Contacts of the strand formed by residues 136 - 146 (chain J) in PDB entry 2IAN
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 136 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160I MET* 3.7 25.6 - - + -
163I MET* 4.0 22.1 - - - -
165I PHE* 3.8 40.2 - - + -
130J GLU* 3.1 27.1 - - - +
131J ILE* 3.5 8.0 + - - -
134J THR* 2.9 31.4 + - - +
135J GLN* 1.3 83.5 - - - +
137J ALA* 1.3 61.1 + - - +
191J ARG* 3.7 18.8 - - - +
192J VAL 3.8 4.0 - - - +
193J SER* 4.9 1.3 - - - -
194J ALA 4.0 1.8 - - - +
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Residues in contact with ALA 137 (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* 3.6 24.0 - - + -
130J GLU* 3.5 3.1 - - - -
131J ILE* 3.9 10.3 - - + -
136J LYS* 1.3 75.1 - - - +
138J THR* 1.3 63.7 + - - +
139J LEU* 4.1 0.4 - - - -
190J LEU 3.9 0.5 - - - +
191J ARG* 3.3 3.0 - - - +
192J VAL* 2.8 41.4 + - + +
193J SER 4.5 2.2 - - - +
194J ALA* 4.6 0.9 - - - -
197J TRP* 3.7 23.3 - - + -
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Residues in contact with THR 138 (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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120I LEU* 3.5 11.3 - - - +
132I LEU* 3.6 28.8 - - + +
158I LEU* 5.3 2.2 - - + -
126J PRO* 3.3 24.4 - - - +
130J GLU* 2.5 34.5 + - - +
137J ALA* 1.3 72.2 - - - +
139J LEU* 1.3 71.3 + - - +
189J ARG* 4.0 18.8 - - + -
190J LEU 3.5 7.6 - - - +
191J ARG* 3.2 23.2 + - + +
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Residues in contact with LEU 139 (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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123J VAL* 4.1 19.5 - - + -
124J PHE 3.6 7.0 - - - +
125J GLU* 5.3 0.7 - - - -
126J PRO* 4.0 13.9 - - + -
138J THR* 1.3 75.9 - - - +
140J VAL* 1.3 62.2 + - - +
155J TRP* 3.9 18.7 - - + -
189J ARG* 3.3 4.3 - - - -
190J LEU* 2.7 46.4 + - + +
192J VAL* 4.3 11.0 - - + -
197J TRP* 3.8 34.3 - - + -
204J PHE* 3.9 37.7 - - + -
235J ALA* 4.8 3.1 - - + -
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Residues in contact with VAL 140 (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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120I LEU* 3.6 23.8 - - + -
130I VAL* 4.2 13.2 - - + -
132I LEU* 3.9 26.5 - - + -
171I VAL* 4.0 25.8 - - + -
123J VAL* 3.4 3.3 - - - +
124J PHE* 2.8 38.3 + - + -
138J THR* 4.0 2.7 + - + -
139J LEU* 1.3 78.5 - - - +
141J CYS* 1.3 70.6 + - - +
142J LEU* 4.2 8.1 - - + -
155J TRP* 4.1 2.9 - - - -
187J SER* 4.8 0.4 - - - -
188J SER 3.4 11.2 - - - +
189J ARG* 4.7 2.5 - - + -
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Residues in contact with CYS 141 (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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121J VAL* 3.6 19.7 - - - -
122J ALA 3.3 5.8 - - - -
123J VAL* 4.0 0.9 - - - +
140J VAL* 1.3 74.3 - - - +
142J LEU* 1.3 69.5 + - - +
143J ALA 4.3 0.2 - - - -
153J LEU* 4.7 5.7 - - + +
155J TRP* 3.4 17.6 - - + -
186J LEU 3.9 0.2 - - - +
187J SER* 3.3 5.2 - - - -
188J SER* 3.0 33.6 + - - +
206J CYS* 2.0 51.4 - - + -
208J VAL* 5.0 0.4 - - - -
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Residues in contact with LEU 142 (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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130I VAL* 3.7 18.8 - - + -
171I VAL* 4.4 2.9 - - + -
173I TRP* 3.6 50.7 - - + +
120J GLU 3.5 1.2 - - - +
121J VAL* 3.5 5.7 - - - -
122J ALA* 2.9 33.0 + - + +
124J PHE* 4.0 21.5 - - + -
140J VAL* 4.2 8.5 - - + -
141J CYS* 1.3 78.6 - - - +
143J ALA* 1.3 61.1 + - - +
144J THR* 3.9 12.8 + - + +
186J LEU 3.4 2.7 - - - +
187J SER* 3.5 30.5 - - - -
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Residues in contact with ALA 143 (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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173I TRP* 5.3 0.2 - - - -
119J PRO* 4.4 7.2 - - + -
120J GLU 3.5 6.3 - - - +
121J VAL* 4.7 1.6 - - - -
141J CYS* 4.3 0.6 - - - -
142J LEU* 1.3 75.1 - - - +
144J THR* 1.3 67.2 + - - +
146J PHE* 3.5 23.8 - - + -
151J VAL* 5.5 0.4 - - + -
153J LEU* 4.9 5.3 - - + +
185J ALA* 3.4 1.4 - - - +
186J LEU* 2.7 40.4 + - + +
208J VAL* 4.7 21.1 - - + -
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Residues in contact with THR 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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173I TRP* 4.6 15.5 - - + +
118J PRO 3.9 0.2 - - - +
119J PRO* 3.4 0.2 - - - +
120J GLU* 2.8 67.5 + - - +
122J ALA 5.4 0.5 + - - -
142J LEU* 3.9 17.8 + - + -
143J ALA* 1.3 83.7 - - - +
145J GLY* 1.3 61.6 + - - +
146J PHE* 3.4 6.6 + - - -
175J GLU* 4.0 10.3 - - - +
184J TYR 3.7 3.1 - - - -
185J ALA* 4.6 7.0 - - + -
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Residues in contact with GLY 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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117J PHE* 3.2 21.8 - - - +
118J PRO 3.5 4.8 - - - +
120J GLU* 4.2 5.4 - - - -
144J THR* 1.3 72.3 - - - +
146J PHE* 1.3 58.4 + - - +
175J GLU* 2.8 29.9 + - - -
183J ARG* 3.3 26.5 + - - -
184J TYR 3.0 5.5 + - - -
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Residues in contact with PHE 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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117J PHE 3.3 10.5 - - - +
118J PRO 3.7 1.3 - - - -
119J PRO* 3.4 39.7 - - + -
143J ALA* 3.5 25.6 - - + -
144J THR 3.4 4.8 - - - -
145J GLY* 1.3 74.7 - - - +
147J PHE* 1.3 60.2 + - - +
148J PRO 3.6 11.7 - - - -
149J ASP* 3.8 18.8 - - - -
151J VAL* 3.6 28.7 - - + -
172J PRO* 4.4 3.8 - - + -
183J ARG* 4.2 0.2 - - - -
184J TYR* 3.1 59.5 + - + -
186J LEU* 4.1 18.2 - - + -
210J PHE* 4.1 4.5 - - + -
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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