -
191F SER 4.0 0.2 - - - +
192F ARG* 3.3 4.2 - - - -
193F LEU* 2.8 44.0 + - + +
195F VAL* 4.5 5.6 - - + -
200F TRP* 4.0 19.3 - - + -
207F PHE* 3.8 46.4 - - + -
238F ALA* 4.3 3.8 - - + -
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Residues in contact with VAL 143 (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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121E LEU* 3.7 22.6 - - + +
131E VAL* 4.1 22.4 - - + -
133E LEU* 4.3 10.5 - - + -
172E VAL* 4.1 29.8 - - + -
126F VAL* 3.4 3.8 - - - +
127F PHE* 2.8 43.4 + - + -
141F THR* 4.1 2.9 + - + -
142F LEU* 1.3 78.8 - - - +
144F CYS* 1.3 70.7 + - - +
145F LEU* 4.3 7.2 - - + -
158F TRP* 4.1 2.7 - - - -
190F SER* 4.9 0.7 - - - -
191F SER 3.4 6.7 - - - +
192F ARG* 4.3 11.0 - - + -
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Residues in contact with CYS 144 (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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124F VAL* 3.6 19.7 - - - -
125F ALA 3.4 5.6 - - - -
126F VAL* 4.4 1.3 - - + +
143F VAL* 1.3 74.3 - - - +
145F LEU* 1.4 66.8 + - - +
156F LEU* 4.1 7.5 - - - +
158F TRP* 3.5 13.9 - - + -
189F LEU 3.9 0.6 - - - +
190F SER* 3.3 6.2 - - - -
191F SER* 2.8 36.1 + - - +
209F CYS* 2.0 54.7 - - + -
211F VAL* 4.9 0.2 - - - -
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Residues in contact with LEU 145 (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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131E VAL* 3.7 20.0 - - + -
172E VAL* 4.5 1.8 - - + -
174E TRP* 3.6 54.7 - - + +
123F GLU 3.5 1.6 - - - +
124F VAL* 3.4 3.1 - - - +
125F ALA* 2.9 33.1 + - + +
127F PHE* 3.8 22.0 - - + -
143F VAL* 4.3 7.6 - - + -
144F CYS* 1.4 76.0 - - - +
146F ALA* 1.3 58.8 + - - +
147F THR* 4.0 12.8 + - + +
189F LEU 3.5 1.8 - - - +
190F SER* 3.6 29.2 - - - -
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Residues in contact with ALA 146 (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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122F PRO* 4.0 13.7 - - + -
123F GLU 3.2 6.3 - - - -
124F VAL* 4.4 0.9 - - + -
144F CYS* 4.3 0.4 - - - -
145F LEU* 1.3 70.8 - - - +
147F THR* 1.3 61.4 + - - +
149F PHE* 3.5 13.4 - - + -
156F LEU* 4.7 4.4 - - + +
188F ALA* 3.2 2.6 - - - -
189F LEU* 2.8 43.4 + - + +
211F VAL* 3.9 30.5 - - + -
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Residues in contact with THR 147 (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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174E TRP* 4.3 15.9 - - + +
122F PRO* 3.4 0.7 - - - +
123F GLU* 2.8 51.3 + - - +
145F LEU* 4.1 22.3 + - + -
146F ALA* 1.3 79.3 - - - +
148F GLY* 1.3 64.4 + - - +
149F PHE 3.3 3.6 + - - -
178F GLU* 3.4 13.2 - - - +
187F TYR 3.6 3.6 - - - -
188F ALA* 4.0 10.1 - - + -
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Residues in contact with GLY 148 (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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120F PHE* 3.4 21.3 - - - +
121F PRO 3.9 3.1 - - - +
147F THR* 1.3 70.9 - - - +
149F PHE* 1.3 61.2 + - - +
178F GLU* 3.0 25.0 + - - -
186F ARG* 3.6 16.8 + - - -
187F TYR 2.9 8.2 + - - -
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Residues in contact with PHE 149 (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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120F PHE 3.3 12.1 - - - +
121F PRO 4.0 0.7 - - - -
122F PRO* 3.6 34.3 - - + -
146F ALA* 3.5 23.6 - - + -
147F THR 3.3 0.6 - - - -
148F GLY* 1.3 78.6 - - - +
150F TYR* 1.3 62.9 + - - +
151F PRO 3.6 13.5 - - - -
152F ASP* 3.5 22.0 - - - -
154F VAL* 3.6 33.0 - - + -
175F PRO* 3.9 13.2 - - + -
186F ARG* 3.5 0.9 - - - -
187F TYR* 2.8 74.4 + - + -
189F LEU* 3.9 11.9 - - + -
213F PHE* 4.5 3.1 - + + -
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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