Contacts of the strand formed by residues 143 - 153 (chain J) in PDB entry 2NX5
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 LYS 143 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168I MET* 3.7 19.5 - - + -
171I MET* 3.8 28.2 - - + +
173I PHE* 3.6 43.0 - - + -
137J GLU* 3.0 22.9 - - - +
138J ILE* 3.8 2.8 + - - -
141J THR* 2.8 33.9 + - - +
142J GLN* 1.3 84.6 - - - +
144J ALA* 1.3 61.9 + - - +
198J ARG* 3.4 30.3 - - + +
199J VAL 3.7 7.0 - - - +
200J SER* 5.1 3.4 - - - -
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Residues in contact with ALA 144 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133J PRO* 3.4 26.2 - - + -
137J GLU* 3.3 3.1 - - - -
138J ILE* 4.0 8.7 - - + -
143J LYS* 1.3 74.3 - - - +
145J THR* 1.3 61.8 + - - +
146J LEU* 4.1 1.0 + - - +
197J LEU 3.8 1.0 - - - +
198J ARG* 3.5 1.5 - - - -
199J VAL* 2.8 38.9 + - - +
201J ALA* 4.2 4.2 - - - +
204J TRP* 3.7 28.7 - - + -
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Residues in contact with THR 145 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128I LEU* 3.3 20.8 - - - +
140I LEU* 3.8 21.2 - - + +
142I THR* 5.5 0.3 + - - -
166I LEU* 4.9 2.7 - - + -
177I SER* 6.1 0.9 - - - -
133J PRO* 3.4 14.5 - - - +
137J GLU* 2.6 34.0 + - - +
144J ALA* 1.3 72.9 - - - +
146J LEU* 1.3 68.0 - - - +
147J VAL* 4.9 0.7 - - + -
196J ARG* 3.8 16.8 - - + -
197J LEU 3.3 19.3 - - - +
198J ARG* 3.4 22.8 - - + +
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Residues in contact with LEU 146 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130J VAL* 4.4 14.4 - - + -
131J PHE 3.6 7.0 - - - +
132J GLU* 5.6 0.4 - - - -
133J PRO* 4.1 19.1 - - + -
144J ALA 4.5 0.4 - - - +
145J THR* 1.3 76.9 - - - +
147J VAL* 1.3 63.5 + - - +
162J TRP* 3.7 21.5 - - + -
196J ARG* 3.3 5.0 - - - -
197J LEU* 2.7 46.6 + - + +
199J VAL* 4.5 10.8 - - + -
204J TRP* 4.2 15.0 - - + -
211J PHE* 3.6 51.8 - - + -
242J ALA* 4.8 2.5 - - + -
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Residues in contact with VAL 147 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128I LEU* 3.7 23.1 - - + -
138I VAL* 4.3 15.5 - - + -
140I LEU* 4.4 12.6 - - + -
179I VAL* 4.1 26.7 - - + -
130J VAL* 3.4 5.9 - - - +
131J PHE* 2.9 44.4 + - + +
145J THR* 4.7 0.9 - - + +
146J LEU* 1.3 80.5 - - - +
148J CYS* 1.3 70.9 + - - +
149J LEU* 4.2 2.0 - - + -
162J TRP* 4.0 2.7 - - - -
194J SER* 4.9 2.0 - - - -
195J SER 3.3 9.2 - - - +
196J ARG* 4.3 14.8 - - + -
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Residues in contact with CYS 148 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128J VAL* 3.8 18.4 - - - -
129J ALA 3.5 5.6 - - - -
130J VAL* 4.9 0.2 - - + -
147J VAL* 1.3 74.2 - - - +
149J LEU* 1.3 63.9 + - - +
150J ALA 4.0 0.2 + - - -
160J LEU* 4.2 6.7 - - - +
162J TRP* 3.4 19.5 - - + -
193J LEU 3.5 1.4 - - - +
194J SER* 3.2 7.3 - - - -
195J SER* 2.7 39.6 + - - +
213J CYS* 2.0 50.3 - - - -
215J VAL* 4.8 0.4 - - - -
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Residues in contact with LEU 149 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138I VAL* 3.6 22.2 - - + -
179I VAL* 4.4 3.6 - - + -
181I TRP* 3.6 64.4 - - + +
127J GLU 3.2 4.7 - - - +
128J VAL* 3.3 2.3 - - - -
129J ALA* 2.8 38.1 + - + +
131J PHE* 3.7 22.2 - - + -
147J VAL* 4.2 2.8 + - + -
148J CYS* 1.3 74.7 - - - +
150J ALA* 1.3 58.6 + - - +
151J THR* 4.3 11.3 + - + +
193J LEU 3.5 4.5 - - - +
194J SER* 3.8 19.5 - - - -
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Residues in contact with ALA 150 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126J PRO* 4.0 18.8 - - + -
127J GLU 3.2 5.8 - - - +
128J VAL* 4.3 1.3 - - + +
148J CYS* 4.0 1.2 + - - -
149J LEU* 1.3 72.3 - - - +
151J THR* 1.3 59.7 + - - +
153J PHE* 3.5 11.5 - - + -
158J VAL* 5.7 0.2 - - + -
160J LEU* 5.1 2.9 - - + +
192J ALA* 3.2 2.6 - - - -
193J LEU* 2.7 47.0 + - + +
215J VAL* 4.1 27.8 - - + -
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Residues in contact with THR 151 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181I TRP* 4.0 22.7 - - + +
125J PRO 4.6 0.3 - - - +
127J GLU* 2.9 51.8 + - - +
149J LEU* 4.3 16.5 + - + +
150J ALA* 1.3 79.1 - - - +
152J GLY* 1.3 61.0 + - - +
153J PHE* 3.5 3.1 - - - -
182J GLU* 3.4 15.9 - - - +
191J TYR 3.9 2.2 - - - -
192J ALA* 3.8 10.5 - - + -
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Residues in contact with GLY 152 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124J PHE* 3.5 6.2 - - - +
125J PRO 4.2 4.0 - - - -
151J THR* 1.3 71.5 - - - +
153J PHE* 1.3 62.5 + - - +
182J GLU* 3.1 18.5 + - - -
190J ARG* 2.6 48.0 + - - +
191J TYR 2.9 10.3 + - - -
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Residues in contact with PHE 153 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124J PHE 3.4 9.9 - - - +
125J PRO 4.0 2.0 + - - -
126J PRO* 3.6 36.3 - - + -
150J ALA* 3.5 24.7 - - + -
151J THR 3.5 1.2 + - - -
152J GLY* 1.3 76.1 - - - +
154J PHE* 1.3 61.0 + - - +
155J PRO 3.6 13.7 - - - -
156J ASP* 3.6 22.7 - - + -
158J VAL* 3.6 34.8 - - + -
179J PRO* 4.0 10.5 - - + -
191J TYR* 2.8 64.8 + - + +
192J ALA* 3.6 3.8 - - - -
193J LEU* 3.9 7.6 - - + -
217J PHE* 4.1 3.6 - + + -
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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