Contacts of the strand formed by residues 153 - 160 (chain A) in PDB entry 5T5W
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 THR 153 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A SER 4.4 0.4 - - - -
152A TRP* 1.3 84.6 - - - +
154A TYR* 1.3 65.3 + - - +
170A THR* 3.3 27.4 - - + +
171A PRO 3.6 8.4 + - - -
172A GLN 5.4 2.8 + - - -
193A GLY* 3.8 0.3 - - - -
194A PHE* 3.0 46.7 + - + +
196A PRO* 3.6 27.1 - - + -
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Residues in contact with TYR 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A PRO* 3.8 23.8 - - + -
131A PHE* 3.9 31.6 + + + -
132A LEU 3.8 0.3 - - - -
133A ALA* 3.3 33.0 + - - +
146A LYS* 3.8 14.0 - - - -
152A TRP* 3.4 32.3 + + - -
153A THR* 1.3 87.4 + - - +
155A ASN* 1.3 59.5 + - - +
170A THR* 3.6 7.4 - - - +
171A PRO* 3.5 24.9 + - + +
173A TYR 3.7 19.3 + - - +
174A ASP* 4.0 19.9 - - + +
191A VAL* 4.1 18.2 - - + -
192A ARG 3.5 8.1 - - - +
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Residues in contact with ASN 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A TYR* 1.3 76.5 - - - +
156A VAL* 1.3 69.2 + - - +
168A GLN* 4.0 12.2 + - - +
169A ILE 3.9 8.8 + - - +
170A THR* 4.3 10.9 + - - -
191A VAL* 3.2 1.9 - - - -
192A ARG* 2.8 82.1 + - + +
194A PHE* 3.8 25.3 - - + -
204A TRP* 3.1 8.3 - - - -
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Residues in contact with VAL 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A MET* 5.5 0.7 - - - -
129A MET* 3.6 29.6 - - + -
131A PHE* 3.5 35.4 - - + -
155A ASN* 1.3 78.6 + - - +
157A GLN* 1.3 68.6 + - - +
158A TYR* 5.1 1.3 - - + -
168A GLN* 3.5 8.2 - - - +
169A ILE* 2.9 48.9 + - + +
171A PRO* 3.6 17.0 - - + -
189A VAL* 5.0 4.3 - - + -
190A GLN 3.3 11.0 - - - +
191A VAL* 4.0 6.5 - - + -
204A TRP* 4.3 0.7 - - - -
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Residues in contact with GLN 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A VAL* 1.3 76.6 - - - +
158A TYR* 1.3 61.6 + - - +
159A TRP* 3.9 5.9 - - + -
166A LYS* 3.3 34.3 - - + +
167A PHE 3.3 5.4 - - - +
168A GLN* 3.0 30.9 + - - +
189A VAL* 3.4 2.6 - - - +
190A GLN* 2.7 63.3 + - + +
204A TRP* 3.6 35.9 + - + +
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Residues in contact with TYR 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A VAL* 5.4 0.7 - - + -
157A GLN* 1.3 75.6 - - - +
159A TRP* 1.3 70.5 + - - +
166A LYS* 3.6 0.7 - - - -
167A PHE* 2.8 77.3 + + + +
168A GLN 4.9 0.2 - - - -
169A ILE* 4.0 24.1 - - + +
178A LEU* 3.7 42.7 - - + +
181A LEU* 4.4 14.9 - - + +
187A TYR* 4.3 18.8 - + + -
188A CYS 3.2 11.9 - - - +
189A VAL* 3.6 18.4 - - + -
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Residues in contact with TRP 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A GLN* 3.9 13.9 - - - -
158A TYR* 1.3 89.6 - - - +
160A LYS* 1.3 84.2 + - - +
161A GLN* 4.1 4.9 - - - +
162A GLY 4.6 3.5 - - - +
163A THR* 4.3 2.2 - - - +
164A ASP* 4.7 9.5 + - - -
165A GLU 3.4 25.4 - - - +
166A LYS* 3.9 34.7 - - + +
167A PHE* 4.6 2.7 - - - -
187A TYR* 3.3 9.1 - - - -
188A CYS* 3.0 64.6 + - + +
190A GLN* 3.8 28.3 - - + -
207A PRO* 4.0 23.8 - - + -
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Residues in contact with LYS 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A TRP* 1.3 76.4 - - - +
161A GLN* 1.3 72.9 + - - +
162A GLY 3.0 0.7 + - - -
163A THR* 2.6 51.5 + - + +
165A GLU 4.9 0.8 + - - -
167A PHE* 5.6 2.8 - - - -
182A GLU* 6.0 4.3 - - + +
185A THR* 3.6 33.0 + - + +
186A THR 3.7 4.9 - - - +
187A TYR* 3.6 21.3 - - + +
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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