Contacts of the strand formed by residues 180 - 193 (chain A) in PDB entry 3IML
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 180 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176A TYR* 3.3 5.9 - - - -
177A VAL 2.8 39.2 + - - +
178A ASP* 4.3 4.7 - - + +
179A GLY* 1.3 78.8 - - - +
181A PRO* 1.3 76.4 - - + +
182A HIS* 4.2 0.7 - - - +
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Residues in contact with PRO 181 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A GLU* 4.1 25.1 - - + +
140A LEU* 3.8 30.7 - - + -
174A VAL* 4.3 6.1 - - + -
175A ARG 4.1 3.1 - - - +
176A TYR* 3.6 24.6 - - + -
180A LYS* 1.3 90.6 - - + +
182A HIS* 1.3 58.7 - - - +
219A LEU* 4.0 13.8 - - + +
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Residues in contact with HIS 182 (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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175A ARG* 2.9 39.9 + - + +
177A VAL* 4.0 34.1 - - + +
180A LYS 4.3 0.2 - - - +
181A PRO* 1.3 73.7 - - - +
183A SER* 1.3 74.6 + - - +
218A ASP 4.4 0.3 - - - +
219A LEU* 3.1 17.2 - - - +
221A LYS* 3.8 32.9 + - + -
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Residues in contact with SER 183 (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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174A VAL* 3.8 7.2 - - - +
175A ARG* 3.1 43.0 + - - +
182A HIS* 1.3 92.4 + - - +
184A ILE* 1.3 69.4 + - - +
185A ASP* 4.8 0.7 + - - -
219A LEU* 3.3 11.4 - - - +
221A LYS* 3.5 29.6 - - - -
223A ASP* 4.3 10.3 + - - -
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Residues in contact with ILE 184 (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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144A LEU* 3.7 26.0 - - + -
172A VAL* 4.2 4.7 - - + -
173A THR 3.9 8.3 - - - +
174A VAL* 3.9 17.9 - - + -
183A SER* 1.3 73.1 - - - +
185A ASP* 1.3 64.3 + - - +
186A THR 4.1 4.3 - - - +
187A VAL* 3.6 31.2 - - + -
215A LEU* 4.2 20.0 - - + -
216A PRO* 5.1 0.4 - - + -
219A LEU* 2.9 41.8 + - + +
221A LYS 5.5 0.7 + - - -
223A ASP* 4.5 4.3 - - - +
224A ILE* 3.3 34.5 - - + +
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Residues in contact with ASP 185 (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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6A LEU* 4.0 28.7 - - + +
173A THR* 2.9 25.9 + - + +
175A ARG* 4.6 7.5 - - + +
183A SER* 3.7 4.3 + - - +
184A ILE* 1.3 72.7 - - - +
186A THR* 1.3 83.4 + - - +
223A ASP* 4.8 11.6 - - - +
224A ILE* 3.7 1.6 - - - +
225A LYS* 2.9 53.5 + - - +
312B THR 4.2 7.4 - - - +
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Residues in contact with THR 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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171A GLN 3.7 1.0 - - - +
172A VAL* 3.6 0.7 - - - -
173A THR* 2.9 41.9 + - - +
184A ILE* 4.1 0.9 - - - +
185A ASP* 1.3 103.3 + - - +
187A VAL* 1.3 75.8 + - - +
188A VAL* 4.2 7.4 - - + -
224A ILE* 5.4 0.2 - - - -
225A LYS* 3.3 22.9 - - + +
227A LEU* 3.9 28.0 - - + -
312B THR* 4.4 16.6 + - + +
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Residues in contact with VAL 187 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A LEU* 3.5 27.6 - - + -
171A GLN 3.4 4.0 - - - +
172A VAL* 4.5 7.2 - - + -
184A ILE* 3.6 21.8 - - + -
186A THR* 1.3 79.1 - - - +
188A VAL* 1.3 64.8 + - - +
