Contacts of the strand formed by residues 197 - 203 (chain B) in PDB entry 1G4M
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 197 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187B THR 3.7 1.2 - - - +
188B ARG* 3.4 2.9 - - - -
189B GLN* 2.8 35.3 + - - +
191B LEU* 4.0 17.7 - - + -
196B PRO* 1.3 75.2 - - - +
198B HIS* 1.3 75.2 + - - +
199B LEU 3.9 2.2 - - - +
220B VAL* 4.0 11.4 - - + -
221B THR 3.6 4.7 - - - +
222B ASN* 3.8 20.0 - - - +
224B THR* 3.6 13.3 - - + +
228B VAL* 3.8 28.5 - - + -
327B LEU* 3.7 22.2 - - + -
329B VAL* 5.1 2.7 - - + -
343B VAL* 4.0 15.9 - - + -
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Residues in contact with HIS 198 (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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186B THR* 3.8 30.6 + - + +
187B THR 3.5 4.0 - - - -
188B ARG* 3.8 28.7 - - + +
196B PRO* 3.8 4.9 + - + +
197B LEU* 1.3 76.9 - - - +
199B LEU* 1.3 62.9 + - - +
200B GLU* 3.8 21.7 - - + +
219B HIS* 3.7 2.6 + - - +
220B VAL* 3.4 5.5 - - - +
221B THR* 2.8 57.3 + - + +
223B ASN* 5.2 2.9 - - - +
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Residues in contact with LEU 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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185B GLU 3.9 0.2 - - - +
186B THR* 3.1 5.7 - - - -
187B THR* 2.8 43.7 + - + -
197B LEU* 3.9 4.2 - - + +
198B HIS* 1.3 73.8 + - - +
200B GLU* 1.3 74.2 + - - +
201B ALA* 4.9 0.4 - - + -
218B VAL* 3.9 27.6 - - + -
219B HIS 3.7 0.7 - - - -
220B VAL* 4.0 11.0 - - + +
325B VAL* 3.8 24.0 - - + +
327B LEU* 4.1 19.1 - - + -
343B VAL* 3.9 15.3 - - + +
344B ALA 3.9 3.4 - - - -
345B VAL* 3.8 31.8 - - + +
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Residues in contact with GLU 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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184B ALA* 3.7 20.1 - - + +
185B GLU 3.4 3.8 - - - +
186B THR* 3.7 23.0 - - + +
198B HIS* 3.8 14.9 - - + +
199B LEU* 1.3 80.1 - - - +
201B ALA* 1.3 65.8 + - - +
217B ASN 3.7 0.3 - - - +
218B VAL* 3.7 0.5 - - - -
219B HIS* 2.7 59.8 + - + +
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Residues in contact with ALA 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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184B ALA* 3.4 2.5 - - - -
185B GLU* 2.9 32.5 + - - -
199B LEU* 4.9 2.0 - - + -
200B GLU* 1.3 79.3 - - - +
202B SER* 1.3 62.1 + - - +
216B VAL* 4.5 1.1 - - + -
217B ASN 3.0 11.7 - - - +
218B VAL* 4.4 4.7 - - + -
325B VAL* 4.2 17.9 - - + -
345B VAL* 4.1 21.5 - - + +
347B LEU* 3.4 14.7 - - + +
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Residues in contact with SER 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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182B PRO 4.5 7.9 - - - -
183B THR 4.3 4.7 - - - -
184B ALA* 3.8 23.4 - - - +
201B ALA* 1.3 78.2 - - - +
203B LEU* 1.3 64.3 + - - +
215B SER 3.9 0.2 - - - +
216B VAL* 3.7 1.9 - - - -
217B ASN* 2.9 42.9 + - - +
347B LEU* 3.4 11.2 - - - +
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Residues in contact with LEU 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B PRO* 2.9 30.1 - - + +
183B THR 5.3 1.2 + - - -
202B SER* 1.3 80.8 + - - +
204B ASP* 1.3 61.1 + - - +
205B LYS 3.7 9.0 - - - +
208B TYR* 3.4 12.8 - - + +
214B ILE* 4.0 7.2 - - + -
215B SER 3.6 1.6 - - - +
216B VAL* 4.0 21.3 - - + -
323B VAL* 3.8 21.3 - - + -
347B LEU* 3.7 31.8 - - + +
348B PRO 3.6 24.2 - - - +
349B PHE* 3.7 23.3 - - + -
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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