Contacts of the strand formed by residues 209 - 216 (chain B) in PDB entry 1MWA
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 HIS 209 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162B TRP* 4.4 1.9 + - + -
163B VAL* 3.3 5.7 - - - +
164B ASN* 2.5 47.4 + - - +
165B GLY 4.7 6.5 + - - -
207B ARG 3.8 0.6 + - - +
208B ASN* 1.3 72.7 - - - +
210B PHE* 1.3 69.6 + - - +
211B ARG* 3.6 36.1 - - + +
240B GLU* 3.0 25.2 + - + +
241B ALA 4.0 3.8 - - - -
242B TRP* 3.3 50.0 - + + +
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Residues in contact with PHE 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B LEU* 4.7 2.2 - - + -
145B LEU* 3.8 28.0 - - + -
161B TRP* 5.1 1.6 - - + -
162B TRP 3.5 4.9 - - - +
163B VAL* 3.9 18.2 - - + -
196B LEU* 4.1 9.6 - - + -
198B VAL* 4.4 14.4 - - + -
202B PHE* 3.7 43.3 - + - -
203B TRP* 3.7 33.0 - + - -
208B ASN* 3.6 22.4 - - + -
209B HIS* 1.3 79.0 - - - +
211B ARG* 1.3 64.2 + - - +
240B GLU* 3.3 6.8 - - - +
241B ALA 3.0 39.0 + - - +
243B GLY* 3.8 5.8 - - - -
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Residues in contact with ARG 211 (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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129B LEU* 4.9 0.4 - - - -
161B TRP* 3.5 10.4 - - - -
162B TRP* 2.8 80.0 + - + +
165B GLY* 5.8 2.6 - - - -
209B HIS* 3.6 21.4 - - + -
210B PHE* 1.3 78.3 - - - +
212B CYS* 1.3 62.0 + - - +
213B GLN* 2.4 35.6 + - - +
236B ASN* 5.7 0.8 - - - +
238B SER* 3.3 27.1 + - - -
239B ALA 3.4 13.9 - - - +
240B GLU* 4.5 5.8 - - + -
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Residues in contact with CYS 212 (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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127B VAL* 4.4 2.1 - - + +
129B LEU* 4.2 5.6 - - + +
147B CYS* 2.0 53.8 - - + -
159B LEU* 3.5 20.4 - - - -
160B SER 3.7 3.8 - - - -
161B TRP* 4.1 13.1 - - + -
211B ARG* 1.3 72.9 - - - +
213B GLN* 1.3 63.7 + - - +
214B VAL* 4.2 4.7 - - - -
237B ILE 4.0 0.2 - - - +
238B SER* 3.0 7.6 - - - -
239B ALA* 2.8 36.3 + - + +
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Residues in contact with GLN 213 (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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158B GLU 3.7 0.8 + - - +
159B LEU* 3.4 1.9 - - - +
160B SER* 2.9 50.1 + - - +
162B TRP* 3.7 7.9 + - + +
211B ARG* 2.4 34.6 + - - +
212B CYS* 1.3 73.0 - - - +
214B VAL* 1.3 73.9 + - - +
215B GLN* 4.0 7.0 - - - +
236B ASN* 3.9 21.8 + - + +
237B ILE 3.6 0.2 - - - -
238B SER* 3.4 17.0 - - - +
1J NAG 2.3 47.8 + - - +
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Residues in contact with VAL 214 (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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125B PRO* 4.1 20.1 - - + +
127B VAL* 4.0 22.4 - - + -
149B ALA* 4.2 17.0 - - + -
157B VAL* 4.1 26.0 - - + -
158B GLU 3.4 6.7 - - - +
159B LEU* 4.0 23.6 - - + -
192B LEU* 5.5 0.7 - - + -
212B CYS* 4.2 8.1 - - - -
213B GLN* 1.3 82.8 - - - +
215B GLN* 1.3 61.9 + - - +
216B PHE* 3.1 3.8 + - - -
235B GLN 3.8 0.7 - - - +
237B ILE 2.9 27.6 + - - +
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Residues in contact with GLN 215 (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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156B HIS 3.9 0.5 - - - +
157B VAL* 3.1 6.6 - - - +
158B GLU* 2.9 59.2 + - + +
213B GLN* 4.0 7.7 - - - +
214B VAL* 1.3 72.3 - - - +
216B PHE* 1.3 62.2 + - - +
217B HIS* 4.0 22.3 + - + +
234B THR* 4.7 9.3 - - + +
235B GLN 3.6 2.7 - - - +
236B ASN* 2.9 21.2 + - - +
1J NAG 2.8 37.4 + - - +
2J NAG 4.7 17.2 + - - +
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Residues in contact with PHE 216 (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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122B VAL* 3.9 17.0 - - + -
123B THR 3.2 24.2 - - - -
124B PRO* 3.8 22.9 - - + -
125B PRO* 3.4 28.3 - - + -
152B PHE* 3.9 6.1 - - + -
153B PHE 4.4 0.2 - - - -
154B PRO* 3.6 27.8 - - + -
156B HIS 3.9 1.3 - - - -
157B VAL* 3.7 17.9 - - + -
214B VAL 3.1 0.8 + - - -
215B GLN* 1.3 73.0 - - - +
217B HIS* 1.3 66.4 + - - +
218B GLY* 3.9 15.5 - - - -
232B PRO 4.0 11.0 - - - -
233B VAL 4.2 11.4 - - - -
234B THR* 3.1 10.4 - - - +
235B GLN* 2.8 38.0 + - + +
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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