Contacts of the strand formed by residues 127 - 132 (chain A) in PDB entry 1N99
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
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Residue Dist Surf HB Arom Phob DC
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117A LEU* 4.4 2.2 - - + -
125A ILE* 3.5 33.0 - - + +
126A GLY* 1.3 76.0 - - - +
128A ARG* 1.3 63.1 + - - +
129A LEU* 3.9 21.3 - - + -
138A VAL* 3.6 33.2 - - + -
140A LEU 3.4 2.5 - - - +
141A VAL* 4.0 12.3 - - + -
147A ALA* 4.0 4.9 - - + -
152A LEU* 3.8 27.4 - - + -
178A LEU* 4.6 10.5 - - + +
188A MSE 4.0 18.4 - - + -
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Residues in contact with ARG 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 77.0 + - - +
129A LEU* 1.3 74.6 + - - +
138A VAL* 3.7 3.6 - - - +
139A GLN* 2.8 41.1 + - + -
140A LEU* 2.9 27.2 + - + +
171A SER 6.1 0.2 - - - -
175A HIS* 3.8 38.2 + - - +
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Residues in contact with LEU 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* 3.9 20.6 - - + -
128A ARG* 1.3 94.2 - - - +
130A LYS* 1.3 62.3 + - - +
136A ILE* 3.8 17.9 - - + -
137A PHE 3.3 9.6 - - - +
138A VAL* 4.0 8.1 - - + -
139A GLN* 4.4 0.4 - - - -
158A VAL* 4.0 21.5 - - + -
161A ILE* 3.9 13.0 - - + -
171A SER* 4.2 15.3 + - - +
174A ALA* 4.3 15.3 - - + -
175A HIS* 5.7 0.8 - - - +
178A LEU* 3.6 32.0 - - + +
188A MSE 3.8 17.0 - - + -
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Residues in contact with LYS 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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129A LEU* 1.3 76.3 - - - +
131A SER* 1.3 72.6 + - - +
132A ILE* 3.5 22.7 + - + +
136A ILE* 3.4 7.2 - - - -
137A PHE* 2.8 42.2 + - - +
139A GLN* 3.4 44.3 + - + +
171A SER* 3.4 9.9 - - - +
272A ALA 5.3 6.7 + - - -
273A PHE 5.3 6.4 - - - -
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Residues in contact with SER 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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130A LYS* 1.3 78.9 - - - +
132A ILE* 1.3 65.8 + - - +
134A ASN* 4.7 8.1 + - - -
135A GLY 3.4 8.3 + - - -
136A ILE* 3.9 4.0 - - - +
168A GLY 5.4 0.2 - - - -
169A TRP 3.1 25.8 + - - -
170A SER* 4.1 3.2 - - - -
171A SER* 2.9 25.7 + - - -
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Residues in contact with ILE 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 LYS* 3.5 31.8 + - + +
131A SER* 1.3 80.8 + - - +
133A ASP* 1.3 83.6 + - + +
134A ASN 3.1 2.0 - - - -
135A GLY* 2.9 21.1 + - - +
137A PHE* 3.6 36.3 - - + -
139A GLN* 5.2 4.0 - - - +
270A MSE 5.7 4.0 - - + -
273A PHE* 3.6 48.2 - - + -
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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