Contacts of the strand formed by residues 130 - 138 (chain A) in PDB entry 3HMX
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 LEU 130 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A ILE* 4.4 11.2 - - + -
124A THR* 4.2 6.3 - - - +
126A ILE* 3.6 38.6 - - + +
127A SER* 4.3 2.0 - - - +
128A THR* 3.1 12.3 - - - +
129A ASP* 1.3 74.8 - - - +
131A THR* 1.3 64.8 + - - +
132A PHE* 4.1 29.8 - - + -
167A TYR* 4.0 25.4 - - + +
193A VAL 3.5 12.3 - - - +
194A HIS* 4.0 18.2 - - + -
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Residues in contact with THR 131 (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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5A LYS* 4.7 12.0 + - - -
129A ASP 4.3 4.3 - - - +
130A LEU* 1.3 80.4 - - - +
132A PHE* 1.3 66.0 + - - +
191A ASP 3.6 2.6 - - - +
193A VAL* 3.1 61.8 + - + +
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Residues in contact with PHE 132 (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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5A LYS* 5.2 1.8 + - - -
94A ILE* 5.4 1.6 - - + -
95A LEU* 4.4 14.4 - - + -
122A TRP* 3.6 33.4 - + + -
124A THR* 4.9 3.4 - - + -
130A LEU* 4.1 31.4 - - + -
131A THR* 1.3 80.7 + - - +
133A SER* 1.3 65.7 + - - +
151A ALA* 4.0 22.0 - - + -
167A TYR* 3.8 33.9 - + - -
190A VAL* 4.0 12.8 - - + -
191A ASP 3.3 12.8 - - - -
192A ALA* 3.7 24.5 - - + -
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Residues in contact with SER 133 (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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5A LYS* 4.5 15.5 - - - -
132A PHE* 1.3 79.6 - - - +
134A VAL* 1.3 65.4 + - - +
135A LYS* 2.7 23.8 + - - -
189A MET 3.5 1.6 - - - +
190A VAL* 3.4 4.5 - - - -
191A ASP* 2.9 39.1 + - - -
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Residues in contact with VAL 134 (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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122A TRP* 3.8 27.8 - - + -
133A SER* 1.3 84.3 + - - +
135A LYS* 1.3 68.2 + - - +
148A CYS* 3.9 33.5 - - + +
149A GLY 4.9 7.2 + - - +
151A ALA* 4.7 7.2 - - + +
169A VAL* 4.1 22.7 - - + -
171A CYS* 4.9 0.2 - - - -
188A VAL* 3.8 28.3 - - + -
189A MET 3.4 3.8 - - - +
190A VAL* 4.3 5.4 - - + -
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Residues in contact with LYS 135 (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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133A SER* 2.7 33.1 + - - -
134A VAL* 1.3 78.7 - - - +
136A SER* 1.3 64.7 + - - +
148A CYS* 4.7 3.4 - - - -
188A VAL* 3.8 0.7 - - - -
189A MET* 2.9 80.4 + - + +
191A ASP* 3.4 28.5 + - - +
1C NAG 4.7 9.4 - - - +
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Residues in contact with SER 136 (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 PHE* 4.4 1.8 - - - -
135A LYS* 1.3 79.8 - - - +
137A SER* 1.3 68.1 + - - +
143A PRO 4.3 5.7 - - - +
146A VAL* 3.4 43.4 + - - +
147A THR* 6.2 0.2 - - - +
148A CYS* 4.1 14.2 - - - -
186A ILE* 3.8 10.7 - - - +
187A GLU 2.5 24.7 + - - -
188A VAL* 4.1 8.2 - - - +
189A MET* 4.4 4.2 - - - +
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Residues in contact with SER 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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136A SER* 1.3 83.0 + - - +
138A ARG* 1.3 60.1 + - - +
139A GLY 3.9 13.6 + - - -
141A SER 5.3 0.2 - - - -
142A ASP 4.4 13.2 - - - -
143A PRO* 4.6 10.5 - - - -
144A GLN 5.3 0.2 - - - -
146A VAL* 3.9 12.5 - - - +
186A ILE* 4.7 1.3 - - - -
187A GLU* 3.0 32.3 + - - +
189A MET* 4.7 9.5 - - - +
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Residues in contact with ARG 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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137A SER* 1.3 70.7 - - - +
139A GLY* 1.3 67.1 + - - +
141A SER* 4.2 7.8 + - - +
142A ASP* 3.9 20.6 + - - +
146A VAL* 4.2 4.9 - - + +
173A GLU* 2.8 47.8 + - - +
182A GLU* 2.8 47.5 + - - +
183A SER 5.5 1.1 - - - +
184A LEU* 2.9 48.2 + - + +
185A PRO 3.6 10.8 - - - +
186A ILE* 3.3 29.7 - - + +
206A PHE* 4.3 1.4 - - - -
207A ILE* 4.1 5.5 - - - +
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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