Contacts of the strand formed by residues 195 - 206 (chain B) in PDB entry 6MGP
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 SER 195 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A THR* 4.6 5.7 + - - -
184A ASP* 4.7 0.2 - - - +
148B GLU* 4.4 13.7 - - - -
149B LEU 3.1 14.1 - - - -
150B ARG* 4.5 3.1 - - - -
186B PRO* 4.9 5.2 - - - +
193B ARG* 3.6 3.1 + - - -
194B ASN* 1.3 80.4 + - - +
196B ALA* 1.3 63.3 + - - +
226B TRP* 3.7 6.9 - - - -
301B GOL 2.9 50.4 + - - -
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Residues in contact with ALA 196 (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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147B LEU 4.4 0.2 - - - -
148B GLU* 3.3 7.4 - - - +
149B LEU* 2.9 34.0 + - + +
183B VAL* 4.3 15.3 - - + -
184B ASP 3.4 25.6 - - - +
185B LEU* 4.5 4.3 - - + -
186B PRO* 4.6 3.1 - - + -
195B SER* 1.3 74.4 - - - +
197B PHE* 1.3 63.8 + - - +
226B TRP* 4.0 10.5 - - + -
301B GOL 4.9 1.8 - - - -
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Residues in contact with PHE 197 (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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180A ALA 5.2 4.0 - - - -
181A LEU* 3.7 24.7 - - + -
182A THR 5.4 9.4 - - - +
199A PHE 3.2 23.6 - - - -
200A GLN* 3.8 27.1 - - + -
146B GLN* 3.7 22.9 - - + -
147B LEU 3.2 19.5 - - - -
148B GLU* 4.1 16.4 - - + -
183B VAL* 3.9 10.4 - - - +
196B ALA* 1.3 77.6 - - - +
198B GLY* 1.3 78.8 + - - +
199B PHE* 3.8 7.0 - - + -
232B ALA* 5.3 1.1 - - + -
301C GOL 4.0 15.7 + - - -
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Residues in contact with GLY 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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146B GLN* 3.3 6.8 - - - +
147B LEU 2.9 31.6 + - - -
181B LEU* 3.5 12.8 - - - -
183B VAL* 3.7 16.1 - - - +
197B PHE* 1.3 81.5 - - - +
199B PHE* 1.3 60.9 + - - -
301C GOL 3.7 9.9 - - - -
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Residues in contact with PHE 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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142A TYR* 3.3 21.3 - - - -
199A PHE* 3.5 31.4 - + - +
200A GLN* 4.4 0.9 - - - -
201A GLY 3.2 28.5 - - - -
142B TYR* 3.9 2.7 - - - -
144B PHE* 3.7 26.5 - + + -
145B PHE 3.6 9.9 - - - -
146B GLN* 3.5 21.1 - - + -
181B LEU* 3.7 3.6 - - - +
197B PHE* 3.8 4.3 - - + -
198B GLY* 1.3 73.7 - - - +
200B GLN* 1.3 67.9 + - - +
197C PHE* 3.1 22.3 - - - -
199C PHE* 3.4 39.9 - + + +
301C GOL 3.2 12.8 + - - -
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Residues in contact with GLN 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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144B PHE* 3.1 4.2 - - - +
145B PHE* 3.0 44.7 + - + +
179B LEU* 3.2 22.3 - - + +
180B ALA 2.8 44.0 + - - +
181B LEU* 4.3 5.1 - - + +
199B PHE* 1.3 82.8 - - - +
201B GLY* 1.3 62.6 + - - +
202B ARG* 4.9 2.3 - - - +
146C GLN* 3.0 41.2 - - - +
148C GLU* 4.4 3.4 + - - -
197C PHE* 3.4 22.4 - - + -
199C PHE* 4.6 1.3 - - + -
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Residues in contact with GLY 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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142B TYR* 4.0 13.9 - - - -
