Contacts of the strand formed by residues 182 - 192 (chain B) in PDB entry 2QH5
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 PHE 182 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142B SER* 5.4 0.2 - - - -
143B ILE* 3.3 29.7 + - + +
152B TYR* 4.2 8.7 - + + -
153B ILE 3.3 14.6 - - - -
154B GLU* 3.4 44.9 - - + -
165B ILE* 4.2 9.2 - - + -
176B PHE* 3.5 71.1 - + + +
179B SER* 4.1 8.5 - - - -
180B GLY* 3.3 17.6 - - - -
181B GLY* 1.3 79.2 - - - +
183B TYR* 1.3 68.9 + - - +
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Residues in contact with TYR 183 (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 GLY* 3.8 18.2 - - - -
141B VAL 3.5 25.1 - - - +
142B SER* 4.1 11.0 - - - -
143B ILE* 4.0 5.6 - - - -
152B TYR* 3.3 6.9 - - - +
153B ILE* 2.7 36.8 + - + +
155B SER* 3.6 28.3 - - - -
156B PRO 5.5 0.9 + - - -
157B ASN 5.0 1.2 - - - -
158B GLY* 4.0 8.0 + - - -
181B GLY* 4.8 2.9 - - - -
182B PHE* 1.3 81.0 - - - +
184B PHE* 1.3 59.3 + - - +
257B MET* 3.6 33.4 - - + -
259B GLU* 3.3 31.5 + - + -
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Residues in contact with PHE 184 (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 GLY* 3.4 6.1 - - - -
141B VAL* 2.8 43.7 + - + +
142B SER 3.8 15.9 - - - -
143B ILE* 3.5 29.5 - - + +
144B ASP* 4.2 9.2 - - - -
145B LYS 3.2 26.7 - - - -
147B ASN* 3.8 9.6 - - - -
150B PHE* 3.7 41.3 - + + -
151B GLY 3.4 0.9 - - - -
152B TYR* 3.5 37.0 - + - -
153B ILE* 4.5 0.7 - - - -
183B TYR* 1.3 72.3 - - - +
185B ASN* 1.3 64.4 + - - +
186B SER 3.4 2.4 + - - -
264B TRP* 5.5 3.8 - + + -
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Residues in contact with ASN 185 (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 THR* 3.4 21.1 + - - -
139B PHE 4.4 0.5 - - - +
150B PHE* 4.1 20.1 - - - -
151B GLY* 2.7 35.7 + - - +
153B ILE* 3.8 13.6 - - + +
164B PHE* 3.4 19.1 - - + -
166B GLU* 4.8 1.0 + - - -
183B TYR 3.7 0.6 + - - -
184B PHE* 1.3 72.5 - - - +
186B SER* 1.3 65.3 + - - +
187B GLY* 3.3 19.0 + - - +
188B MET 4.8 0.3 - - - +
189B PHE* 4.2 3.5 - - - -
245B ASP* 3.0 28.1 + - - -
264B TRP* 4.6 0.7 - - - -
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Residues in contact with SER 186 (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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112B HIS* 3.1 26.7 + - - -
139B PHE* 3.1 41.8 + - - +
141B VAL* 4.5 6.5 - - - -
184B PHE 3.4 1.3 + - - -
185B ASN* 1.3 72.6 + - - +
187B GLY* 1.3 55.7 + - - +
188B MET* 3.0 23.6 + - - +
260B LEU* 4.3 13.9 - - - -
264B TRP* 3.4 22.6 - - - -
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Residues in contact with GLY 187 (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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8B LEU* 5.7 1.2 - - - +
107B VAL* 4.4 1.6 - - - +
109B PRO* 3.2 27.3 - - - +
112B HIS* 4.7 0.4 - - - -
185B ASN* 3.2 23.1 + - - -
186B SER* 1.3 77.6 + - - +
188B MET* 1.3 59.1 + - - +
189B PHE* 3.8 18.3 - - - -
245B ASP* 5.1 1.3 - - - -
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Residues in contact with MET 188 (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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44B ARG* 6.0 0.7 - - - -
106B ILE* 5.3 1.3 - - + -
107B VAL 3.3 7.4 - - - +
108B THR* 3.7 13.7 - - + -
109B PRO* 4.1 13.5 - - + -
112B HIS* 4.3 9.0 - - - +
114B ILE* 4.5 9.2 - - - -
120B TYR* 3.4 42.0 - - + +
124B ILE* 3.9 15.3 - - + -
138B THR* 3.9 5.2 + - - -
139B PHE* 3.7 27.4 + - + -
186B SER* 3.0 22.6 + - - +
187B GLY* 1.3 79.9 + - - +
189B PHE* 1.3 77.8 + - - +
260B LEU* 4.3 13.9 - - + -
264B TRP* 5.0 0.9 - - - -
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Residues in contact with PHE 189 (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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8B LEU* 6.5 0.2 - - + -
92B ILE* 4.4 13.9 - - + -
105B LEU 3.9 0.4 - - - +
106B ILE* 3.5 0.5 - - - +
107B VAL* 2.7 44.3 + - + +
137B VAL 3.3 14.4 - - - +
138B THR* 3.6 19.7 - - - -
139B PHE* 4.5 1.8 - - - -
164B PHE* 4.8 1.6 - + - -
185B ASN* 4.2 8.1 - - - -
187B GLY* 3.8 17.7 - - - -
188B MET* 1.3 85.5 - - - +
190B VAL* 1.3 66.3 + - - +
191B PHE* 3.4 24.2 - + + -
244B ILE* 3.5 29.8 - - + -
245B ASP* 3.4 25.6 - - - -
249B MET* 4.1 23.8 - - + -
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Residues in contact with VAL 190 (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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104B LEU* 5.3 1.6 - - + -
105B LEU 3.3 13.9 - - - +
106B ILE* 4.0 22.4 - - + -
124B ILE* 4.7 4.0 - - + +
127B ALA* 3.8 30.1 - - + +
128B ILE* 3.9 25.4 - - + -
131B ALA* 4.0 15.5 - - + -
137B VAL* 2.8 37.6 + - + +
139B PHE* 3.9 12.5 - - + -
189B PHE* 1.3 77.9 - - - +
191B PHE* 1.3 69.6 + - - +
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Residues in contact with PHE 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ILE* 3.9 23.6 - - + -
104B LEU* 4.5 1.1 - - - -
105B LEU* 2.9 43.7 + - + +
107B VAL* 3.5 33.2 - - + -
131B ALA* 3.8 12.6 - - - -
135B PHE 3.9 6.1 - - - +
136B LEU* 3.4 39.3 - - + -
137B VAL 4.8 0.7 - - - -
189B PHE* 3.4 26.0 - + + -
190B VAL* 1.3 83.9 - - - +
192B GLN* 1.3 69.3 + - - +
195B VAL* 5.4 0.2 - - + -
196B PHE* 4.3 18.2 - + + -
249B MET* 4.4 9.4 - - + -
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Residues in contact with GLN 192 (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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101B LYS 3.2 16.3 + - - +
102B GLU* 3.5 35.0 + - - +
103B ASP 3.7 4.7 - - - +
104B LEU* 3.8 20.6 - - + +
131B ALA* 4.3 9.1 + - - +
132B GLN* 6.0 0.2 - - - -
135B PHE 4.9 0.2 + - - -
191B PHE* 1.3 76.1 - - - +
193B ALA* 1.3 63.8 + - - +
194B GLY* 3.2 6.6 + - - -
195B VAL* 3.0 42.3 + - + +
196B PHE* 3.2 21.7 + - - +
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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