Contacts of the strand formed by residues 136 - 143 (chain A) in PDB entry 1H3Z
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 PHE 136 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A LYS* 3.9 4.2 - - - +
133A MET* 2.7 74.8 + - + +
134A SER 3.7 10.3 - - - -
135A GLY* 1.3 86.2 - - - +
137A PRO* 1.3 79.7 - - + +
139A TRP* 4.0 22.0 - + + -
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Residues in contact with PRO 137 (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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131A THR 4.0 2.1 - - - +
132A LYS* 5.4 0.2 - - + -
135A GLY 4.1 3.6 - - - +
136A PHE* 1.3 95.1 - - + +
138A TRP* 1.3 72.8 + - + +
139A TRP* 2.9 33.9 + - + +
199A LYS 4.5 4.7 - - - +
200A PRO* 3.4 37.5 - - + -
202A THR* 5.1 0.4 - - + -
205A LEU* 4.4 5.2 - - + -
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Residues in contact with TRP 138 (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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130A LEU* 2.8 55.6 - - + +
131A THR 3.7 0.2 - - - -
132A LYS* 2.9 41.5 - - + +
136A PHE 3.8 0.2 + - - -
137A PRO* 1.3 74.8 - - + +
139A TRP* 1.3 59.1 + - - +
181A ASP 4.1 5.2 - - - -
182A SER* 2.7 35.9 - - - -
183A LEU 3.9 2.2 - - - -
184A THR* 3.1 36.6 - - + -
205A LEU* 3.8 10.9 - - - +
209A TYR* 3.8 5.4 + - - -
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Residues in contact with TRP 139 (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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130A LEU* 2.8 6.6 - - - +
131A THR* 2.7 38.1 + - - +
133A MET* 5.9 0.9 - - + -
136A PHE* 4.0 24.0 - + + -
137A PRO* 2.9 34.3 + - + +
138A TRP* 1.3 72.0 - - - +
140A PRO* 1.3 79.5 - - + +
141A SER 2.9 6.6 + - - -
169A PHE* 3.2 39.2 - + + -
170A PHE 2.9 26.5 + - - -
171A PRO* 4.9 0.4 - - - +
202A THR* 3.4 14.8 - - + -
204A SER* 3.7 11.4 + - - -
205A LEU* 3.1 54.5 - - + -
208A ALA* 3.3 4.4 - - - +
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Residues in contact with PRO 140 (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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129A VAL 3.8 2.2 - - - +
130A LEU* 3.1 8.0 - - + -
139A TRP* 1.3 90.8 - - + +
141A SER* 1.3 59.4 + - - +
169A PHE* 3.9 0.7 - - - -
170A PHE* 3.1 29.5 + - - -
186A LEU* 4.0 7.9 - - + -
205A LEU* 3.9 2.9 - - + -
208A ALA* 3.1 36.8 - - + -
209A TYR* 3.5 42.8 - - + +
212A ALA* 4.0 15.0 - - + -
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Residues in contact with SER 141 (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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128A ARG* 4.7 0.9 - - - -
129A VAL* 2.3 48.2 + - - +
131A THR* 2.5 44.5 + - - +
139A TRP 2.9 0.8 + - - -
140A PRO* 1.3 74.5 - - - +
142A MET* 1.3 59.5 + - - +
167A VAL* 3.4 5.3 - - - +
168A ILE 2.9 15.0 - - - -
169A PHE* 3.4 19.1 - - - -
170A PHE* 4.1 2.2 - - - -
186A LEU* 4.7 0.4 - - - +
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Residues in contact with MET 142 (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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126A GLY* 3.4 17.0 - - - -
127A MET 3.0 20.2 - - - +
128A ARG* 4.0 17.5 - - + -
129A VAL 3.9 0.9 - - - +
141A SER* 1.3 74.5 - - - +
143A VAL* 1.3 64.3 + - - +
144A VAL* 3.1 2.1 - - - +
167A VAL* 2.9 5.9 - - - -
168A ILE* 2.7 47.8 + - + -
170A PHE* 3.7 25.5 - - + -
215A THR* 4.1 7.2 - - + +
217A ASP* 3.6 22.0 - - - +
218A LEU* 3.1 36.8 - - - -
221A LEU* 5.1 1.6 - - + -
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Residues in contact with VAL 143 (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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123A TYR* 3.4 35.7 - - + +
124A LYS 3.2 23.6 - - - +
125A PRO* 3.0 5.0 - - + +
126A GLY 2.7 29.8 + - - -
127A MET 3.0 6.2 + - - +
129A VAL* 3.6 26.5 - - + -
142A MET* 1.3 69.6 - - - +
144A VAL* 1.3 67.3 + - - +
165A TYR* 4.7 16.2 - - + -
166A PRO* 3.8 7.0 - - + +
167A VAL* 4.1 7.6 - - + +
183A LEU* 4.6 2.5 - - + -
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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