Contacts of the strand formed by residues 137 - 145 (chain P) in PDB entry 1HH2
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 VAL 137 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136P THR* 1.3 85.0 + - - +
138P THR* 1.3 64.9 + - - +
179P LYS* 3.4 34.1 - - + -
180P VAL 3.2 14.6 - - - +
181P TYR* 4.2 13.9 - - + -
203P PHE* 4.0 11.7 - - + +
206P GLY* 3.4 32.8 - - - +
207P LEU* 4.0 7.4 - - + +
210P LEU* 3.8 29.4 - - + +
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Residues in contact with THR 138 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133P LEU* 5.3 12.2 - - + +
136P THR* 5.3 2.7 - - - -
137P VAL* 1.3 76.4 - - - +
139P THR* 1.3 81.4 + - - +
154P ILE* 4.1 25.6 - - + +
179P LYS* 3.4 6.9 - - - +
180P VAL* 3.0 46.0 + - + +
182P ILE* 4.1 13.9 - - + -
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Residues in contact with THR 139 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138P THR* 1.3 91.3 + - - +
140P ALA* 1.3 73.5 + - - +
153P ARG 4.5 0.3 - - - +
154P ILE* 4.3 7.8 - - - +
177P LEU* 4.0 24.5 - - + -
178P VAL 3.4 12.3 - - - +
179P LYS* 2.9 27.0 - - + -
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Residues in contact with ALA 140 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139P THR* 1.3 79.3 - - - +
141P GLU* 1.3 61.3 + - - +
142P VAL 4.0 0.2 + - - -
152P ILE* 3.6 31.2 - - + -
153P ARG 3.1 13.9 - - - +
154P ILE* 3.6 11.0 - - + +
177P LEU* 3.4 6.4 - - - -
178P VAL* 2.9 37.4 + - + +
180P VAL* 4.2 6.7 - - + -
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Residues in contact with GLU 141 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140P ALA* 1.3 73.1 - - - +
142P VAL* 1.3 83.6 + - - +
143P ILE* 3.4 8.3 + - + +
152P ILE* 2.9 5.8 - - - -
153P ARG* 2.5 76.6 + - + +
175P GLY* 3.3 24.5 - - - +
176P ASP 4.0 1.8 - - - -
177P LEU* 3.9 17.7 - - + -
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Residues in contact with VAL 142 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141P GLU* 1.3 73.8 + - - +
143P ILE* 1.3 60.4 + - - +
144P ARG 4.2 8.3 - - - +
145P VAL* 4.4 4.3 - - + -
150P ALA* 4.5 2.2 - - + -
151P ASP 3.8 9.2 - - - +
152P ILE* 3.9 10.1 - - + -
172P ILE* 3.6 28.3 - - + -
173P LYS 3.4 26.5 - - - +
174P ALA* 3.4 5.1 - - - +
175P GLY 2.7 28.6 + - - -
176P ASP* 3.0 28.1 + - + +
178P VAL* 3.8 23.6 - - + -
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Residues in contact with ILE 143 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141P GLU* 3.8 17.9 - - + +
142P VAL* 1.3 74.6 - - - +
144P ARG* 1.3 93.1 + - + +
151P ASP* 2.7 20.0 + - - +
153P ARG* 3.6 34.8 - - + +
158P GLU* 3.3 31.0 - - + +
174P ALA* 4.9 0.4 - - - -
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Residues in contact with ARG 144 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142P VAL* 3.6 2.8 + - - -
143P ILE* 1.3 107.4 + - + +
145P VAL* 1.3 63.1 + - - +
146P MET* 3.9 18.7 - - - +
150P ALA* 3.8 0.9 - - - +
151P ASP* 3.0 46.4 + - - +
158P GLU* 5.8 3.2 + - - -
174P ALA* 3.4 28.0 - - + +
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Residues in contact with VAL 145 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142P VAL* 4.4 5.2 - - + -
144P ARG* 1.3 78.8 - - - +
146P MET* 1.3 66.9 + - - +
147P GLY* 3.8 12.6 - - - +
149P TRP 3.7 7.4 - - - +
150P ALA* 3.9 9.2 - - + +
163P LYS* 6.2 0.2 - - - +
166P TRP* 4.7 12.8 - - + -
172P ILE 3.7 25.8 - - - +
173P LYS* 3.7 16.6 - - - -
174P ALA* 3.9 5.4 - - + +
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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