Contacts of the strand formed by residues 180 - 190 (chain B) in PDB entry 3DIF
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 180 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B LYS 5.4 0.2 - - - +
123B THR* 3.7 27.4 - - + +
150B GLY* 3.6 37.7 - - - +
151B TYR 3.7 5.6 - - - -
152B PHE* 4.3 0.9 - - + -
175B VAL 3.6 1.7 - - - +
176B LEU* 3.4 5.0 - - - +
177B GLN* 2.9 36.2 + - - +
178B SER* 4.2 7.4 - - - +
179B ASP* 1.3 87.0 - - + +
181B TYR* 1.3 61.0 + - - +
182B THR* 4.9 2.1 - - - +
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Residues in contact with TYR 181 (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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116B THR* 5.5 4.7 - - - +
150B GLY 2.9 22.3 + - - -
151B TYR* 2.6 50.8 + + + +
152B PHE* 3.5 30.5 - + - -
153B PRO* 4.1 2.0 - - + -
154B GLU* 3.6 45.8 - - + +
174B ALA* 4.0 15.5 - - + -
175B VAL 3.4 1.6 - - - -
176B LEU* 3.6 43.1 - - + +
180B LEU* 1.3 73.4 - - - +
182B THR* 1.3 60.7 + - - +
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Residues in contact with THR 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A LEU* 4.9 7.6 - - + -
162A SER* 5.7 0.2 + - - -
178A THR* 5.8 2.6 - - - +
147B LEU* 4.1 9.4 - - - +
148B VAL 3.3 11.6 + - - -
149B LYS* 3.8 35.7 + - - +
150B GLY 4.1 2.7 - - - +
151B TYR* 4.3 0.9 - - - -
173B PRO 4.6 0.3 - - - +
174B ALA* 3.4 2.2 - - - -
175B VAL* 3.0 54.8 + - + +
177B GLN* 5.5 4.9 - - + -
180B LEU 4.9 2.7 - - - +
181B TYR* 1.3 78.1 - - - +
183B LEU* 1.3 65.8 + - - +
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Residues in contact with LEU 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B LEU* 3.9 2.8 - - - +
148B VAL* 2.9 52.7 + - + +
151B TYR* 3.6 22.7 - - + +
154B GLU* 4.9 2.0 - - - +
156B VAL* 4.9 14.8 - - + +
158B VAL* 4.2 8.1 - - + -
171B THR* 4.1 15.7 - - + -
172B PHE* 3.3 23.1 - - - +
173B PRO* 4.2 2.7 - - + -
174B ALA* 3.7 15.5 - - + +
182B THR* 1.3 75.7 - - - +
184B SER* 1.3 81.9 + - - +
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Residues in contact with SER 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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133A VAL* 4.3 9.8 - - - +
135A PHE* 3.9 24.7 - - - -
176A SER* 5.1 5.4 - - - -
178A THR* 4.6 4.7 + - - -
130B LEU* 5.3 0.2 - - - -
146B CYS 3.3 10.8 - - - -
147B LEU* 3.3 21.8 - - - +
171B THR* 3.8 0.2 - - - -
172B PHE* 3.0 37.3 + - - +
183B LEU* 1.3 86.4 + - - +
185B SER* 1.3 60.6 + - - +
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Residues in contact with SER 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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135A PHE* 4.3 3.4 - - - -
146B CYS* 2.9 34.3 + - - -
158B VAL* 3.9 14.3 - - - +
160B TRP* 3.0 32.4 + - - -
169B VAL* 3.6 4.0 - - - +
170B HIS 3.6 4.3 - - - -
171B THR* 2.6 35.8 + - - -
183B LEU* 4.6 0.2 - - - +
184B SER* 1.3 74.4 - - - +
186B SER* 1.3 59.2 + - - +
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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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135A PHE* 3.7 30.4 - - - -
137A ASN* 3.2 26.2 + - - -
143B THR* 4.2 3.4 - - - -
144B LEU 3.2 9.6 - - - -
145B GLY* 4.2 0.9 - - - -
160B TRP* 4.5 0.2 - - - -
168B GLY 4.2 0.4 - - - -
169B VAL* 3.3 6.9 - - - +
170B HIS* 2.9 46.1 + - - +
172B PHE* 4.0 1.6 - - - -
185B SER* 1.3 74.8 - - - +
187B VAL* 1.3 61.6 - - - +
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Residues in contact with VAL 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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142B VAL 3.7 1.6 - - - +
143B THR* 3.6 0.8 - - - -
144B LEU* 2.7 51.7 + - + +
160B TRP* 3.4 47.6 - - + -
165B LEU* 4.1 15.3 - - + +
168B GLY 3.2 7.0 - - - +
169B VAL* 3.8 20.0 - - + -
186B SER* 1.3 76.4 - - - +
188B THR* 1.3 62.3 - - - +
189B VAL* 3.8 20.7 + - + +
199B VAL* 4.7 4.7 - - + -
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Residues in contact with THR 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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114A THR* 6.1 0.8 - - + +
137A ASN* 4.5 8.8 + - - +
141B MET* 3.8 39.5 - - + +
142B VAL 3.5 5.8 - - - +
143B THR* 2.8 27.9 + - - +
168B GLY* 2.9 29.6 + - - -
170B HIS* 5.6 1.8 - - - -
186B SER* 5.6 0.2 + - - -
187B VAL* 1.3 70.7 - - - +
189B VAL* 1.3 66.1 + - - +
190B PRO* 4.7 1.0 - - - +
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Residues in contact with VAL 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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141B MET* 4.2 3.8 - - - -
142B VAL* 2.6 61.4 + - + +
144B LEU* 4.9 9.6 - - + -
165B LEU* 4.2 28.0 - - + -
187B VAL* 4.0 22.2 - - + +
188B THR* 1.3 80.3 - - - +
190B PRO* 1.3 68.0 - - + +
193B THR* 3.8 14.8 - - - +
194B TRP* 4.2 10.1 - - + -
199B VAL* 5.0 6.1 - - + -
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Residues in contact with PRO 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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140B SER 3.7 8.7 - - - +
141B MET* 4.0 14.1 - - + -
142B VAL* 4.0 0.9 - - - +
188B THR 4.7 1.1 - - - +
189B VAL* 1.3 91.9 - - + +
191B SER* 1.3 63.5 + - - +
192B SER* 3.2 14.6 - - - +
193B THR* 2.6 36.8 + - + +
194B TRP 3.6 3.6 + - - -
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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