Contacts of the strand formed by residues 138 - 148 (chain F) in PDB entry 4PJ7
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 138 (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 10.8 - - + -
164E MET* 4.2 22.4 - - - +
166E PHE* 3.7 45.1 - - + +
132F GLU* 3.6 8.5 - - - +
133F ILE* 3.4 22.7 + - - -
136F THR* 3.2 27.1 + - - +
137F GLN* 1.3 81.9 - - - +
139F ALA* 1.3 59.5 + - - +
193F ARG* 3.6 36.1 - - - +
194F VAL 3.4 9.2 - - - +
195F SER* 4.9 1.6 - - - -
196F ALA 4.0 3.4 - - - +
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Residues in contact with ALA 139 (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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128F PRO* 3.7 26.2 - - + -
132F GLU* 3.8 1.3 - - - -
133F ILE* 3.9 9.2 - - + -
138F LYS* 1.3 74.7 - - - +
140F THR* 1.3 61.8 + - - +
141F LEU* 4.0 1.4 + - + +
192F LEU 3.5 2.3 - - - +
193F ARG* 3.3 2.3 - - - -
194F VAL* 2.7 45.3 + - + +
195F SER 4.5 2.0 - - - +
196F ALA* 4.8 0.2 - - - -
199F TRP* 3.8 25.1 - - + -
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Residues in contact with THR 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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121E LEU* 3.4 10.7 - - - +
133E LEU* 3.8 25.1 - - + +
135E THR* 5.3 1.3 + - - +
159E LEU* 5.1 1.8 - - + -
170E SER* 5.9 0.9 - - - +
128F PRO* 3.3 22.8 - - - +
132F GLU* 2.7 34.4 + - - +
139F ALA* 1.3 70.3 - - - +
141F LEU* 1.3 71.2 + - - +
142F VAL* 4.6 1.1 - - + -
191F ARG* 3.9 23.8 - - + -
192F LEU 3.4 4.0 - - - +
193F ARG* 3.1 26.4 + - + +
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Residues in contact with LEU 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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125F VAL* 5.3 4.3 - - + -
126F PHE 3.5 10.1 - - - +
127F GLU* 5.1 0.9 - - - -
128F PRO* 3.8 15.7 - - + -
139F ALA 4.5 1.3 - - - +
140F THR* 1.3 75.3 - - - +
142F VAL* 1.3 61.6 + - - +
157F TRP* 3.8 21.9 - - + -
190F SER 4.0 0.2 - - - +
191F ARG* 3.4 5.2 - - - -
192F LEU* 2.8 42.7 + - + +
194F VAL* 4.4 11.0 - - + -
199F TRP* 4.1 25.1 - - + -
206F PHE* 4.0 44.9 - - + -
237F ALA* 4.2 13.5 - - + -
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Residues in contact with VAL 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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121E LEU* 3.6 26.4 - - + +
131E VAL* 4.0 15.5 - - + -
133E LEU* 4.3 14.1 - - + -
172E VAL* 4.1 23.8 - - + -
125F VAL* 3.3 4.7 - - - +
126F PHE* 2.8 38.5 + - + -
140F THR* 4.6 3.1 - - + -
141F LEU* 1.3 78.6 - - - +
143F CYS* 1.3 64.9 + - - +
144F LEU* 4.0 25.6 - - + -
157F TRP* 4.2 1.8 - - - -
189F SER* 5.0 0.9 - - - -
190F SER 3.4 6.5 - - - +
191F ARG* 4.4 6.5 - - + -
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Residues in contact with CYS 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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123F VAL* 3.8 19.1 - - - -
124F ALA 3.5 6.1 - - - -
125F VAL* 4.3 0.9 - - + -
142F VAL* 1.3 74.3 - - - +
144F LEU* 1.4 64.8 + - - +
145F ALA 4.2 0.2 - - - -
155F LEU* 4.4 7.5 - - - +
157F TRP* 3.5 15.5 - - + -
188F LEU 3.7 0.7 - - - +
189F SER* 3.2 8.3 - - - -
190F SER* 2.9 34.5 + - - +
208F CYS* 2.0 50.5 - - + -
210F VAL* 5.0 0.7 - - - -
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Residues in contact with LEU 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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129E LYS* 3.8 14.7 - - + -
131E VAL* 3.8 11.0 - - + -
172E VAL* 4.2 2.5 - - + -
174E TRP* 3.5 49.1 - - + -
122F GLU 3.2 4.5 - - - +
123F VAL* 3.4 1.1 - - - -
124F ALA* 3.0 31.8 + - + +
126F PHE* 3.8 26.2 - - + -
142F VAL* 4.0 12.1 - - + -
143F CYS* 1.4 77.2 - - - +
145F ALA* 1.3 59.1 + - - +
146F THR* 3.9 12.8 + - + -
188F LEU 3.4 2.0 - - - +
189F SER* 3.6 27.1 - - - -
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Residues in contact with ALA 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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121F PRO* 4.1 14.1 - - + -
122F GLU 3.1 7.0 - - - -
123F VAL* 4.5 1.6 - - + +
143F CYS* 4.2 0.6 - - - -
144F LEU* 1.3 71.0 - - - +
146F THR* 1.3 60.0 + - - +
148F PHE* 3.7 12.8 - - + -
153F VAL* 5.8 0.2 - - + -
155F LEU* 4.8 4.2 - - + +
187F ALA* 3.2 2.8 - - - -
188F LEU* 2.7 47.1 + - + +
210F VAL* 4.1 29.2 - - + -
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Residues in contact with THR 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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129E LYS* 3.4 35.8 + - - -
174E TRP* 3.9 17.7 - - + +
120F PRO 4.3 0.3 - - - +
121F PRO* 3.4 1.6 - - - +
122F GLU* 2.7 50.8 + - - +
144F LEU* 4.2 9.0 + - + -
145F ALA* 1.3 78.4 - - - +
147F GLY* 1.3 62.9 + - - +
148F PHE* 3.4 3.1 - - - -
177F GLU* 3.6 15.5 - - - +
186F TYR 3.5 4.7 - - - -
187F ALA* 3.9 11.2 - - + -
188F LEU 5.1 0.2 - - - +
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Residues in contact with GLY 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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119F PHE* 3.2 12.6 - - - +
120F PRO 3.8 5.0 - - - +
122F GLU* 5.8 0.2 - - - -
146F THR* 1.3 74.7 - - - +
148F PHE* 1.3 57.8 + - - +
177F GLU* 3.4 20.6 + - - -
185F ARG* 2.8 40.2 + - - -
186F TYR 2.9 7.2 + - - -
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Residues in contact with PHE 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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119F PHE 3.3 12.8 - - - +
120F PRO 4.0 0.4 - - - -
121F PRO* 3.6 36.3 - - + -
145F ALA* 3.7 22.4 - - + -
146F THR 4.2 0.7 - - - -
147F GLY* 1.3 78.4 - - - +
149F TYR* 1.3 61.6 + - - +
150F PRO 3.4 19.1 - - - -
151F ASP* 3.8 15.0 - - - -
153F VAL* 3.6 38.1 - - + -
174F PRO* 4.0 12.6 - - + -
185F ARG* 3.4 1.1 - - - -
186F TYR* 2.7 79.8 + - + -
187F ALA 4.0 0.7 - - - -
188F LEU* 4.0 9.2 - - + -
212F PHE* 4.3 2.0 - + + -
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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