Contacts of the strand formed by residues 126 - 130 (chain A) in PDB entry 5NJ8
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 VAL 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A LEU* 5.0 7.9 - - + -
122A LEU* 4.2 8.3 - - + -
125A PHE* 1.3 78.7 - - - +
127A LEU* 1.3 71.0 + - - +
137A TYR* 4.3 7.3 - - + -
138A ALA* 3.5 5.5 - - - -
139A SER* 2.8 43.0 + - - +
267A ALA 3.6 13.5 - - - +
268A ILE* 4.4 3.1 - - + -
164B LEU* 5.3 2.0 - - + -
167B LEU* 3.5 36.6 - - + -
168B ILE* 3.3 31.9 - - + -
171B ALA* 5.7 2.0 - - + -
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Residues in contact with LEU 127 (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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125A PHE* 3.6 30.2 + - + -
126A VAL* 1.3 72.7 - - - +
128A VAL* 1.3 66.9 + - - +
129A VAL* 4.7 12.8 - - + -
135A VAL* 3.3 27.6 - - + -
137A TYR 3.2 16.4 - - - +
138A ALA* 3.9 10.3 - - + -
142A ILE* 5.3 3.4 - - + -
153A VAL* 5.4 0.9 - - + -
158A VAL* 5.4 7.2 - - + -
161A LEU* 5.7 3.6 - - + -
170A PHE* 6.0 1.1 - - + -
224A LEU* 4.6 6.7 - - + -
239A PHE* 3.7 29.8 - - + -
265A LEU 3.6 1.5 - - - +
266A PHE* 3.6 0.5 - - - -
267A ALA* 2.9 40.7 + - + +
269A ALA 6.0 1.1 - - - +
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Residues in contact with VAL 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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127A LEU* 1.3 78.6 - - - +
129A VAL* 1.3 60.5 + - - +
135A VAL* 3.3 4.5 - - - +
136A PHE* 2.5 52.2 + - + -
137A TYR* 2.9 43.3 + - + +
264A ALA* 4.8 1.8 - - + -
265A LEU 3.3 3.8 - - - +
266A PHE* 3.3 50.0 - - + -
167B LEU* 4.1 12.1 - - + -
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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 LEU* 4.7 13.2 - - + -
128A VAL* 1.3 80.4 - - - +
130A THR* 1.3 80.2 + - - +
133A ALA* 3.7 8.5 - - - -
134A LEU 3.6 4.3 - - - +
135A VAL* 4.5 2.9 - - - -
158A VAL* 3.5 44.4 - - + -
170A PHE* 4.5 10.3 - - + -
174A LEU* 3.8 19.5 - - + -
264A ALA* 3.0 8.7 - - - +
265A LEU* 2.9 38.2 + - + +
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Residues in contact with THR 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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78A ARG* 4.7 14.6 - - - +
129A VAL* 1.3 84.3 - - - +
131A THR* 1.3 56.2 + - - +
132A ASP* 3.3 23.1 + - - +
133A ALA* 2.4 31.0 + - - -
134A LEU* 3.3 19.4 + - + +
136A PHE* 4.0 23.1 - - + -
174A LEU* 4.1 5.1 - - - +
246A LEU* 5.1 3.8 - - + -
262A GLN* 4.6 9.2 - - - +
263A LEU 4.0 9.4 - - - +
264A ALA* 4.8 6.5 - - + -
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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