Contacts of the strand formed by residues 155 - 163 (chain F) in PDB entry 4R2G
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 GLY 155 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133F PRO* 3.8 6.1 - - - -
153F ASP 3.6 0.6 + - - -
154F SER* 1.3 76.8 + - - +
156F THR* 1.3 63.7 + - - -
157F TRP* 3.7 4.9 - - - -
172F ILE 3.6 1.6 - - - +
173F ASP* 4.6 1.1 - - - -
174F ILE* 2.9 38.4 + - - +
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Residues in contact with THR 156 (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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131F ARG 4.6 0.7 - - - +
132F SER 4.7 0.3 - - - -
133F PRO* 3.9 18.3 - - - +
155F GLY* 1.3 70.5 - - - -
157F TRP* 1.3 69.1 + - - +
158F THR* 4.0 4.7 + - - -
171F LYS* 4.0 36.3 - - + +
172F ILE 3.5 5.4 - - - +
173F ASP* 2.6 26.5 + - - +
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Residues in contact with TRP 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F LEU* 4.3 22.2 - - + -
116F LEU* 5.5 5.6 - - + -
130F CYS* 4.4 14.4 - - + -
131F ARG 3.5 9.2 - - - -
132F SER* 3.6 32.8 - - - -
133F PRO* 3.6 4.5 - - + +
136F LYS* 5.5 0.4 - - + -
138F ILE* 3.4 33.4 - - + -
146F VAL* 4.8 7.4 - - + -
149F LEU* 5.3 1.3 - - + -
153F ASP* 2.8 50.6 + - + -
155F GLY 3.7 14.1 - - - -
156F THR* 1.3 74.6 - - - +
158F THR* 1.3 61.8 + - - +
159F CYS* 4.0 10.3 - - - -
170F PHE 3.7 1.2 - - - +
171F LYS* 3.2 8.5 - - - +
172F ILE* 2.9 38.5 + - + +
174F ILE* 3.4 25.8 - - + +
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Residues in contact with THR 158 (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 GLN 3.7 2.3 - - - +
131F ARG* 2.9 67.5 + - - +
156F THR* 4.0 5.6 + - - +
157F TRP* 1.3 73.3 + - - +
159F CYS* 1.3 63.0 + - - +
160F THR* 4.1 4.4 + - - +
169F GLU* 4.2 24.5 - - + +
170F PHE 3.9 3.4 - - - +
171F LYS* 3.9 25.9 - - + +
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Residues in contact with CYS 159 (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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100F LEU* 3.9 22.0 - - + -
116F LEU* 3.9 4.7 - - - -
128F VAL* 4.5 1.3 - - + -
129F GLN 3.3 5.2 - - - +
130F CYS* 2.0 42.8 - - - -
157F TRP* 4.8 3.4 - - - -
158F THR* 1.3 73.3 - - - +
160F THR* 1.3 63.4 + - - +
161F VAL 4.1 0.6 + - - -
168F VAL 3.6 0.5 - - - +
169F GLU* 3.2 7.4 - - - +
170F PHE* 2.9 43.1 + - + +
172F ILE* 3.7 26.7 - - - -
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Residues in contact with THR 160 (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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127F SER 3.6 1.7 - - - +
128F VAL* 3.6 2.2 - - - -
129F GLN* 2.9 42.9 + - - +
158F THR* 4.6 5.4 + - - +
159F CYS* 1.3 74.7 + - - +
161F VAL* 1.3 64.1 + - - +
162F LEU* 3.8 2.6 + - + +
167F LYS* 3.8 35.4 - - + -
168F VAL 3.3 9.6 - - - +
169F GLU* 4.1 19.7 + - + +
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Residues in contact with VAL 161 (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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5F LEU* 4.1 1.6 - - - +
98F PHE* 4.1 21.5 - - + -
100F LEU* 3.9 17.7 - - + -
118F LEU* 4.1 9.6 - - + -
126F PRO* 3.9 26.7 - - + -
127F SER 3.3 5.6 - - - +
128F VAL* 4.2 6.1 - - + -
160F THR* 1.3 73.0 - - - +
162F LEU* 1.3 63.1 + - - +
166F LYS 3.9 0.3 - - - +
167F LYS* 3.4 4.5 - - - -
168F VAL* 2.9 43.7 + - + +
170F PHE* 3.6 31.0 - - + -
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Residues in contact with LEU 162 (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 SER 4.5 0.3 - - - +
126F PRO* 3.4 3.8 - - - +
127F SER* 2.9 51.0 + - - +
160F THR* 3.8 3.0 + - + +
161F VAL* 1.3 73.1 - - - +
163F GLN* 1.3 67.4 + - - +
165F GLN* 3.7 15.0 - - + +
166F LYS 3.2 29.6 - - - +
167F LYS* 3.6 24.5 - - + +
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Residues in contact with GLN 163 (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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5F LEU* 4.0 15.3 - - + +
96F LEU* 3.5 25.2 - - + +
98F PHE* 3.6 19.6 - - + -
123F GLY 5.1 0.6 + - - -
124F SER* 3.4 12.6 - - - +
125F SER* 3.1 37.6 + - - +
126F PRO* 3.2 13.6 - - - +
161F VAL* 5.3 0.2 - - + -
162F LEU* 1.3 77.4 - - - +
164F ASN* 1.3 98.7 + - - +
165F GLN 3.3 1.3 - - - -
166F LYS* 2.9 23.9 + - - +
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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