Contacts of the strand formed by residues 152 - 160 (chain F) in PDB entry 3QS7
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 TYR 152 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144F PHE* 3.5 4.7 - - - +
145F ILE* 2.9 50.9 + - + +
150F THR* 4.2 3.1 - - - -
151F ASN* 1.4 74.4 - - - +
153F THR* 1.4 61.7 + - - +
154F ILE* 5.9 3.4 - - + -
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Residues in contact with THR 153 (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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142F LEU* 6.4 0.2 - - - -
143F LEU 3.7 7.0 - - - -
144F PHE* 4.1 10.5 - - - +
152F TYR* 1.4 76.5 - - - +
154F ILE* 1.4 65.6 + - - +
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Residues in contact with ILE 154 (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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93F VAL* 3.8 19.3 - - + -
95F VAL* 6.0 6.7 - - + -
142F LEU* 3.1 8.5 - - - +
143F LEU* 2.9 64.8 + - + +
145F ILE* 4.3 9.9 - - + -
152F TYR* 5.7 3.4 - - + -
153F THR* 1.4 78.9 - - - +
155F LEU* 1.4 64.6 + - - +
156F PHE* 3.7 26.5 - - + -
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Residues in contact with LEU 155 (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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79F ALA* 4.5 13.0 - - - +
141F TYR 3.7 6.7 - - - +
142F LEU* 4.1 7.4 - - + +
154F ILE* 1.4 79.5 - - - +
156F PHE* 1.3 68.2 + - - +
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Residues in contact with PHE 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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79F ALA* 3.7 17.3 - - - +
81F VAL* 4.5 14.6 - - + -
91F LEU* 5.7 10.8 - - + -
93F VAL* 4.0 33.7 - - + -
105F TRP* 3.7 31.6 - + - -
139F GLY 3.2 4.0 - - - +
140F GLU* 3.7 3.1 - - - -
141F TYR* 2.9 55.5 + - + +
143F LEU* 4.5 3.6 - - + -
154F ILE* 3.7 35.0 - - + -
155F LEU* 1.3 77.8 - - - +
157F THR* 1.4 59.3 + - - +
158F VAL* 3.9 4.7 - - + -
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Residues in contact with THR 157 (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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79F ALA 3.1 12.7 + - - -
80F ALA* 3.8 6.0 - - - +
81F VAL* 2.9 28.4 + - - +
139F GLY 3.7 5.8 - - - -
140F GLU* 5.1 1.3 - - - +
156F PHE* 1.4 70.3 - - - +
158F VAL* 1.4 62.7 + - - +
159F SER* 3.6 2.4 + - - -
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Residues in contact with VAL 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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81F VAL* 3.8 24.9 - - + -
83F VAL* 3.6 29.2 - - + -
91F LEU* 4.7 12.6 - - + -
133F MET* 6.0 0.4 - - + -
137F GLN 4.5 4.7 - - - +
138F ALA* 3.7 25.0 - - + +
139F GLY* 2.9 42.7 + - - +
141F TYR* 3.8 20.9 - - + -
156F PHE* 4.9 5.8 - - + +
157F THR* 1.4 68.8 - - - +
159F SER* 1.3 57.4 - - - +
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Residues in contact with SER 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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81F VAL 2.9 17.4 + - - -
82F GLU* 4.6 2.0 - - - -
83F VAL* 3.0 31.4 + - - +
138F ALA* 5.4 0.4 - - - -
157F THR 3.6 2.9 + - - -
158F VAL* 1.3 73.1 - - - +
160F ILE* 1.3 66.7 + - - +
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Residues in contact with ILE 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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82F GLU* 5.5 2.0 - - - -
83F VAL* 3.3 31.6 - - + +
85F VAL* 5.1 6.1 - - - +
133F MET 4.5 11.2 - - - +
134F THR 4.7 3.1 - - - +
135F GLU* 4.8 11.2 - - + -
137F GLN 5.3 0.9 - - - +
138F ALA* 3.8 26.7 - - + -
158F VAL* 5.1 0.2 - - + -
159F SER* 1.3 84.9 - - - +
161F ARG* 1.4 53.8 + - - +
162F ASN* 2.9 29.0 + - + +
163F THR 4.8 0.2 + - - -
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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