Contacts of the strand formed by residues 128 - 133 (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 ARG 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A GLY 4.4 1.0 + - - -
127A MET* 1.3 83.3 - - - +
129A VAL* 1.3 61.4 + - - +
141A SER 4.2 0.4 - - - -
142A MET* 4.0 21.8 - - + +
170A PHE* 5.8 3.6 - - + -
185A PRO* 4.5 0.2 - - - +
186A LEU* 2.9 51.5 + - + +
187A THR* 5.7 0.4 - - - +
188A SER* 4.2 17.7 + - - +
191A ILE* 4.7 12.8 - - + -
212A ALA* 5.0 4.0 - - + +
215A THR 3.9 11.7 - - - +
216A PRO* 3.1 35.3 + - - +
217A ASP* 3.3 16.4 + - - -
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Residues in contact with VAL 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A TYR* 3.3 31.9 - - + -
127A MET* 3.5 17.0 - - + +
128A ARG* 1.3 80.1 - - - +
130A LEU* 1.3 58.2 + - - +
140A PRO 3.7 0.9 - - - -
141A SER* 2.3 65.1 + - - +
142A MET 4.3 0.4 - - - -
143A VAL* 3.6 16.6 - - + +
167A VAL* 4.8 0.4 - - + -
183A LEU* 3.1 29.6 - - + -
184A THR 3.1 12.6 - - - +
185A PRO* 4.5 1.1 - - + -
186A LEU* 3.3 11.0 - - - +
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Residues in contact with LEU 130 (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* 1.3 73.1 - - - +
131A THR* 1.3 59.2 + - - +
138A TRP* 2.8 45.7 - - + -
139A TRP 2.8 38.1 - - - -
140A PRO* 3.1 4.7 - - + -
182A SER 3.4 0.3 - - - +
183A LEU* 3.5 1.4 - - - -
184A THR* 2.7 46.8 + - + -
185A PRO 5.7 0.2 - - - +
186A LEU* 3.6 21.5 - - + +
190A ALA* 6.3 0.7 - - + -
209A TYR* 3.0 28.0 - - - +
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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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130A LEU* 1.3 71.8 - - - +
132A LYS* 1.3 63.4 + - - +
133A MET* 3.8 1.6 + - - +
137A PRO 4.0 0.3 - - - +
139A TRP* 2.7 31.0 + - - +
141A SER* 2.5 32.6 + - - +
167A VAL* 4.1 3.4 - - + -
169A PHE* 2.6 32.7 - - - -
176A LEU* 4.3 2.2 - - - -
178A THR* 3.2 24.7 - - + -
182A SER 3.5 3.8 - - - -
183A LEU* 2.9 32.3 - - + -
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Residues in contact with LYS 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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131A THR* 1.3 74.0 - - - +
133A MET* 1.3 65.9 + - - +
136A PHE 3.9 3.4 - - - +
137A PRO 4.1 0.2 - - - -
138A TRP* 2.9 63.5 - - + +
176A LEU* 5.9 0.7 - - - +
178A THR* 4.8 2.6 + - - -
181A ASP* 5.3 4.4 + - - +
182A SER* 3.1 44.2 + - - +
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Residues in contact with MET 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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131A THR 3.8 1.7 + - - +
132A LYS* 1.3 79.7 - - - +
134A SER* 1.3 57.7 + - - +
135A GLY 3.1 0.9 + - - -
136A PHE* 2.7 68.6 + - + +
139A TRP* 5.9 0.9 - - + -
169A PHE* 3.9 23.6 - - + -
176A LEU* 3.7 35.4 - - + -
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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