Contacts of the strand formed by residues 188 - 195 (chain A) in PDB entry 3P1I
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 GLY 188 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A PHE* 3.4 16.6 - - - -
97A ILE 3.0 13.9 - - - -
99A ARG* 3.9 5.2 - - - -
136A GLU* 3.4 6.8 - - - +
137A ALA 3.0 25.0 + - - -
184A LEU* 6.0 0.2 - - - -
186A LYS 3.1 4.2 + - - +
187A ALA* 1.3 79.6 - - - +
189A PHE* 1.3 67.6 + - - +
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Residues in contact with PHE 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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42A LEU* 4.3 4.9 - - + -
96A PHE* 3.5 5.1 - - - -
97A ILE* 2.8 79.3 + - + +
99A ARG* 4.0 14.6 - - + -
105A VAL* 3.9 35.0 - - + -
134A TYR* 4.9 0.4 - - + -
135A TYR 3.1 17.5 - - - +
136A GLU* 4.1 8.3 - - + +
181A PHE* 3.8 26.0 - + + -
184A LEU* 4.0 14.4 - - + -
188A GLY* 1.3 77.7 - - - +
190A TYR* 1.3 76.7 + - - +
191A LEU* 3.9 7.9 - - + -
207A ALA* 4.4 4.5 - - + -
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Residues in contact with TYR 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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93A ARG* 3.9 24.9 - - + -
94A THR* 3.2 25.4 - - - +
95A GLY* 3.5 8.3 - - - -
96A PHE* 3.6 32.5 - + - -
97A ILE* 5.1 0.2 - - - -
134A TYR* 3.2 7.8 - - - +
135A TYR* 2.7 64.1 + + + +
137A ALA* 4.3 6.7 - - + -
140A ASP* 2.6 27.4 + - - -
141A VAL* 3.2 8.3 + - + -
142A ALA* 2.9 36.9 + - + -
150A MET* 5.4 0.2 - - - -
154A TYR* 5.4 0.4 - - + -
189A PHE* 1.3 76.6 - - - +
191A LEU* 1.3 63.9 + - - +
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Residues in contact with LEU 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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43A MET* 4.4 8.5 - - + -
93A ARG* 3.5 3.6 - - - +
94A THR* 3.0 43.3 + - + -
97A ILE* 4.3 3.8 - - + +
107A VAL* 4.0 20.2 - - + -
132A LEU* 4.4 11.0 - - + -
133A PHE 3.4 12.6 - - - +
134A TYR* 4.1 1.6 - - + -
181A PHE* 3.7 36.1 - - + -
189A PHE* 3.9 9.6 - - + -
190A TYR* 1.3 79.0 - - - +
192A ALA* 1.3 63.8 + - - +
193A PHE* 4.5 2.5 - - + -
205A VAL* 4.0 27.1 - - + -
207A ALA* 4.4 13.7 - - + -
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Residues in contact with ALA 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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91A TRP* 4.2 11.7 - - + -
92A LEU 3.0 13.9 - - - +
93A ARG* 4.3 2.9 - - + -
132A LEU* 3.6 4.7 - - - +
133A PHE* 2.8 41.8 + - + +
148A PHE* 5.2 0.2 - - + -
154A TYR* 3.9 32.5 - - + -
191A LEU* 1.3 77.4 - - - +
193A PHE* 1.3 67.2 + - - +
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Residues in contact with PHE 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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54A TRP* 4.0 10.1 - + - -
62A TRP* 3.7 22.2 + - + -
90A ASN 3.5 1.3 - - - +
91A TRP* 3.2 10.3 - - - +
92A LEU* 2.8 44.6 + - + +
94A THR* 4.0 23.3 - - + -
109A LEU* 3.8 16.4 - - + -
130A PHE* 3.9 22.7 - + + -
131A ASN 3.2 7.2 - - - +
132A LEU* 3.5 28.9 - - + -
191A LEU* 4.6 2.5 - - + -
192A ALA* 1.3 80.6 - - - +
194A GLN* 1.3 60.3 + - - +
202A LEU* 3.9 18.4 - - + -
205A VAL* 3.8 27.4 - - + -
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Residues in contact with GLN 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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2A SO4 4.6 2.7 + - - -
62A TRP* 4.5 0.9 - - - -
89A ASN* 2.9 25.6 + - - +
90A ASN 3.4 2.9 - - - -
91A TRP* 3.5 30.7 - - + +
130A PHE* 3.4 8.6 - - - +
131A ASN* 2.8 55.1 + - + +
133A PHE* 3.6 24.7 - - + -
193A PHE* 1.3 73.2 - - - +
195A ASP* 1.3 61.9 + - - +
196A GLN* 3.5 29.9 + - + +
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Residues in contact with ASP 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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62A TRP* 3.8 17.2 - - + +
80A VAL* 3.4 31.2 - - + +
82A ASN 5.3 0.9 + - - -
89A ASN* 3.6 0.5 + - - -
90A ASN* 2.7 63.2 + - + +
129A THR 4.9 0.6 - - - +
130A PHE* 4.7 6.1 - - + +
194A GLN* 1.3 74.4 - - - +
196A GLN* 1.3 64.0 + - - +
197A GLY* 3.3 9.4 + - - -
198A ALA* 2.8 40.0 + - - +
200A MET* 4.9 1.1 - - - +
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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