Contacts of the strand formed by residues 185 - 194 (chain A) in PDB entry 2IL1
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 185 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A ASP* 3.4 13.9 - - + +
137A PHE* 4.5 15.9 - - + -
180A VAL 3.4 1.9 - - - +
181A GLU* 3.3 5.9 - - - -
182A LEU 2.8 39.8 + - - +
183A ARG* 4.2 6.7 - - + +
184A GLY* 1.3 79.4 - - - +
186A LYS* 1.3 60.0 + - - +
187A ILE* 3.8 19.9 + - + +
301A LEU* 5.2 4.7 - - + -
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Residues in contact with LYS 186 (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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134A PRO* 3.6 27.6 - - + +
135A ALA* 3.7 14.3 - - + +
136A ASP* 2.7 40.4 + - - +
137A PHE 3.3 4.7 + - - -
179A THR* 3.7 25.6 - - + -
180A VAL 3.5 4.5 - - - +
181A GLU* 4.7 10.3 - - + +
184A GLY 4.1 1.4 + - - -
185A LYS* 1.3 71.7 - - - +
187A ILE* 1.3 60.8 + - - +
188A ARG 4.2 0.4 - - - -
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Residues in contact with ILE 187 (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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135A ALA* 4.6 0.9 - - - -
137A PHE* 3.3 41.1 - - + +
139A LEU* 3.7 33.0 - - + -
178A LYS 3.5 0.2 - - - +
179A THR* 3.4 3.0 - - - -
180A VAL* 2.8 53.5 + - + +
182A LEU* 4.7 4.3 - - + -
185A LYS* 4.0 16.8 - - + +
186A LYS* 1.3 79.6 - - - +
188A ARG* 1.3 68.7 + - - +
189A LEU* 3.3 7.2 + - + +
297A VAL* 4.3 13.7 - - + -
301A LEU* 3.8 18.6 - - + -
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Residues in contact with ARG 188 (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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135A ALA* 3.9 16.9 - - + +
137A PHE 2.7 14.9 + - - +
138A LYS* 3.3 39.3 - - + +
139A LEU 3.0 24.1 + - - +
177A ILE* 3.7 50.3 - - + +
178A LYS 3.9 2.2 - - - -
179A THR* 4.3 13.5 - - - +
187A ILE* 1.3 70.6 - - - +
189A LEU* 1.3 60.3 + - - +
190A GLN* 3.8 7.0 + - - +
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Residues in contact with LEU 189 (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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139A LEU* 3.5 22.4 - - + +
141A VAL* 3.9 21.5 - - + -
158A PHE* 4.1 16.6 - - + -
176A LYS 3.7 0.9 - - - +
177A ILE* 3.3 6.6 - - - +
178A LYS* 2.7 48.2 + - + +
180A VAL* 4.7 10.8 - - + -
187A ILE* 3.3 7.5 + - + +
188A ARG* 1.3 73.4 - - - +
190A GLN* 1.3 59.2 + - - +
191A ILE* 3.9 29.1 + - + +
293A PHE* 4.4 9.6 - - + -
294A LEU* 6.4 0.2 - - + -
297A VAL* 3.8 32.3 - - + -
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Residues in contact with GLN 190 (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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139A LEU 2.8 14.7 + - - +
140A GLN* 3.3 28.1 + - + +
141A VAL* 3.0 28.5 + - - +
175A PHE* 3.6 32.9 - - + -
176A LYS 3.7 2.7 - - - -
177A ILE* 3.7 19.6 - - + +
188A ARG* 3.8 8.0 + - - +
189A LEU* 1.3 72.3 - - - +
191A ILE* 1.3 61.4 - - - +
192A TRP* 3.4 36.1 + - + +
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Residues in contact with ILE 191 (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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141A VAL* 3.5 18.6 - - + -
143A ILE* 3.6 33.9 - - + -
155A MET* 3.7 16.1 - - + +
158A PHE* 3.8 32.8 - - + -
159A THR* 4.0 17.5 - - + -
175A PHE* 3.1 5.9 - - - -
176A LYS 2.9 34.8 + - - +
178A LYS* 4.8 3.4 - - + -
189A LEU* 3.9 13.7 - - + +
190A GLN* 1.3 76.5 - - - +
192A TRP* 1.3 61.5 + - - +
293A PHE* 3.8 16.2 - - + -
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Residues in contact with TRP 192 (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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140A GLN* 2.6 36.6 + - + -
141A VAL 2.9 19.2 + - - -
142A ILE* 3.5 24.1 - - + +
143A ILE* 2.9 31.0 + - - +
170A THR* 5.4 2.9 - - + -
173A VAL* 4.1 15.3 - - + -
174A ASP 3.5 10.1 - - - -
175A PHE* 3.6 33.7 - + + -
190A GLN* 3.4 34.8 + - + -
191A ILE* 1.3 72.8 - - - +
193A ASP* 1.3 61.1 + - - +
194A THR* 4.0 7.6 + - + -
207A TYR* 3.6 42.1 - + + -
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Residues in contact with ASP 193 (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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143A ILE* 4.5 5.0 - - + +
151A LYS* 3.9 21.4 - - - +
152A THR* 2.4 39.5 + - - +
155A MET* 3.6 32.4 - - + +
172A GLY 4.7 0.2 - - - -
173A VAL* 3.3 4.4 - - - -
174A ASP* 2.8 51.4 + - + +
191A ILE 3.9 0.6 + - - -
192A TRP* 1.3 73.1 - - - +
194A THR* 1.3 68.0 + - - +
402A MG 4.0 2.5 - - - -
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Residues in contact with THR 194 (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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142A ILE* 4.7 11.2 - - + -
143A ILE 2.9 23.9 + - - +
144A ILE* 3.7 21.5 - - + +
151A LYS* 3.4 17.8 - - - -
172A GLY 3.5 4.5 - - - -
173A VAL* 4.0 15.7 - - + -
192A TRP* 4.4 10.3 - - + +
193A ASP* 1.3 81.4 + - - +
195A ALA* 1.3 69.1 + - - +
204A THR* 4.0 22.0 - - - +
207A TYR* 5.0 6.1 - - + -
208A TYR* 5.4 0.7 - - + -
232A TRP* 6.1 0.5 - - - -
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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