Contacts of the strand formed by residues 127 - 133 (chain A) in PDB entry 5IVK
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 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A THR* 3.5 19.5 + - - -
119A ASN* 2.9 32.9 + - - -
120A ASN* 3.9 21.7 + - - +
123A PRO* 4.0 22.5 - - - +
125A THR* 3.8 7.4 - - + +
126A LYS* 1.3 79.2 - - - +
128A PRO* 1.3 76.8 - - + +
157A ASP* 3.1 50.9 + - + +
158A VAL* 3.9 7.8 + - - +
159A VAL* 4.5 5.4 - - + +
206A GLY 2.9 11.3 + - - +
207A GLY* 3.5 2.3 - - - -
208A ASN* 2.7 27.8 + - - +
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Residues in contact with PRO 128 (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 LYS 4.6 1.1 - - - +
127A ARG* 1.3 89.2 - - + +
129A VAL* 1.3 59.0 + - - +
130A LEU* 4.3 4.7 - - + -
157A ASP 3.8 10.8 - - - +
158A VAL* 3.6 11.1 - - + +
159A VAL 3.1 23.7 + - - -
211A ASN* 3.6 18.3 - - + +
508A ALA* 4.2 26.0 - - + +
509A THR* 3.4 35.4 - - + +
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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
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127A ARG 3.7 3.8 - - - +
128A PRO* 1.3 73.5 - - - +
130A LEU* 1.3 58.5 + - - +
131A VAL* 4.1 12.8 - - + -
159A VAL* 3.5 13.0 - - + +
161A ILE* 3.9 27.8 - - + -
198A ILE* 4.2 8.7 - - + -
202A CYS* 4.0 15.7 - - + -
207A GLY* 3.6 31.2 - - - -
208A ASN 3.7 7.6 - - - +
211A ASN 3.0 10.2 + - - +
212A ILE* 3.3 8.5 - - + -
213A THR* 2.7 34.7 + - - +
508A ALA* 5.4 0.2 - - - +
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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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128A PRO* 4.2 3.6 - - + +
129A VAL* 1.3 76.0 - - - +
131A VAL* 1.3 60.7 + - - +
132A TYR 4.1 0.2 - - - -
153A PHE* 4.0 29.8 - - + -
158A VAL* 3.8 31.9 - - + -
159A VAL 2.8 8.7 + - - +
160A LEU* 3.4 13.7 - - + +
161A ILE* 2.9 26.0 + - - +
213A THR* 3.4 11.2 - - + -
215A PHE* 3.9 21.3 - - + -
504A TRP* 4.2 21.8 - - + +
505A THR* 4.7 1.8 - - - +
508A ALA* 3.5 26.5 - - + -
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Residues in contact with VAL 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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129A VAL* 4.1 4.9 - - + -
130A LEU* 1.3 75.8 - - - +
132A TYR* 1.3 64.2 + - - +
133A ILE* 4.9 5.2 - - + -
161A ILE* 3.4 10.1 - - + +
163A ILE* 4.1 12.8 - - + -
195A LEU* 4.0 15.7 - - + -
198A ILE* 3.5 42.4 - - + -
212A ILE* 3.8 26.2 - - + -
213A THR 2.8 11.6 + - - +
214A VAL* 3.5 8.9 - - + +
215A PHE* 2.9 28.9 + - - +
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Residues in contact with TYR 132 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A LEU 4.1 0.4 - - - -
131A VAL* 1.3 72.7 - - - +
133A ILE* 1.3 68.4 + - - +
134A HIS* 3.5 24.8 + - + -
135A GLY 4.5 0.7 + - - -
148A TYR* 3.7 22.1 + + - -
160A LEU* 4.7 1.8 - - + -
161A ILE 2.9 10.9 + - - +
162A ASN* 3.8 25.6 - - + +
163A ILE* 3.4 26.3 + - - +
215A PHE* 3.3 43.6 - + + -
216A GLY* 3.5 15.9 - - - -
217A GLU* 3.3 29.3 + - + +
243A MET* 4.8 3.4 - - - -
475A LEU* 3.6 11.0 - - + +
479A PHE* 3.6 25.1 - + + -
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Residues in contact with ILE 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 VAL* 4.7 3.8 - - + +
132A TYR* 1.3 77.6 - - - +
134A HIS* 1.3 66.8 + - - +
163A ILE* 4.0 20.0 - - + -
165A TYR* 3.7 24.0 - - + -
191A GLN* 3.8 22.7 - - + +
195A LEU* 5.2 4.0 - - + -
214A VAL* 3.7 31.9 - - + -
215A PHE 2.9 7.6 + - - +
216A GLY* 3.2 12.6 - - - -
220A GLY* 3.2 18.8 - - - +
223A SER* 3.6 24.0 - - - -
224A THR* 4.1 8.3 - - - +
227A MET* 4.3 9.6 - - + -
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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