Contacts of the strand formed by residues 127 - 132 (chain A) in PDB entry 4F4I
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 127 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A PHE 3.5 1.0 + - - -
5A ILE* 3.3 26.4 - - + +
6A THR 2.8 24.8 + - - +
125A PRO* 3.2 3.5 - - - +
126A ASP* 1.3 82.1 - - - +
128A THR* 1.3 63.0 + - - +
129A ILE* 4.3 21.3 - - + -
177A ARG* 3.6 20.2 - - - +
179A LYS* 4.5 28.9 - - + -
197A THR* 4.3 8.3 - - + +
198A ILE* 4.3 9.9 - - + -
201A TYR* 3.8 42.0 - - + -
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Residues in contact with THR 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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6A THR* 2.7 25.6 + - - +
8A GLU* 3.8 19.7 - - + -
95A ASP* 4.2 1.1 - - - +
125A PRO* 3.3 6.9 - - - +
127A LEU* 1.3 73.0 - - - +
129A ILE* 1.3 67.7 + - - +
130A TYR 3.9 0.2 + - - -
177A ARG* 2.9 37.3 + - - +
178A PHE* 3.3 34.5 - - + -
179A LYS* 3.1 26.9 + - - +
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Residues in contact with ILE 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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5A ILE* 4.5 6.5 - - + -
6A THR 2.6 16.7 + - - +
7A PHE* 3.3 14.3 - - + +
8A GLU* 2.6 35.2 + - - +
127A LEU* 4.3 9.2 - - + -
128A THR* 1.3 75.1 - - - +
130A TYR* 1.3 57.0 + - - +
131A LEU* 4.2 12.7 - - + +
179A LYS* 3.5 5.8 - - + +
181A VAL* 3.6 27.6 - - + -
194A THR* 3.9 21.5 - - + +
197A THR* 3.6 33.2 - - + -
198A ILE* 4.1 20.2 - - + -
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Residues in contact with TYR 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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8A GLU* 3.4 12.6 - - + -
9A GLY* 4.2 5.2 - - - -
10A PRO* 4.4 4.0 - - + +
128A THR 3.9 0.6 + - - -
129A ILE* 1.3 71.0 - - - +
131A LEU* 1.3 72.3 + - - +
132A ASN* 3.1 26.2 + - + -
133A VAL 5.3 1.2 + - - -
164A ILE* 4.2 8.5 + - - +
167A TYR* 3.3 49.3 - + + +
168A GLN* 2.7 29.1 + - - +
171A ILE* 3.6 32.5 - - + -
178A PHE* 4.3 19.1 - + + -
179A LYS 2.9 13.6 + - - +
180A SER* 3.2 15.0 - - - +
181A VAL 3.0 22.9 + - - -
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Residues in contact with LEU 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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7A PHE* 5.3 4.5 - - + -
8A GLU 3.0 11.9 + - - +
10A PRO* 3.8 11.3 - - - +
13A SER* 3.4 29.9 - - - +
14A GLY 4.3 0.9 - - - -
15A LYS* 3.2 52.5 - - + +
18A VAL* 4.1 9.4 - - + -
129A ILE* 4.2 10.1 - - + +
130A TYR* 1.3 71.9 - - - +
132A ASN* 1.3 59.5 + - - +
133A VAL 3.2 8.0 + - - -
181A VAL* 3.7 10.5 - - + -
183A ALA* 3.6 4.0 - - + -
190A VAL* 3.5 29.2 - - + -
194A THR* 3.6 16.8 - - - +
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Residues in contact with ASN 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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130A TYR* 3.1 32.3 + - + +
131A LEU* 1.3 67.3 - - - +
133A VAL* 1.3 63.1 + - - +
134A SER 4.2 0.5 + - - -
164A ILE* 5.9 0.2 - - - +
168A GLN* 3.2 22.3 + - - +
171A ILE* 4.6 5.5 - - - +
180A SER* 4.5 12.1 - - - -
181A VAL 2.9 18.6 + - - +
182A ASN* 3.6 10.8 - - - +
183A ALA* 2.9 19.6 + - - +
184A ASP* 4.3 0.9 - - - +
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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