189A LEU* 5.0 0.4 - - + -
211A ILE* 3.7 38.3 - - + +
215A LEU* 4.2 13.5 - - + -
224A ILE* 5.1 0.6 - - + +
225A LYS 2.8 9.5 + - - +
226A PHE* 3.5 11.0 - - + +
227A LEU 2.7 32.2 + - - -
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Residues in contact with VAL 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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170A SER* 3.3 6.3 - - - -
171A GLN* 2.9 54.4 + - + +
186A THR* 4.2 7.4 - - + -
187A VAL* 1.3 79.5 - - - +
189A LEU* 1.3 67.9 + - - +
190A SER* 4.6 7.2 - - - +
227A LEU* 3.2 23.8 - - + +
230A PRO* 4.7 5.6 - - + -
123B GLN* 3.7 21.1 - - + +
305B ALA* 3.9 29.8 - - + -
306B ILE* 5.2 2.0 - - + -
312B THR* 4.7 0.9 - - + -
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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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148A LEU* 4.2 25.1 - - + +
149A VAL* 5.6 1.3 - - + -
152A GLN* 5.1 7.4 - - + -
168A ALA* 4.8 5.6 - - + -
169A LYS 3.3 10.3 - - - +
170A SER* 4.6 4.5 - - - -
187A VAL 4.1 0.2 - - - -
188A VAL* 1.3 74.7 - - - +
190A SER* 1.3 75.9 + - - +
191A THR* 4.0 14.1 - - + -
206A VAL* 3.9 25.1 - - + -
210A VAL* 3.8 28.7 - - + -
211A ILE* 4.2 16.4 - - + -
227A LEU 2.9 9.0 + - - +
228A VAL* 3.1 8.1 - - + +
229A ASN* 2.9 23.2 + - - +
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Residues in contact with SER 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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168A ALA* 3.1 6.3 - - - +
169A LYS* 2.9 44.7 + - - +
188A VAL* 4.3 4.6 - - - +
189A LEU* 1.3 74.6 - - - +
191A THR* 1.3 60.3 + - - +
229A ASN* 3.3 8.8 - - - -
230A PRO* 4.0 8.1 - - - +
234A PHE* 4.3 17.0 - - - -
123B GLN* 5.0 2.2 + - - -
306B ILE* 3.9 25.1 - - - +
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Residues in contact with THR 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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152A GLN* 3.0 25.4 + - - -
164A LEU* 3.5 19.1 - - + +
167A ASP 3.7 4.0 - - - -
168A ALA* 4.0 6.3 - - - -
189A LEU* 4.0 10.1 - - + -
190A SER* 1.3 75.6 - - - +
192A GLN* 1.3 75.7 + - - +
193A HIS* 3.5 3.6 - - - -
202A LEU* 4.2 19.5 - - + -
206A VAL* 4.3 11.2 - - + -
229A ASN* 2.9 36.6 + - - +
234A PHE* 3.3 7.6 - - - -
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Residues in contact with GLN 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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79A TYR* 3.7 12.6 + - - -
164A LEU* 3.9 2.4 - - - +
165A ARG* 3.2 35.9 + - + +
166A PRO* 3.6 6.5 - - - +
167A ASP* 2.8 46.5 + - + +
191A THR* 1.3 87.7 + - - +
193A HIS* 1.3 64.9 + - - +
234A PHE* 3.2 23.5 - - + +
235A VAL 3.1 23.5 + - - +
237A GLY* 3.1 27.9 + - - +
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Residues in contact with HIS 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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163A TRP* 3.2 16.6 - - + +
165A ARG* 3.6 11.3 - - - +
191A THR 3.5 11.0 - - - -
192A GLN* 1.3 78.1 - - - +
194A ALA* 1.3 87.5 + - - +
195A PRO* 3.7 2.4 - - + +
197A ILE* 3.5 20.4 - - + +
199A LEU* 4.7 7.4 - - + +
202A LEU* 3.3 33.4 - - + +
229A ASN* 3.7 5.8 + - - -
233A ARG* 3.6 13.4 - - + -
234A PHE 3.0 43.9 + - - +
235A VAL* 3.7 27.7 - - + +
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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