Contacts of the strand formed by residues 198 - 205 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68I VAL* 4.1 17.5 - - + -
70I ILE* 5.2 1.6 - - + -
78I LEU* 4.8 8.3 - - + -
127I ILE* 3.7 18.4 - - + +
128I ALA 2.7 17.8 + - - +
129I ILE* 4.3 14.4 - - + -
130I ALA* 2.9 26.9 + - - +
190I ALA* 3.7 27.1 - - + -
191I LEU 3.6 3.6 - - - +
192I LEU* 4.0 6.0 - - + +
196I GLY 4.1 0.4 + - - -
197I GLU* 1.3 68.2 - - - +
199I ILE* 1.3 59.8 + - - +
200I GLY 3.4 24.0 - - - +
201I ILE* 3.7 22.0 - - + -
221I SER* 3.3 19.5 + - - +
224I ALA* 5.5 0.9 - - + -
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Residues in contact with ILE 199 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130I ALA* 3.9 18.6 - - + -
131I ASP 5.7 0.4 - - - +
132I SER* 3.8 4.3 - - - -
135I LEU* 3.9 40.2 - - + -
140I PHE 4.9 1.3 - - - +
141I ALA* 4.1 10.5 - - + -
159I VAL* 4.2 7.4 - - + -
176I ILE* 3.2 15.6 - - - +
191I LEU* 2.8 46.7 + - + +
192I LEU 3.9 13.5 - - - +
193I ASN* 4.0 15.7 - - + +
197I GLU 3.4 6.0 + - - +
198I LEU* 1.3 77.7 - - - +
200I GLY* 1.3 58.7 + - - +
221I SER* 3.0 25.5 + - - +
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Residues in contact with GLY 200 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176I ILE* 4.5 0.7 - - - -
191I LEU* 2.9 35.5 + - - -
198I LEU* 3.4 11.9 - - - +
199I ILE* 1.3 82.1 - - - +
201I ILE* 1.4 66.0 + - - -
218I ALA* 4.2 5.4 - - - -
219I ILE 3.1 13.9 - - - -
220I PRO* 4.3 0.2 - - - -
221I SER* 3.8 7.0 - - - -
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Residues in contact with ILE 201 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68I VAL* 4.0 9.0 - - + -
78I LEU* 3.6 38.6 - - + -
79I THR 4.7 7.6 - - - +
80I ASN* 3.9 18.4 - - - +
113I ILE* 5.3 2.9 - - + -
188I GLY* 3.6 22.4 - - - +
189I GLY 3.2 12.3 - - - +
198I LEU* 3.7 24.5 - - + -
200I GLY* 1.4 71.4 - - - +
202I ASN* 1.3 62.5 + - - +
203I THR* 2.6 24.5 + - - +
218I ALA* 3.8 1.5 - - - +
219I ILE* 2.9 31.3 + - + +
224I ALA* 4.4 8.1 - - + -
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Residues in contact with ASN 202 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80I ASN* 3.0 1.6 - - - +
143I ALA* 3.6 12.6 - - - +
144I VAL 4.3 2.1 + - - +
178I THR* 4.7 0.2 - - - +
182I ILE* 3.5 40.0 - - + +
186I ASN* 3.7 18.4 - - - +
187I SER* 3.5 3.0 - - - -
188I GLY* 2.9 28.2 + - - -
189I GLY 3.1 6.1 + - - +
190I ALA 3.0 28.1 + - - +
191I LEU* 3.6 22.6 - - - +
201I ILE* 1.3 68.2 - - - +
203I THR* 1.3 58.3 + - - +
217I PHE 3.8 4.4 + - - -
218I ALA* 3.7 9.3 - - - +
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Residues in contact with THR 203 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80I ASN* 3.3 21.9 + - - +
82I HIS* 3.3 13.3 + - - -
112I ASP* 3.8 5.4 - - - +
170I GLU* 3.7 22.7 - - - +
175I PHE* 3.9 20.4 - - + -
182I ILE* 5.5 2.1 - - - +
187I SER* 3.1 18.5 + - - -
201I ILE 2.6 21.3 + - - -
202I ASN* 1.3 71.1 - - - +
204I ALA* 1.3 60.9 + - + +
217I PHE 2.8 13.5 + - - -
219I ILE* 3.2 21.1 - - + +
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Residues in contact with ALA 204 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169I LEU* 3.9 37.0 - - + -
170I GLU* 5.3 1.6 - - - +
175I PHE* 5.0 1.6 - - + -
182I ILE* 4.8 1.9 - - - +
203I THR* 1.3 86.7 - - + +
205I ILE* 1.3 66.8 + - - +
217I PHE* 2.8 37.0 + - + +
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Residues in contact with ILE 205 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169I LEU* 5.0 5.4 - - - +
182I ILE* 3.5 50.0 - - + +
183I ASN* 4.6 10.1 - - - -
184I ARG* 5.2 3.6 - - + +
204I ALA* 1.3 82.9 - - - +
206I LEU* 1.3 67.4 + - - +
207I ALA* 3.7 26.3 + - + -
210I GLY 4.4 8.5 - - - +
211I GLY 4.3 1.3 - - - -
212I SER* 4.3 12.6 - - - +
215I ILE 3.4 10.1 - - - +
216I GLY* 4.1 6.1 - - - -
217I PHE* 4.2 4.9 - - - -
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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