Contacts of the strand formed by residues 198 - 206 (chain A) in PDB entry 3STJ
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 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A VAL* 4.2 10.5 - - + -
70A ILE* 5.3 1.1 - - + -
78A LEU* 4.6 11.2 - - + -
127A ILE* 3.8 17.4 - - + +
128A ALA 2.7 18.9 + - - +
129A ILE* 4.3 16.8 - - + -
130A ALA* 3.0 23.9 + - - +
190A ALA* 3.8 27.1 - - + -
191A LEU 3.7 3.8 - - - +
192A LEU* 4.2 3.8 - - + +
196A GLY 4.1 1.0 + - - -
197A GLU* 1.4 68.8 - - - +
199A ILE* 1.4 59.5 + - - +
200A GLY 3.3 24.5 - - - +
201A ILE* 4.0 25.8 - - + -
221A SER* 3.4 18.7 + - - +
224A ALA* 5.5 0.4 - - + -
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Residues in contact with ILE 199 (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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130A ALA* 3.9 17.9 - - + -
131A ASP 5.7 0.4 - - - +
132A SER* 3.7 4.1 - - - -
135A LEU* 3.9 42.2 - - + -
140A PHE 4.9 3.4 - - - +
141A ALA* 4.2 9.9 - - + -
159A VAL* 4.1 14.6 - - + -
176A ILE* 3.1 17.3 - - - +
191A LEU* 2.7 49.4 + - + +
192A LEU 4.2 6.1 - - - +
193A ASN* 4.1 13.7 - - + +
197A GLU 3.4 6.7 + - - +
198A LEU* 1.4 77.2 - - - +
200A GLY* 1.3 55.0 + - - +
220A PRO* 3.6 0.2 - - - +
221A SER* 2.9 25.2 + - - +
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Residues in contact with GLY 200 (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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176A ILE* 4.3 0.9 - - - -
191A LEU* 3.1 34.0 + - - +
198A LEU* 3.3 13.6 - - - +
199A ILE* 1.3 81.0 - - - +
201A ILE* 1.3 64.3 + - - -
218A ALA* 4.2 6.3 - - - -
219A ILE 3.0 14.8 - - - -
220A PRO* 4.2 0.2 - - - -
221A SER* 3.8 6.1 - - - +
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Residues in contact with ILE 201 (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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68A VAL* 3.6 30.5 - - + -
78A LEU* 4.1 20.0 - - + -
79A THR 4.4 9.0 - - - +
80A ASN* 3.9 17.3 - - - +
113A ILE* 5.2 2.5 - - + -
188A GLY* 3.8 28.9 - - - +
189A GLY 3.5 2.0 - - - +
198A LEU* 4.0 13.2 - - + -
200A GLY* 1.3 77.0 - - - +
202A ASN* 1.3 55.4 + - - +
203A THR* 2.7 24.1 + - - +
218A ALA* 3.9 2.2 - - - -
219A ILE* 2.8 36.1 + - + +
224A ALA* 4.1 21.8 - - + -
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Residues in contact with ASN 202 (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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80A ASN* 2.9 2.4 - - - +
143A ALA* 3.8 10.2 - - - +
144A VAL 4.2 2.9 + - - +
182A ILE* 3.7 33.5 - - + +
186A ASN* 3.8 18.5 - - - +
187A SER* 3.4 3.5 - - - -
188A GLY 2.9 27.4 + - - -
189A GLY 3.0 11.1 + - - +
190A ALA 3.1 22.8 - - - +
191A LEU* 3.4 31.5 - - - +
201A ILE* 1.3 67.0 - - - +
203A THR* 1.3 57.8 + - - +
217A PHE 3.8 4.0 - - - -
218A ALA* 3.7 9.5 - - - +
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Residues in contact with THR 203 (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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80A ASN* 3.1 22.5 + - - +
82A HIS* 3.3 18.9 + - - -
112A ASP* 3.5 24.0 - - - +
170A GLU* 3.6 13.9 - - - +
175A PHE* 4.0 15.3 - - + -
182A ILE* 5.5 2.4 - - - +
187A SER* 3.5 9.4 + - - -
201A ILE 2.7 17.8 + - - -
202A ASN* 1.3 71.7 - - - +
204A ALA* 1.3 59.5 + - + +
217A PHE 2.9 13.6 + - - -
219A ILE* 3.2 18.2 + - + +
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Residues in contact with ALA 204 (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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169A LEU* 3.9 37.9 - - + -
170A GLU* 5.3 1.3 - - - +
175A PHE* 5.0 1.8 - - + -
182A ILE* 4.8 1.6 - - - +
203A THR* 1.3 86.3 + - + +
205A ILE* 1.3 66.5 + - - +
217A PHE* 2.7 38.1 + - + +
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Residues in contact with ILE 205 (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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169A LEU* 5.0 5.5 - - - +
182A ILE* 3.4 49.8 - - + +
183A ASN* 4.6 10.1 - - - -
184A ARG* 5.2 3.1 - - + +
204A ALA* 1.3 82.6 - - - +
206A LEU* 1.3 69.2 + - - +
207A ALA* 3.6 26.6 + - + -
210A GLY 4.5 8.5 - - - +
211A GLY 4.2 1.3 - - - -
212A SER* 4.1 12.8 - - - +
215A ILE 3.4 9.9 - - - +
216A GLY* 4.1 5.8 - - - -
217A PHE* 4.2 4.7 - - - -
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Residues in contact with LEU 206 (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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167A LEU* 5.8 5.6 - - + +
169A LEU* 5.3 12.3 - - + -
205A ILE* 1.3 76.6 - - - +
207A ALA* 1.3 60.6 + - - +
208A PRO* 4.4 2.2 - - - -
213A VAL* 3.3 22.6 + - - +
215A ILE* 3.0 25.6 + - + +
217A PHE* 3.8 18.3 - - + -
148C PHE* 3.9 30.3 - - + +
150C LEU* 3.8 30.1 - - + -
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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