Contacts of the strand formed by residues 129 - 139 (chain N) in PDB entry 3INU
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 THR 129 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145M LYS* 4.7 8.7 - - - +
124N GLN* 3.3 33.9 - - - +
125N LEU* 4.5 4.0 - - - +
127N SER* 2.7 20.1 + - - +
128N GLY* 1.3 78.9 + - - +
130N ALA* 1.3 67.1 + - - +
131N SER* 4.7 0.7 - - - +
180N THR* 3.7 29.2 - - + -
181N LEU 3.8 7.4 - - - +
182N SER* 5.0 1.3 - - - -
183N LYS* 4.0 4.9 - - - +
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Residues in contact with ALA 130 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120N PRO* 4.4 11.7 - - + -
124N GLN* 3.9 1.1 - - - -
125N LEU* 5.4 2.5 - - + -
129N THR* 1.3 75.3 - - - +
131N SER* 1.3 61.2 + - - +
132N VAL* 4.1 2.3 - - + +
179N LEU 3.6 1.0 - - - +
180N THR* 3.4 4.0 - - - +
181N LEU* 2.7 43.8 + - + +
183N LYS* 4.8 2.9 - - + -
186N TYR* 3.6 45.3 - - + -
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Residues in contact with SER 131 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124M LEU* 5.8 1.2 - - - +
143M LEU* 3.8 19.0 - - - +
145M LYS* 3.2 22.0 - - - -
118N PHE 4.2 0.9 - - - +
119N PRO 4.4 0.2 - - - -
120N PRO* 3.7 21.0 - - - +
124N GLN* 3.0 29.1 + - - +
130N ALA* 1.3 68.9 - - - +
132N VAL* 1.3 63.9 + - - +
133N VAL* 3.9 5.0 + - - +
178N THR* 3.8 10.2 - - - +
179N LEU 3.3 3.1 - - - -
180N THR* 3.5 15.6 + - - +
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Residues in contact with VAL 132 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117N ILE* 3.7 4.0 - - + -
118N PHE 3.4 12.8 - - - +
119N PRO* 4.6 0.4 - - + -
120N PRO* 4.4 7.9 - - + -
130N ALA 5.2 1.6 - - - +
131N SER* 1.3 75.3 - - - +
133N VAL* 1.3 60.1 + - - +
148N TRP* 3.7 26.3 - - + -
177N SER 3.7 0.3 - - - +
178N THR* 3.3 5.9 - - - +
179N LEU* 2.8 49.0 + - + +
181N LEU* 6.5 0.9 - - + -
186N TYR* 4.5 11.9 - - + -
192N TYR* 4.6 10.5 - - + -
209N PHE* 3.3 40.6 - - + -
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Residues in contact with VAL 133 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124M LEU* 3.7 36.6 - - + -
143M LEU* 4.4 14.8 - - + -
188M SER* 5.2 3.8 - - - +
117N ILE* 3.5 2.9 - - - +
118N PHE* 2.7 48.0 + - + +
131N SER 3.9 6.5 + - - +
132N VAL* 1.3 79.2 - - - +
134N CYS* 1.3 72.0 + - - +
135N LEU* 4.7 1.8 - - + +
148N TRP* 4.2 2.7 - - - -
176N SER* 4.6 12.3 - - - -
177N SER 3.4 7.2 - - - +
178N THR* 3.7 23.6 - - + +
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Residues in contact with CYS 134 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115N VAL* 3.9 7.9 - - - -
116N PHE 3.3 9.0 - - - -
117N ILE* 4.6 0.4 - - + +
133N VAL* 1.3 76.1 - - - +
135N LEU* 1.3 61.6 + - - +
136N LEU* 3.8 22.5 + - - +
146N VAL* 4.2 2.7 - - - -
148N TRP* 3.6 14.8 - - + -
175N LEU 3.7 1.0 - - - +
176N SER* 3.2 4.7 - - - -
177N SER* 2.8 41.7 + - - +
194N CYS* 2.0 43.5 - - + -
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Residues in contact with LEU 135 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139M ALA* 4.1 13.5 - - + -
174M PHE* 3.5 37.7 - - + -
190M VAL* 4.0 28.0 - - + -
192M THR* 5.6 0.4 - - + -
114N SER 3.3 5.4 - - - +
115N VAL* 3.4 3.8 - - - +
116N PHE* 2.8 64.0 + - + +
118N PHE* 4.3 11.4 - - + -
133N VAL* 4.2 2.2 - - + -
134N CYS* 1.3 73.5 - - - +
136N LEU* 1.3 72.2 + - - +
137N ASN* 4.1 15.3 - - - +
175N LEU 3.6 2.9 - - - +
176N SER* 4.5 3.4 - - - -
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Residues in contact with LEU 136 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113N PRO* 3.9 15.0 - - + -
114N SER 3.5 4.0 - - - -
115N VAL* 4.6 2.9 - - + -
134N CYS* 3.8 22.9 - - - +
135N LEU* 1.3 78.4 - - - +
137N ASN* 1.3 60.3 + - - +
139N PHE* 3.4 14.4 - - + -
144N ALA* 3.9 24.7 - - + -
146N VAL* 3.9 20.2 - - + -
174N SER* 3.3 5.9 - - - -
175N LEU* 2.7 51.9 + - + +
196N VAL* 3.6 36.6 - - + -
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Residues in contact with ASN 137 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172M HIS* 3.5 12.5 + - - -
190M VAL* 4.7 2.0 - - - +
192M THR* 3.0 35.2 - - - +
113N PRO* 3.6 1.2 - - - +
114N SER* 2.9 43.6 + - - +
116N PHE* 4.2 12.0 - - + -
135N LEU* 4.1 17.2 - - + +
136N LEU* 1.3 73.3 - - - +
138N ASN* 1.3 90.8 + - - +
139N PHE* 3.5 2.1 + - - -
174N SER* 2.9 17.4 + - - -
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Residues in contact with ASN 138 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172M HIS* 3.6 23.4 + - - -
111N ALA* 4.5 4.5 - - - +
112N ALA 3.8 8.7 - - - +
114N SER* 5.7 0.9 - - - +
137N ASN* 1.3 101.9 + - + +
139N PHE* 1.3 57.1 + - - +
167N ASP* 4.6 4.2 + - - +
170N ASP* 3.3 17.0 + - - +
172N THR* 3.1 34.5 + - + +
173N TYR 3.0 15.9 + - - -
174N SER* 3.1 3.4 + - - -
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Residues in contact with PHE 139 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111N ALA* 3.3 15.0 - - - +
113N PRO* 3.5 34.3 - - + -
136N LEU* 3.4 31.4 - - + -
138N ASN* 1.3 74.5 - - - +
140N TYR* 1.3 62.2 + - - +
141N PRO 3.2 20.0 - - - -
142N ARG* 3.3 30.5 - - - -
144N ALA* 3.9 13.2 - - + -
163N VAL* 5.0 2.2 - - + -
172N THR* 3.4 4.0 - - - -
173N TYR* 2.8 55.7 + - + -
174N SER* 3.7 4.5 - - - -
175N LEU* 3.8 19.1 - - + -
198N HIS* 3.4 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