Contacts of the strand formed by residues 172 - 183 (chain B) in PDB entry 4DF3
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 172 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B VAL* 3.7 19.1 - - + +
150B GLY* 3.7 15.5 - - - -
151B LEU* 4.1 8.2 - - + +
168B ALA* 3.0 42.1 + - + +
171B PHE* 1.3 75.9 - - - +
173B ARG* 1.3 73.0 + - - +
174B ASP* 3.7 1.2 + - - -
176B GLY* 3.7 23.6 - - - +
177B TYR 3.6 28.5 - - - +
178B MET* 4.4 11.9 - - + -
209B LEU* 4.6 9.6 - - + -
230B VAL* 6.1 0.2 - - + -
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Residues in contact with ARG 173 (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 GLY* 3.6 34.8 + - - +
148B VAL 3.0 28.2 + - - +
149B ASP* 4.2 15.3 + - - -
171B PHE 3.3 0.4 + - - +
172B LEU* 1.3 79.7 - - - +
174B ASP* 1.3 59.3 + - - +
175B GLY 3.2 0.5 + - - -
176B GLY* 2.8 29.1 + - - +
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Residues in contact with ASP 174 (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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172B LEU 3.7 1.6 + - - -
173B ARG* 1.3 76.4 - - - +
175B GLY* 1.3 63.5 + - - +
176B GLY 3.3 0.3 + - - -
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Residues in contact with GLY 175 (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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173B ARG 3.2 0.2 + - - -
174B ASP* 1.3 78.0 + - - +
176B GLY* 1.3 65.2 + - - +
177B TYR* 3.8 0.7 + - - +
230B VAL* 4.1 26.5 - - - +
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Residues in contact with GLY 176 (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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149B ASP* 3.1 18.6 - - - -
172B LEU* 3.7 16.3 - - - +
173B ARG* 2.8 19.9 + - - -
174B ASP 3.1 2.0 + - - -
175B GLY* 1.3 81.6 - - - +
177B TYR* 1.3 64.1 + - - -
230B VAL* 3.4 16.5 - - - +
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Residues in contact with TYR 177 (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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74B PRO* 3.3 34.3 - - + -
75B VAL* 3.5 12.6 - - + -
79B ASP* 2.5 31.9 + - - -
81B ILE* 3.3 28.2 - - + +
149B ASP* 3.1 17.7 + - + -
150B GLY* 3.2 20.0 - - - -
151B LEU 2.9 28.4 + - - -
152B TYR* 6.1 1.1 - - + -
172B LEU* 3.6 4.2 - - - +
175B GLY 3.8 1.7 + - - +
176B GLY* 1.3 74.8 - - - -
178B MET* 1.3 60.3 + - - +
179B LEU* 4.3 15.3 - - + -
228B TYR* 3.8 24.2 - - + +
229B ALA 3.5 4.9 - - - -
230B VAL 4.2 3.8 - - - +
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Residues in contact with MET 178 (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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151B LEU* 3.2 16.8 - - + +
164B VAL* 3.6 30.5 - - + -
168B ALA* 5.8 0.2 - - + -
172B LEU* 4.4 4.5 - - + -
177B TYR* 1.3 76.2 - - - +
179B LEU* 1.3 68.2 + - - +
180B MET* 3.6 22.4 - - + +
204B LEU* 3.9 15.7 - - + -
209B LEU* 4.1 23.8 - - + -
227B ILE* 3.9 20.4 - - + -
228B TYR* 3.5 5.4 - - - -
229B ALA* 2.8 53.9 + - + +
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Residues in contact with LEU 179 (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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62B LEU* 4.3 12.6 - - + -
70B LEU* 4.2 12.8 - - + -
74B PRO* 4.1 23.3 - - + -
75B VAL* 4.7 7.0 - - + -
151B LEU 2.9 8.2 + - - +
152B TYR* 3.3 30.8 - - + -
153B ALA 2.8 31.1 + - - -
177B TYR* 4.3 16.5 - - + -
178B MET* 1.3 77.6 - - - +
180B MET* 1.3 55.5 + - - +
226B MET* 4.1 19.5 - - + -
227B ILE 3.1 7.2 - - - +
228B TYR* 3.7 35.0 - - + -
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Residues in contact with MET 180 (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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153B ALA* 3.5 4.5 - - + +
160B GLN* 3.8 28.5 - - + +
161B ALA* 4.0 13.7 - - + +
164B VAL* 3.7 25.4 - - + -
178B MET* 3.6 18.1 - - + -
179B LEU* 1.3 76.0 - - - +
181B ALA* 1.3 64.0 - - - +
182B ILE* 3.5 31.2 + - + -
200B GLU* 4.0 20.2 - - + +
204B LEU* 4.3 13.0 - - + -
226B MET* 3.5 3.5 - - - -
227B ILE* 2.7 52.1 + - + +
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Residues in contact with ALA 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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61B LYS* 3.5 33.0 - - + -
152B TYR* 5.1 1.1 - - + +
153B ALA 3.0 12.2 + - - +
154B ASP* 3.7 16.6 - - + +
160B GLN* 2.9 22.9 + - - +
180B MET* 1.3 70.7 - - - +
182B ILE* 1.3 59.6 + - - +
183B LYS 4.3 0.3 + - - -
217B LEU* 5.6 0.2 - - + -
224B HIS* 4.3 6.0 - - + -
225B ALA 3.3 9.6 - - - +
226B MET* 3.9 16.7 - - + -
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Residues in contact with ILE 182 (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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160B GLN* 4.6 2.2 - - - -
180B MET* 3.5 12.7 + - + -
181B ALA* 1.3 73.5 - - - +
183B LYS* 1.4 71.0 + - + +
184B ALA* 4.3 0.9 - - + -
197B TYR* 3.6 35.0 - - + +
200B GLU* 3.6 35.2 - - + +
201B ILE* 4.8 0.9 - - + -
224B HIS* 3.1 6.9 - - - -
225B ALA* 2.9 55.7 + - + +
227B ILE* 3.6 33.2 - - + -
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Residues in contact with LYS 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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11A ASP* 3.9 24.3 + - - +
12A ARG* 3.7 34.8 - - - +
14A ARG* 4.0 13.6 + - - +
156B ALA* 3.9 30.5 + - - +
157B GLN* 5.3 3.5 - - - +
158B PRO* 5.4 5.3 - - - +
181B ALA 4.3 0.2 + - - -
182B ILE* 1.4 82.6 - - + +
184B ALA* 1.3 61.2 + - - +
197B TYR* 4.3 5.4 - - - +
223B ASP* 3.4 10.8 - - + +
224B HIS* 3.6 24.0 - - + +
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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