Contacts of the strand formed by residues 157 - 164 (chain F) in PDB entry 5MS0
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 ARG 157 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E LEU 5.6 0.9 - - - +
103E GLY* 6.3 2.0 - - - -
150F GLU 4.6 0.7 - - - +
151F VAL* 4.7 0.3 - - - -
152F ASP* 3.2 36.1 + - + +
155F LYS* 4.3 10.8 - - + +
156F SER* 1.3 78.8 - - - +
158F LEU* 1.3 61.5 + - - +
159F LYS 4.2 0.4 + - - -
172F GLU* 4.4 19.3 - - + -
173F LEU 3.4 8.3 - - - +
174F ASP* 5.4 0.2 - - - -
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Residues in contact with LEU 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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148F VAL* 3.9 19.3 - - + -
150F GLU 4.9 1.1 - - - -
151F VAL* 5.7 0.9 - - - +
152F ASP 5.5 0.2 - - - +
157F ARG* 1.3 75.1 - - - +
159F LYS* 1.3 58.0 + - - +
160F VAL* 3.1 11.2 + - + +
171F VAL 3.3 0.2 - - - +
172F GLU* 3.9 0.9 - - - -
173F LEU* 2.5 44.3 + - + +
174F ASP 4.9 6.3 - - - +
175F PHE* 6.0 1.1 - - - -
178F VAL* 5.9 5.2 - - + -
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Residues in contact with LYS 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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147F VAL 2.9 15.0 - - - +
148F VAL* 3.3 11.7 - - - +
149F GLU* 3.4 5.9 + - + +
150F GLU* 4.1 26.0 + - + +
157F ARG 4.2 0.6 - - - -
158F LEU* 1.3 66.8 - - - +
160F VAL* 1.3 59.6 + - - +
161F SER* 5.3 0.3 - - - -
170F PRO* 5.0 9.8 - - + +
171F VAL 3.2 10.1 - - - +
172F GLU* 3.8 11.9 - - + +
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Residues in contact with VAL 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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134F VAL* 6.2 3.1 - - + -
145F ASN* 5.3 3.1 - - - -
146F GLY 4.9 10.1 - - - +
147F VAL 3.4 11.7 - - - +
148F VAL* 4.9 1.8 - - + +
158F LEU* 3.1 9.1 + - + +
159F LYS* 1.3 71.3 - - - +
161F SER* 1.3 57.2 + - - +
162F VAL* 3.5 2.9 + - - +
169F THR 3.1 3.5 - - - +
170F PRO* 3.9 0.4 - - - -
171F VAL* 2.4 52.2 + - + +
173F LEU* 5.2 7.0 - - + -
178F VAL* 6.2 3.1 - - + -
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Residues in contact with SER 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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131F GLY* 4.9 1.7 - - - -
145F ASN 2.9 13.7 - - - +
146F GLY* 3.3 6.8 - - - -
147F VAL* 3.4 19.0 + - - +
159F LYS 3.9 0.8 + - - -
160F VAL* 1.3 68.7 - - - +
162F VAL* 1.3 64.1 + - - +
163F SER* 3.6 2.4 + - - -
168F ALA* 4.4 16.4 - - - +
169F THR 3.4 5.8 - - - -
170F PRO* 3.7 15.7 - - - -
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Residues in contact with VAL 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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141F PHE* 4.9 12.1 - - + -
144F PHE* 4.6 16.4 - - + -
145F ASN 3.3 11.4 - - - +
160F VAL 3.5 3.4 + - - +
161F SER* 1.3 70.1 - - - +
163F SER* 1.3 59.8 + - - +
164F ILE* 3.2 9.5 + - + +
167F ARG 3.0 4.3 - - - +
168F ALA* 4.2 0.9 - - - -
169F THR* 2.6 50.0 + - - +
171F VAL* 5.9 2.5 - - + -
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Residues in contact with SER 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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130F PRO* 4.1 38.3 - - - +
131F GLY* 4.5 3.5 - - - +
144F PHE* 5.8 1.6 - - - +
145F ASN 3.9 4.2 + - - +
161F SER 3.6 4.3 + - - -
162F VAL* 1.3 69.6 - - - +
164F ILE* 1.3 59.0 + - - +
165F PHE 4.1 0.9 + - - -
166F GLY* 4.5 5.3 + - - -
167F ARG 3.3 15.9 - - - -
168F ALA* 4.4 3.4 - - - +
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Residues in contact with ILE 164 (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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162F VAL* 3.2 10.6 + - + +
163F SER* 1.3 71.6 - - - +
165F PHE* 1.3 66.7 + - + +
166F GLY 3.2 2.2 - - - -
167F ARG* 2.9 30.3 + - - +
169F THR* 5.5 5.6 - - - -
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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