Contacts of the strand formed by residues 189 - 195 (chain A) in PDB entry 5INQ
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 PHE 189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A GLU 3.4 4.8 + - - -
163A VAL* 2.8 51.2 + - + +
164A ILE 4.0 3.6 - - - -
165A PRO* 4.0 24.2 - - + -
168A CYS* 4.1 7.4 - - - -
182A THR* 3.8 19.5 - - + -
183A GLY 4.1 1.6 - - - -
184A ASN* 3.7 46.4 - - + +
185A GLU 4.0 11.4 - - - -
186A GLU 3.5 19.7 - - - -
187A GLY 3.9 11.0 - - - -
188A TYR* 1.3 83.8 - - - +
190A THR* 1.3 75.1 + - - +
215A MET 6.0 0.7 - - - -
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Residues in contact with THR 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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160A LEU 3.2 14.8 - - - +
161A GLN* 3.9 20.0 - - + -
163A VAL* 4.5 0.4 - - - -
183A GLY* 2.9 26.1 + - - -
189A PHE* 1.3 85.9 - - - +
191A ALA* 1.3 65.7 + - - +
217A ASN* 4.4 9.2 + - - +
219A LEU* 3.6 23.7 - - - +
234A THR* 3.8 9.7 + - + -
235A SER* 4.1 7.9 - - - -
236A HIS* 4.1 23.8 - - + +
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Residues in contact with ALA 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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158A VAL 3.8 0.2 - - - +
159A PHE* 3.7 0.3 - - - -
160A LEU* 2.8 35.6 + - + +
163A VAL* 4.2 18.2 - - + -
171A LEU* 5.9 0.4 - - + -
180A ILE* 4.3 4.3 - - + -
181A ILE 3.1 16.4 - - - +
182A THR* 4.3 11.0 - - + -
190A THR* 1.3 77.7 - - - +
192A ILE* 1.3 67.1 - - - +
193A LEU* 4.2 16.8 - - + -
219A LEU* 3.9 2.5 - - - -
234A THR* 4.2 1.4 - - - +
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Residues in contact with ILE 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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157A VAL* 3.8 25.6 - - + -
158A VAL 3.3 3.8 - - - +
159A PHE* 4.0 18.4 - - + -
179A THR 3.7 1.6 - - - +
181A ILE* 2.8 35.9 + - - +
191A ALA* 1.3 78.3 - - - +
193A LEU* 1.3 63.5 + - - +
194A LEU* 3.9 15.7 - - + +
219A LEU* 3.9 19.5 - - + +
221A VAL* 3.8 26.2 - - + -
232A LEU* 3.5 26.9 - - + +
234A THR* 3.8 14.8 - - + +
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Residues in contact with LEU 193 (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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150A LEU* 4.3 15.3 - - + -
157A VAL* 3.3 11.6 - - - +
158A VAL* 2.8 50.3 + - + +
160A LEU* 4.1 21.8 - - + -
171A LEU* 4.3 21.5 - - + -
175A ALA* 4.9 2.0 - - + -
178A TYR* 3.8 34.0 - - + -
179A THR 3.2 2.9 - - - -
180A ILE* 4.1 29.6 - - + -
191A ALA* 4.2 6.7 - - + -
192A ILE* 1.3 80.1 - - - +
194A LEU* 1.3 60.4 + - - +
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Residues in contact with LEU 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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156A ASP 3.9 2.0 - - - -
157A VAL* 4.2 11.7 - - + -
178A TYR* 3.4 4.4 - - - -
179A THR* 2.9 44.6 + - - +
181A ILE* 4.4 8.1 - - + -
192A ILE* 3.9 22.9 - - + +
193A LEU* 1.3 81.2 - - - +
195A LYS* 1.3 65.9 + - - +
196A LYS* 3.2 1.6 + - - -
199A VAL* 4.0 24.7 - - + +
201A PHE* 3.9 37.5 - - + +
221A VAL* 4.0 6.3 - - + -
223A VAL* 4.0 18.8 - - + -
232A LEU* 4.5 2.9 - - + -
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Residues in contact with LYS 195 (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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150A LEU 5.5 0.4 + - - -
154A SER* 3.4 26.7 + - - +
155A PRO 3.9 3.1 - - - +
156A ASP* 2.9 28.0 + - - +
177A SER* 2.9 36.6 + - - +
178A TYR* 3.5 32.1 + - + -
194A LEU* 1.3 70.9 - - - +
196A LYS* 1.3 73.8 + - - +
198A ARG* 3.2 31.9 + - + +
199A VAL* 3.1 25.1 + - - +
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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