Contacts of the helix formed by residues 134 - 141 (chain B) in PDB entry 1N1E
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 PHE 134 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B GLY 3.6 12.6 - - - -
127B ILE* 3.6 20.4 - - + -
132B LEU 4.7 2.7 - - - -
133B LYS* 1.3 74.8 - - - +
135B PRO* 1.3 75.9 - - + +
136B ALA 3.3 0.4 - - - -
137B GLU* 2.9 38.2 + - + +
138B ILE* 3.0 11.8 + - - +
201B VAL* 6.1 0.7 - - + -
204B GLU* 3.6 55.9 - - + +
205B VAL* 3.7 26.9 - - + -
208B ALA* 4.0 2.5 - - + -
209B VAL* 6.1 0.2 - - + -
244B LEU* 5.1 2.2 - - + -
248B LEU* 3.8 26.2 - - + -
311B LEU* 4.1 19.5 - - + -
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Residues in contact with PRO 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B THR* 3.9 7.6 - - + +
98B LEU* 3.8 10.9 - - + +
122B VAL* 3.8 12.3 - - + -
124B THR* 3.4 51.8 - - + +
125B LYS* 4.9 0.4 - - - -
126B GLY 3.1 22.0 - - - +
133B LYS 4.7 0.2 - - - +
134B PHE* 1.3 87.8 - - + +
136B ALA* 1.3 61.4 + - - +
138B ILE* 3.2 9.1 + - + +
139B ILE* 3.0 26.7 + - - +
204B GLU* 5.2 6.5 - - + +
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Residues in contact with ALA 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B VAL* 4.0 20.5 - - + +
134B PHE 3.3 0.8 - - - -
135B PRO* 1.3 80.3 - - - +
137B GLU* 1.3 56.6 - - + +
139B ILE* 4.4 1.3 - - - -
140B GLY* 2.8 23.2 + - - -
148B LEU* 3.5 18.6 - - + +
150B VAL* 4.1 20.9 - - + -
204B GLU* 3.9 17.6 + - - +
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Residues in contact with GLU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B LEU 4.4 1.0 - - - +
133B LYS* 3.4 29.3 + - + +
134B PHE* 2.9 47.1 + - + +
136B ALA* 1.3 75.0 - - + +
138B ILE* 1.3 66.1 + - - +
140B GLY* 3.3 9.7 + - - +
141B GLU* 3.4 15.2 + - - +
204B GLU* 4.2 11.8 - - - +
248B LEU* 6.1 1.0 - - - +
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Residues in contact with ILE 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B THR* 3.8 25.8 - - + +
98B LEU* 4.2 17.3 - - + -
99B ARG* 4.0 39.7 - - + +
102B PHE* 5.4 0.9 - - + -
128B GLU* 3.6 40.4 - - + +
133B LYS* 4.1 8.3 - - + +
134B PHE 3.0 12.6 + - - +
135B PRO* 3.2 7.4 + - + +
137B GLU* 1.3 76.1 - - - +
139B ILE* 1.3 63.2 + - + +
141B GLU* 3.1 28.0 + - - +
142B PHE* 3.4 13.2 - - + -
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Residues in contact with ILE 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B PHE* 3.9 26.0 - - + -
98B LEU* 4.2 14.1 - - + -
102B PHE* 3.8 27.6 - - + -
120B VAL* 4.7 0.2 - - + -
122B VAL* 3.6 33.7 - - + -
135B PRO 3.0 15.5 + - - +
136B ALA* 3.8 5.4 - - - +
138B ILE* 1.3 75.5 - - + +
140B GLY* 1.3 57.0 + - - +
141B GLU 3.1 0.2 - - - -
142B PHE* 2.9 9.3 + - - +
143B LEU* 2.9 42.0 + - + -
148B LEU* 3.8 25.8 - - + -
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Residues in contact with GLY 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B ALA 2.8 18.3 + - - -
137B GLU* 3.7 5.2 - - - -
138B ILE 3.2 0.6 - - - -
139B ILE* 1.3 75.4 - - - +
141B GLU* 1.3 57.9 + - - +
142B PHE 3.2 0.4 - - - -
143B LEU 3.2 20.6 - - - +
145B SER* 5.3 5.4 + - - -
148B LEU* 3.8 9.8 - - - +
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Residues in contact with GLU 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B ARG* 2.8 44.5 + - - -
131B THR* 5.3 0.3 - - - +
133B LYS* 2.5 38.5 + - - +
137B GLU 3.4 7.7 + - - +
138B ILE* 3.1 11.0 + - - +
140B GLY* 1.3 77.5 - - - +
142B PHE* 1.3 72.7 + - + +
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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