Contacts of the strand formed by residues 214 - 220 (chain A) in PDB entry 4TR8
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 GLU 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A SER* 4.1 12.8 + - - -
130A ILE* 3.4 26.3 + - - -
131A ALA* 3.4 22.4 + - - +
132A GLN* 3.0 17.9 + - - +
210A GLU* 4.8 0.4 + - - +
212A ASP 4.8 4.9 - - - +
213A GLY* 1.3 77.5 - - - +
215A VAL* 1.3 60.9 + - - +
227A THR 4.4 0.4 - - - +
228A THR* 3.9 11.3 - - - +
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Residues in contact with VAL 215 (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 SER* 3.3 4.6 - - - -
130A ILE* 2.8 61.5 + - + +
132A GLN* 3.8 21.8 - - + -
135A LEU* 4.0 10.3 - - + -
208A LEU* 4.0 14.6 - - + -
214A GLU* 1.3 74.2 - - - +
216A GLY* 1.3 72.6 + - - +
217A ILE* 3.9 4.3 + - + -
226A ALA* 3.9 15.3 - - + -
227A THR 3.5 17.7 - - - +
228A THR* 3.7 12.6 - - + -
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Residues in contact with GLY 216 (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 PHE 3.7 5.6 - - - -
129A SER* 4.4 5.8 - - - -
215A VAL* 1.3 71.5 - - - +
217A ILE* 1.4 59.3 + - - +
218A VAL* 5.5 2.5 - - - -
225A ARG 3.6 1.0 - - - +
226A ALA* 3.2 6.8 - - - -
227A THR* 2.8 42.7 + - - -
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Residues in contact with ILE 217 (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 LEU 3.9 0.3 - - - +
127A ASN* 3.2 7.1 - - - +
128A PHE* 2.7 80.8 + - + +
130A ILE* 4.3 12.1 - - + -
135A LEU* 3.6 28.5 - - + -
204A LEU* 5.3 0.4 - - + -
215A VAL* 3.9 6.5 - - + +
216A GLY* 1.4 75.8 - - - +
218A VAL* 1.3 66.1 + - - +
219A LEU* 3.8 20.9 - - + -
224A ILE* 4.2 14.1 - - + -
225A ARG 3.3 4.0 - - - +
226A ALA* 3.7 26.0 - - + -
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Residues in contact with VAL 218 (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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124A GLY* 3.8 26.9 - - - +
126A LEU 3.5 5.6 - - - +
127A ASN* 4.2 15.7 - - + +
216A GLY 5.5 1.8 - - - -
217A ILE* 1.3 78.8 - - - +
219A LEU* 1.3 65.0 + - - +
220A GLY* 3.8 1.6 + - - +
223A HIS 4.6 0.2 - - - -
224A ILE* 3.3 8.3 - - - +
225A ARG* 2.9 74.5 + - + +
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Residues in contact with LEU 219 (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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124A GLY 3.5 0.5 - - - -
125A SER* 2.8 34.4 + - - -
126A LEU* 2.7 45.7 + - + +
128A PHE* 4.2 12.3 - - + -
160A LEU* 5.5 7.4 - - + +
162A VAL* 4.1 16.8 - - + -
167A LEU* 6.0 1.1 - - + -
192A HIS* 4.5 14.1 - - + +
194A VAL* 3.9 33.2 - - + -
217A ILE* 3.8 9.2 - - + -
218A VAL* 1.3 73.2 - - - +
220A GLY* 1.3 55.2 + - - +
223A HIS 4.1 1.6 - - - -
224A ILE* 3.8 30.3 - - + -
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Residues in contact with GLY 220 (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 GLY 5.4 2.0 - - - -
123A PRO 4.0 15.0 - - - -
124A GLY* 4.3 2.9 - - - -
125A SER* 4.1 5.7 - - - -
194A VAL* 4.1 7.3 - - - +
218A VAL* 3.8 3.0 + - - +
219A LEU* 1.3 76.5 - - - +
221A GLN* 1.3 64.0 + - - -
222A HIS 3.3 3.1 - - - -
223A HIS* 2.7 24.1 + - - +
237A LEU* 3.5 9.5 - - - +
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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