Contacts of the strand formed by residues 172 - 177 (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 THR 172 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A PHE* 3.4 27.6 - - + -
164A PRO 2.6 28.1 + - - +
165A ALA* 3.0 16.8 + - - +
167A MET* 3.7 35.7 - - + -
170A MET* 4.1 1.5 + - + -
171A HIS* 1.3 74.3 - - - +
173A ASN* 1.3 61.7 + - - +
196A VAL* 4.3 6.7 - - + -
197A THR 3.6 4.3 - - - +
198A ASN* 4.2 0.7 - - + +
199A LYS* 3.5 14.8 - - - -
204A PHE* 5.1 3.1 - - + -
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Residues in contact with ASN 173 (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 5.3 0.6 + - - -
123A HIS* 3.1 27.6 + - - +
124A GLY 4.6 0.2 - - - -
125A ASP* 3.3 27.8 + - - -
126A ALA* 3.6 15.8 + - - +
129A TRP* 4.2 3.5 - - - -
163A PHE* 3.6 10.3 - - - -
171A HIS 3.9 0.2 + - - -
172A THR* 1.3 75.1 - - - +
174A GLN* 1.3 75.8 + - - +
197A THR* 2.8 24.4 + - - +
198A ASN 4.0 15.0 - - - +
199A LYS* 2.7 34.8 + - + +
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Residues in contact with GLN 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A TYR* 2.7 31.3 + - - -
120A TRP* 3.3 27.3 - - + +
123A HIS* 2.9 31.9 - - - +
125A ASP 3.1 14.3 - - - +
126A ALA* 4.6 0.7 - - - -
129A TRP* 3.8 29.7 - - + +
163A PHE* 3.7 8.0 - - - -
173A ASN* 1.3 90.4 - - - +
175A PHE* 1.3 64.4 + - - +
196A VAL* 3.3 4.9 - - - +
197A THR* 2.9 35.4 + - - +
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Residues in contact with PHE 175 (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* 5.2 0.4 - - + -
120A TRP* 4.2 1.3 - - - -
129A TRP* 3.1 22.2 + + - -
131A ILE* 3.5 47.5 - - + +
159A LEU 4.8 3.4 - - - -
163A PHE* 3.3 40.6 - + + -
174A GLN* 1.3 75.9 - - - +
176A LEU* 1.3 79.5 + - - +
194A VAL* 3.9 19.3 - - + -
195A GLN 3.0 14.6 - - - +
196A VAL* 3.9 15.9 - - + -
208A PHE* 3.7 45.5 - + - -
219A PHE* 4.0 7.0 - + - -
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Residues in contact with LEU 176 (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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95A VAL* 4.4 10.1 - - + +
96A ASP* 3.7 22.9 - - + +
111A GLY* 3.5 32.3 - - - +
113A TYR* 3.8 13.9 - - - +
120A TRP* 3.4 46.4 - - + +
129A TRP* 4.2 1.6 - - - +
131A ILE* 4.3 5.4 - - - -
175A PHE* 1.3 85.4 - - - +
177A GLY* 1.3 68.3 + - - +
194A VAL* 3.2 10.3 - - - +
195A GLN* 2.8 35.4 + - + +
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Residues in contact with GLY 177 (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* 4.2 9.0 + - - +
98A THR* 3.3 16.8 - - - -
109A LEU* 4.1 27.0 + - - +
110A VAL* 5.9 1.2 - - - +
131A ILE* 4.7 0.6 - - - +
176A LEU* 1.3 80.4 - - - +
178A GLY* 1.3 58.4 + - - -
179A ALA 3.1 8.8 + - - -
192A TYR* 5.5 0.2 - - - -
193A PRO 4.1 6.3 - - - -
194A VAL* 4.3 1.3 - - - -
195A GLN* 3.1 17.3 + - - -
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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