Contacts of the strand formed by residues 190 - 198 (chain A) in PDB entry 1MS4
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 LEU 190 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ILE* 4.2 22.7 - - + -
102A LYS* 3.7 34.5 - - + +
107A TYR* 3.8 29.8 - - + -
183A ILE 3.8 2.9 - - - -
184A VAL* 4.4 2.0 - - + -
188A GLY 4.4 1.1 - - - +
189A ASN* 1.3 73.5 - - - +
191A VAL* 1.3 59.2 + - - +
192A TYR 4.2 0.2 - - - -
209A TYR* 3.1 9.5 - - - +
210A SER* 2.9 36.0 + - - +
213A GLU* 3.7 10.5 - - - +
214A GLY* 3.7 31.0 - - - +
217A TRP* 3.8 20.2 - - + -
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Residues in contact with VAL 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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100A ILE* 3.6 4.7 - - - +
182A ALA* 3.2 21.8 - - - +
183A ILE* 2.8 30.8 + - + +
185A ALA* 3.9 20.0 - - + +
189A ASN 3.7 11.2 - - - +
190A LEU* 1.3 78.6 - - - +
192A TYR* 1.3 66.3 + - - +
193A PRO* 3.7 3.8 - - + +
207A ILE* 3.8 29.4 - - + -
208A PHE 3.7 1.8 - - - -
209A TYR* 4.3 0.9 - - + -
233A ALA* 5.7 3.1 - - + -
240A LEU* 4.1 18.2 - - + -
259A MET* 3.9 18.2 - - + -
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Residues in contact with TYR 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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98A THR* 3.2 45.0 + - + -
100A ILE* 3.6 20.6 - - + -
107A TYR* 2.9 35.9 + - + +
109A LEU* 3.5 32.9 + - + -
133A LEU* 3.7 5.1 - - + +
177A GLY* 5.5 0.2 - - - -
182A ALA* 3.7 7.2 - - + -
191A VAL* 1.3 75.5 - - - +
193A PRO* 1.3 67.4 - - + +
194A VAL* 3.3 15.2 + - + -
207A ILE 3.7 0.2 - - - -
208A PHE* 2.7 44.6 + + + +
217A TRP* 3.5 39.3 - + - -
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Residues in contact with PRO 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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98A THR* 5.3 3.1 - - + -
177A GLY* 4.1 1.0 - - - -
178A GLY 3.3 18.4 + - - +
181A VAL 6.0 0.2 - - - +
182A ALA* 3.9 14.8 - - + -
191A VAL* 3.7 9.6 - - + +
192A TYR* 1.3 86.8 - - + +
194A VAL* 1.3 59.8 + - - +
206A LYS 3.3 8.1 - - - +
207A ILE* 4.4 10.8 - - + -
231A PRO* 3.8 31.8 - - + +
232A VAL* 4.2 0.4 - - - -
233A ALA* 3.7 39.0 - - + +
242A ILE* 4.7 4.0 - - + -
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Residues in contact with VAL 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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109A LEU* 4.6 1.6 - - + -
175A PHE* 3.9 17.0 - - + -
176A LEU 3.2 17.5 - - - +
177A GLY* 4.3 2.5 - - - -
192A TYR* 3.7 6.7 - - + +
193A PRO* 1.3 79.7 - - - +
195A GLN* 1.3 58.2 + - - +
196A VAL* 3.9 10.5 - - + -
205A SER* 3.1 6.2 - - - -
206A LYS* 2.6 47.0 + - + +
208A PHE* 3.6 29.8 - - + -
219A PHE* 3.7 28.5 - - + -
231A PRO* 3.6 6.7 - - - +
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Residues in contact with GLN 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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96A ASP* 3.2 21.0 + - - -
119A TYR* 5.4 1.5 + - - -
120A TRP* 3.5 29.8 + - + +
175A PHE* 3.0 4.5 - - - +
176A LEU* 2.8 48.9 + - + +
177A GLY 3.1 19.3 + - - +
178A GLY* 4.3 0.4 - - - -
194A VAL* 1.3 71.2 - - - +
196A VAL* 1.3 62.3 + - - +
203A VAL* 4.5 3.8 - - + -
204A PHE 3.5 6.3 - - - +
228A CYS 5.0 0.2 - - - +
229A SER* 3.2 17.1 - - - -
230A GLU* 2.9 38.0 + - - +
231A PRO* 4.0 11.6 - - + +
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Residues in contact with VAL 196 (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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120A TRP* 4.4 0.2 - - - -
163A PHE* 3.8 25.1 - - + -
167A MET* 4.6 2.9 - - + -
172A THR* 4.3 4.7 - - + -
174A GLN 3.3 11.7 - - - +
175A PHE* 4.0 3.6 - - + -
194A VAL* 3.9 16.4 - - + +
195A GLN* 1.3 79.8 - - - +
197A THR* 1.3 69.5 + - - +
203A VAL* 3.3 6.8 - - - +
204A PHE* 2.8 61.8 + - + +
206A LYS* 3.7 28.0 - - + -
219A PHE* 4.4 3.1 - - + -
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Residues in contact with THR 197 (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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120A TRP* 3.4 29.2 - - + +
121A THR* 4.1 22.2 - - + +
172A THR* 3.6 4.3 - - - -
173A ASN* 2.8 33.9 + - - +
174A GLN* 2.9 40.0 + - - +
196A VAL* 1.3 81.2 - - - +
198A ASN* 1.3 62.5 + - - +
201A LYS* 5.0 3.6 - - - -
202A GLN 3.3 12.1 - - - +
203A VAL* 4.4 6.5 - - + -
204A PHE* 4.1 3.5 - - - -
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Residues in contact with ASN 198 (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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123A HIS 5.5 0.2 - - - +
170A MET* 3.5 34.7 - - + +
171A HIS 3.1 16.6 - - - +
172A THR* 4.2 0.7 - - - +
173A ASN* 3.9 11.6 + - - +
197A THR* 1.3 76.7 - - - +
199A LYS* 1.3 59.2 + - - +
200A LYS* 2.8 20.7 + - - +
201A LYS* 2.8 21.8 + - - +
202A GLN* 2.9 47.9 + - - +
204A PHE* 4.0 9.5 - - + -
226A PHE* 3.7 6.3 - - - -
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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