Contacts of the strand formed by residues 138 - 144 (chain A) in PDB entry 4RA2
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 HIS 138 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A VAL* 4.3 11.1 - - + +
133A LEU 3.8 0.7 - - - +
134A ILE* 3.5 1.9 - - - -
135A SER* 2.8 38.4 + - - +
137A GLN* 1.3 105.6 - - + +
139A THR* 1.3 60.4 + - - +
140A TYR* 3.5 31.3 + - + -
223A ASP* 2.7 37.7 + - - +
224A ILE 3.5 3.1 - - - -
225A GLU* 3.8 25.3 + - + +
226A ARG* 3.7 7.2 - - - +
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Residues in contact with THR 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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132A VAL* 5.2 1.6 - - - -
133A LEU 3.7 3.6 - - - -
134A ILE* 4.3 14.1 - - + +
138A HIS* 1.3 73.7 - - - +
140A TYR* 1.3 60.6 + - - +
141A PHE* 3.7 19.6 + - - -
151A LEU* 5.0 4.4 - - + +
222A HIS 3.4 2.3 - - - +
224A ILE* 2.8 49.8 + - - +
226A ARG* 3.6 24.2 - - + -
231A ASP* 4.9 3.6 - - - +
234A ILE* 4.4 5.8 - - + -
291A PHE* 4.0 22.2 - - + -
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Residues in contact with TYR 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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53A TRP* 5.0 4.5 - + - -
92A PRO 5.3 1.6 + - - -
93A SER 5.0 0.5 - - - -
94A VAL* 3.9 21.9 + - + +
97A VAL* 3.6 45.9 - - + +
98A LYS* 4.9 1.6 - - + -
101A ILE* 4.5 5.2 - - + -
132A VAL* 3.2 5.0 - - - +
133A LEU* 2.8 57.9 + - + +
135A SER* 4.1 14.5 + - - -
138A HIS* 3.5 34.0 + - + -
139A THR* 1.3 71.3 - - - +
141A PHE* 1.3 63.6 + - - +
142A ILE* 3.7 2.9 + - - +
221A VAL* 4.5 16.8 - - + -
222A HIS 3.3 5.4 - - - +
223A ASP* 3.9 31.0 - - + -
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Residues in contact with PHE 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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130A VAL* 5.7 0.2 - - + -
131A GLY 3.6 5.6 - - - -
132A VAL* 3.5 27.1 - - + -
139A THR* 4.0 14.4 - - - -
140A TYR* 1.3 73.7 - - - +
142A ILE* 1.3 59.5 + - - +
149A GLY* 3.9 5.4 - - - -
150A LEU* 3.8 29.8 - - - -
151A LEU* 3.7 26.5 - - + -
159A PHE* 3.5 29.8 - + + -
161A THR* 3.9 14.1 - - + -
220A GLU 3.6 1.2 - - - +
221A VAL* 3.2 7.4 - - - +
222A HIS* 2.8 33.8 + - + +
224A ILE* 3.7 31.0 - - + -
234A ILE* 4.1 11.0 - - + -
236A LEU* 4.6 1.6 - - + -
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Residues in contact with ILE 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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55A PHE* 4.1 24.7 - - + -
79A ILE* 4.7 4.9 - - + -
101A ILE* 3.7 42.4 - - + -
105A PHE* 3.6 35.7 - - + -
129A ALA 5.5 0.9 - - - +
130A VAL* 3.3 8.9 - - - +
131A GLY 2.8 40.6 + - - +
133A LEU* 4.4 10.5 - - + +
140A TYR 3.8 10.3 - - - +
141A PHE* 1.3 79.2 - - - +
143A ASN* 1.3 64.9 + - - +
161A THR* 5.0 0.7 - - - -
219A PRO* 4.1 6.1 - - + -
220A GLU 3.5 3.4 - - - +
221A VAL* 4.5 1.3 - - + -
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Residues in contact with ASN 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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129A ALA 3.7 2.7 + - - -
130A VAL* 3.4 20.6 - - - +
142A ILE* 1.3 77.0 - - - +
144A CYS* 1.3 64.6 + - - +
145A GLY 3.1 20.5 + - - +
147A SER 3.2 23.9 + - - -
161A THR* 3.9 25.9 + - + -
162A GLN 3.3 18.1 - - - +
164A HIS* 3.2 14.7 + - + -
219A PRO* 3.4 2.4 - - - +
220A GLU* 2.8 44.3 + - + +
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Residues in contact with CYS 144 (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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105A PHE* 3.5 27.6 - - + -
128A THR* 3.2 5.7 - - - -
129A ALA 2.8 36.1 + - - +
143A ASN* 1.3 75.4 - - - +
145A GLY* 1.3 58.4 + - - +
164A HIS* 3.7 4.5 - - - -
195A ARG* 3.9 8.4 - - - +
196A ALA* 3.7 30.7 - - - -
197A LEU* 4.6 1.6 - - - -
217A PRO* 3.8 25.8 - - - -
218A GLU 4.1 3.1 - - - -
219A PRO* 4.3 2.9 - - + -
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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