Contacts of the strand formed by residues 274 - 279 (chain A) in PDB entry 1DG6
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 274 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A HIS* 3.4 33.9 - + + +
126A ILE 3.2 14.8 - - - +
127A THR* 4.0 3.6 - - + -
154A TRP* 3.5 8.3 - - - -
185A TYR* 3.8 26.2 - + - -
186A SER* 2.9 21.0 + - - -
187A GLN* 2.9 59.2 + - + +
243A TYR* 4.6 7.6 - + - -
270A HIS 4.2 4.9 - - - -
271A GLU* 3.6 20.0 - - - -
272A ALA 4.2 0.2 - - - -
273A SER* 1.3 80.4 - - - +
275A PHE* 1.3 61.7 + - - +
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Residues in contact with PHE 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ALA 4.6 0.2 - - - -
125A HIS* 3.6 1.0 - - - -
126A ILE* 2.8 44.8 + - + +
154A TRP* 3.8 31.6 - - + -
172A GLY 4.2 7.9 - - - -
174A LEU* 3.8 28.7 - - + +
184A ILE* 4.1 23.3 - - + -
185A TYR* 3.4 20.6 - - - -
186A SER* 4.2 0.4 - - - +
210A ILE* 4.7 3.1 - - + -
256A ILE* 3.5 41.7 - - + -
257A PHE* 3.8 11.7 - - - -
258A VAL* 3.5 20.0 - - + -
274A PHE* 1.3 77.0 - - - +
276A GLY* 1.3 63.6 + - - +
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Residues in contact with GLY 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ALA 3.1 15.3 - - - -
174A LEU* 4.4 8.1 - - - -
184A ILE* 3.5 5.0 - - - +
185A TYR* 2.9 49.9 + - - +
275A PHE* 1.3 78.3 - - - +
277A ALA* 1.3 64.8 + - - +
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Residues in contact with ALA 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ALA* 3.3 1.9 - - - +
124A ALA* 2.9 33.2 + - - +
167A LEU* 4.6 14.8 - - + +
174A LEU* 4.6 6.3 - - + -
176A ILE* 5.8 1.8 - - + -
182A TYR* 4.4 13.2 - - + -
183A TYR 3.0 13.7 - - - +
184A ILE* 4.2 16.2 - - + -
185A TYR* 3.8 3.4 - - - -
250A LEU* 6.0 0.2 - - + -
256A ILE* 6.4 2.0 - - + -
276A GLY* 1.3 76.6 - - - +
278A PHE* 1.3 66.4 + - - +
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Residues in contact with PHE 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A VAL 3.5 11.4 - - - +
123A ALA* 3.9 10.8 - - + +
182A TYR* 3.3 8.2 - - - -
183A TYR* 2.9 73.9 + + + -
185A TYR* 4.8 9.9 - + - -
277A ALA* 1.3 78.5 - - - +
279A LEU* 1.3 75.5 + - - +
280A VAL* 4.4 11.4 - - + -
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Residues in contact with LEU 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A GLN 5.4 4.5 - - - +
122A VAL* 3.0 49.5 + - + +
178A GLU* 5.0 7.0 - - + -
179A LYS 4.3 4.9 - - - +
180A GLY* 3.9 9.2 - - - -
181A PHE 3.4 16.8 - - - +
182A TYR* 3.7 27.3 - - + +
278A PHE* 1.3 79.0 - - - +
280A VAL* 1.3 60.0 + - - +
281A GLY* 3.7 22.7 - - - +
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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