143B VAL 3.1 11.9 - - - -
144B PHE* 3.9 8.1 - - - -
179B LEU* 4.3 4.3 - - - -
199B PHE* 4.1 0.6 - - - -
200B GLN* 1.3 76.3 - - - +
202B ARG* 1.3 66.5 + - - +
144C PHE* 4.0 2.1 - - - -
146C GLN* 3.7 8.8 - - - +
199C PHE* 3.2 27.3 - - - -
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Residues in contact with ARG 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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142B TYR* 3.6 6.4 - - - -
143B VAL* 2.8 33.1 + - - +
178B ALA 3.3 26.6 + - - -
179B LEU* 3.5 13.0 - - + -
200B GLN* 4.9 2.0 - - - +
201B GLY* 1.3 74.4 - - - +
203B LEU* 1.3 65.1 + - - +
204B LEU* 3.6 21.8 + - + +
94C GLN* 3.5 21.4 - - - +
96C VAL* 4.8 1.8 - - - +
117C GLY* 4.6 14.8 - - - -
144C PHE* 3.9 11.0 - - + -
146C GLN* 3.6 31.4 + - - +
231C GLY 3.3 24.5 + - - -
232C ALA* 4.6 1.2 - - - +
234C VAL* 3.7 20.1 - - + +
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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
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140B VAL* 4.1 13.0 - - + -
141B TYR 3.3 4.5 - - - +
142B TYR* 3.7 27.6 - - + +
202B ARG* 1.3 72.3 - - - +
204B LEU* 1.3 67.1 + - - +
240B VAL* 4.2 7.4 - - + -
92C PHE* 4.2 19.5 - - + -
93C ALA 3.6 25.8 - - - +
94C GLN* 2.8 42.9 + - + +
117C GLY* 5.7 1.2 - - - -
119C SER* 6.2 1.8 - - - -
144C PHE* 4.1 6.5 - - + -
237C LEU 4.1 16.2 - - - +
238C PHE* 3.7 23.1 - - + -
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Residues in contact with LEU 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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140B VAL* 3.4 3.7 - - - -
141B TYR* 2.9 34.8 + - - +
143B VAL* 4.0 22.0 - - + -
165B LEU* 3.8 28.5 - - + -
167B LEU* 4.5 5.2 - - + -
178B ALA* 4.0 24.5 - - + +
179B LEU* 5.1 1.6 - - + -
202B ARG* 3.6 28.9 - - + +
203B LEU* 1.3 82.3 - - - +
205B HIS* 1.3 61.8 + - - +
206B LEU* 3.5 21.6 + - + +
212B LEU* 6.1 0.2 - - + -
117C GLY* 6.5 0.9 - - - -
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Residues in contact with HIS 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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138B ALA* 5.1 5.2 - - + +
139B GLY* 3.5 23.1 + - - -
140B VAL* 4.0 20.0 - - + +
167B LEU* 5.0 4.2 - - - +
170B LEU* 5.7 2.9 - - - +
204B LEU* 1.3 71.7 - - - +
206B LEU* 1.3 70.9 + - - +
207B SER* 4.1 9.8 + - - -
210B GLN* 3.9 4.7 + - - +
60Z ARG* 6.3 2.9 - - + -
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Residues in contact with LEU 206 (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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135B VAL* 3.7 28.7 - - + -
137B LYS 4.4 0.3 - - - +
138B ALA* 3.2 4.7 - - - +
139B GLY 2.8 31.6 + - - -
141B TYR* 3.8 21.8 - - + -
143B VAL* 4.5 2.0 - - + -
167B LEU* 3.9 32.5 - - + -
204B LEU* 4.0 18.6 - - + +
205B HIS* 1.3 78.7 + - - +
207B SER* 1.3 61.2 + - - +
210B GLN* 3.2 12.3 - - + +
212B LEU* 4.1 8.7 - - + -
237B LEU* 3.6 32.1 - - + -
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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