Contacts of the strand formed by residues 172 - 177 (chain B) in PDB entry 1OFD
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 THR 172 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47B MET* 2.8 40.7 - - - +
48B THR 3.3 7.7 + - - -
50B ILE* 3.8 5.4 - - - +
74B VAL* 4.7 2.4 - - - +
167B SER* 4.3 9.9 + - - -
169B SER* 3.4 35.3 + - - +
171B ARG* 1.3 79.9 - - + +
173B ILE* 1.3 60.9 + - - +
174B VAL* 5.9 0.2 - - + -
200B PHE* 4.6 4.9 - - - -
222B ARG 4.4 16.2 - - - +
283B ARG* 6.0 3.8 - - - +
335B SER 5.0 3.6 - - - +
336B ASP 5.3 3.8 - - - +
337B GLY* 4.9 6.3 - - - -
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Residues in contact with ILE 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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46B VAL 3.8 0.7 - - - +
47B MET* 3.2 2.9 - - - -
48B THR* 2.9 50.4 + - - +
49B ALA 3.7 9.9 - - - +
50B ILE* 4.6 4.5 - - + -
51B PRO* 3.8 14.8 - - + -
55B LEU* 6.1 0.9 - - + -
74B VAL* 4.0 26.0 - - + +
76B MET* 4.1 14.6 - - + +
130B GLN* 3.6 28.0 - - - +
167B SER* 3.5 11.7 - - - +
172B THR* 1.3 78.4 + - - +
174B VAL* 1.3 66.6 + - - +
175B TYR* 4.1 12.6 + - + +
196B TYR* 3.5 12.6 - - - +
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Residues in contact with VAL 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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46B VAL 3.5 8.1 - - - +
47B MET* 3.8 22.0 - - + -
76B MET* 3.2 26.9 - - - +
166B CYS* 4.0 16.5 - - + +
167B SER* 3.2 19.0 + - - +
172B THR* 5.0 0.9 - - - +
173B ILE* 1.3 76.1 - - - +
175B TYR* 1.3 63.2 + - - +
176B LYS* 3.8 23.2 + - + -
220B PRO* 3.4 27.1 - - + +
221B MET 3.4 22.9 - - - +
222B ARG* 5.0 1.1 - - - +
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Residues in contact with TYR 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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45B GLY* 3.3 2.4 - - - -
46B VAL* 2.9 39.0 + - + +
48B THR* 6.0 0.2 - - + -
51B PRO* 4.7 5.2 - - + +
54B LEU* 5.0 0.2 - - - +
55B LEU* 6.0 0.2 - - - +
76B MET* 3.8 14.1 - - + -
108B ARG* 4.0 1.0 + - - -
110B VAL* 4.2 1.3 - - + -
130B GLN* 2.8 24.1 + - - -
173B ILE* 4.1 17.0 - - + -
174B VAL* 1.3 74.1 - - - +
176B LYS* 1.3 59.8 + - - +
184B LEU* 3.9 3.8 - - - +
188B TYR* 3.5 37.9 - + + -
190B ASP* 2.6 41.3 + - + +
191B LEU* 4.0 23.1 - - + -
196B TYR* 3.3 36.9 - + - -
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Residues in contact with LYS 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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44B ALA 3.3 11.7 - - - +
45B GLY* 3.7 7.9 - - - -
76B MET* 5.5 0.2 - - - +
78B PHE* 3.5 16.0 - - + -
164B TYR* 3.2 30.7 + - - -
166B CYS* 4.0 12.2 + - - +
174B VAL* 3.8 11.5 + - + -
175B TYR* 1.3 75.7 - - - +
177B GLY* 1.3 59.2 + - - +
184B LEU* 4.1 1.3 - - - -
188B TYR* 2.7 32.8 + - - -
215B TRP 3.9 8.7 - - - +
216B PRO 3.0 20.1 + - - -
218B ALA* 2.8 34.5 + - + +
219B GLN 3.8 4.3 - - - +
220B PRO 3.4 25.2 + - - +
221B MET* 4.5 3.6 - - - +
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Residues in contact with GLY 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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43B GLY* 3.3 2.4 - - - -
44B ALA 2.9 33.5 + - - +
176B LYS* 1.3 77.2 - - - +
178B MET* 1.3 64.9 + - - -
179B VAL* 3.0 13.7 + - - +
184B LEU* 4.1 2.3 - - - +
188B TYR* 5.0 0.7 - - - -
215B TRP* 3.4 20.9 - - - -
218B ALA* 3.9 4.1 - - - +
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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