Contacts of the strand formed by residues 198 - 205 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B VAL* 4.1 15.7 - - + -
70B ILE* 5.2 1.1 - - + -
78B LEU* 4.8 9.0 - - + -
127B ILE* 3.7 17.7 - - + +
128B ALA 2.8 17.4 + - - +
129B ILE* 4.3 17.9 - - + -
130B ALA* 2.9 24.3 + - - +
190B ALA* 3.7 28.0 - - + -
191B LEU 3.7 3.6 - - - +
192B LEU* 4.0 6.5 - - + +
196B GLY 4.1 0.4 + - - -
197B GLU* 1.3 69.3 - - - +
199B ILE* 1.3 60.5 + - - +
200B GLY 3.5 23.1 - - - +
201B ILE* 4.0 20.4 - - + -
221B SER* 3.3 18.7 + - - +
224B ALA* 5.6 0.7 - - + -
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Residues in contact with ILE 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ALA* 3.9 17.7 - - + -
131B ASP 5.6 0.4 - - - +
132B SER* 3.8 3.3 - - - -
135B LEU* 3.9 42.0 - - + -
140B PHE 4.9 2.0 - - - +
141B ALA* 4.1 16.6 - - + -
159B VAL* 4.2 7.6 - - + -
176B ILE* 3.2 15.9 - - - +
191B LEU* 2.8 46.9 + - + +
192B LEU 3.9 7.4 - - - +
193B ASN* 3.9 21.1 - - + +
197B GLU 3.4 0.4 + - - +
198B LEU* 1.3 78.2 - - - +
200B GLY* 1.3 56.9 + - - +
221B SER* 2.9 25.8 + - - +
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Residues in contact with GLY 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B ILE* 4.5 0.4 - - - -
190B ALA* 3.7 0.3 - - - -
191B LEU* 2.8 41.5 + - - +
198B LEU* 3.5 12.1 - - - +
199B ILE* 1.3 81.1 - - - +
201B ILE* 1.3 63.6 + - - -
218B ALA* 4.3 4.7 - - - -
219B ILE 3.1 13.2 - - - -
220B PRO* 4.3 0.2 - - - -
221B SER* 3.8 6.3 - - - -
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Residues in contact with ILE 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B VAL* 3.7 30.3 - - + -
78B LEU* 4.2 19.7 - - + -
79B THR 4.5 9.2 - - - +
80B ASN* 4.0 13.9 - - - +
113B ILE* 5.1 2.5 - - + -
188B GLY* 3.8 26.9 - - - +
189B GLY 3.3 2.2 - - - +
198B LEU* 4.0 18.6 - - + -
200B GLY* 1.3 71.2 - - - +
202B ASN* 1.3 60.4 + - - +
203B THR* 2.7 24.5 + - - +
218B ALA* 3.9 1.3 - - - -
219B ILE* 2.8 34.9 + - + +
224B ALA* 3.9 24.9 - - + -
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Residues in contact with ASN 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B ASN* 3.0 2.4 - - - +
143B ALA* 3.7 10.7 - - - +
144B VAL 4.2 2.9 + - - +
178B THR* 4.7 0.2 - - - +
182B ILE* 3.4 40.3 - - + +
186B ASN* 3.8 17.7 - - + +
187B SER* 3.6 3.5 - - - -
188B GLY* 2.9 27.4 + - - -
189B GLY 2.8 13.2 + - - +
190B ALA 2.9 27.3 - - - +
191B LEU* 3.6 23.2 - - - +
200B GLY 4.0 0.2 + - - -
201B ILE* 1.3 68.5 - - - +
203B THR* 1.4 58.2 + - - +
217B PHE 3.9 3.3 + - - +
218B ALA* 3.8 8.1 - - - +
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Residues in contact with THR 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B ASN* 3.2 28.1 + - - +
82B HIS* 3.3 18.0 - - - -
112B ASP* 3.5 18.2 - - - +
170B GLU* 3.7 13.7 - - - +
175B PHE* 4.1 14.8 - - + -
182B ILE* 5.6 2.2 - - - +
187B SER* 3.7 9.2 + - - -
201B ILE 2.7 21.6 + - - -
202B ASN* 1.4 71.7 - - - +
204B ALA* 1.3 59.6 + - + +
217B PHE 2.9 13.5 + - - -
219B ILE* 3.2 17.8 - - + +
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Residues in contact with ALA 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B LEU* 3.9 37.9 - - + -
170B GLU* 5.3 1.1 - - - +
175B PHE* 5.0 2.0 - - + -
182B ILE* 4.7 2.1 - - - +
203B THR* 1.3 86.3 - - + +
205B ILE* 1.3 65.7 + - - +
217B PHE* 2.8 38.4 + - + +
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Residues in contact with ILE 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B LEU* 4.9 5.7 - - - +
182B ILE* 3.4 50.3 - - + +
183B ASN* 4.6 10.3 - - - -
184B ARG* 5.2 3.8 - - + +
204B ALA* 1.3 84.1 - - - +
206B LEU* 1.4 68.7 + - - +
207B ALA* 3.7 27.0 + - + -
210B GLY 4.5 8.3 - - - +
211B GLY 4.3 1.3 - - - -
212B SER* 4.1 13.7 - - - +
215B ILE 3.4 9.6 - - - +
216B GLY* 4.0 6.7 - - - -
217B PHE* 4.2 4.7 - - - -
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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