Contacts of the strand formed by residues 241 - 247 (chain A) in PDB entry 5HMG
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 ASP 241 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A PRO* 3.6 2.3 - - - +
170A ASN 2.8 23.7 + - - -
206A THR* 3.5 13.0 - - - +
207A ARG* 2.9 49.6 + - - +
208A ARG* 3.7 23.2 + - - +
237A VAL* 3.8 10.7 - - + -
238A LYS* 3.1 27.1 + - + +
239A PRO 3.2 1.6 + - - +
240A GLY* 1.3 80.3 - - - +
242A VAL* 1.3 75.5 + - - +
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Residues in contact with VAL 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A THR* 3.1 28.5 - - - +
168A MET 3.9 2.2 - - - -
169A PRO* 4.0 20.0 - - + -
205A SER 3.6 0.3 - - - +
206A THR* 3.2 28.8 - - - +
207A ARG* 3.6 29.2 - - - +
237A VAL* 4.1 4.0 - - - -
240A GLY 4.7 0.4 - - - +
241A ASP* 1.3 86.1 + - - +
243A LEU* 1.3 60.4 + - - +
244A VAL* 4.1 1.1 - - + -
221E PRO* 4.3 12.3 - - + +
2G NAG 3.8 24.5 - - + -
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Residues in contact with LEU 243 (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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125A PHE* 4.4 6.7 - - + -
167A THR* 3.1 8.0 + - - -
168A MET* 2.9 42.4 + - + +
178A TYR* 3.7 39.0 - - + -
180A TRP* 6.3 0.7 - - + -
204A VAL* 3.5 29.8 - - + -
205A SER 3.5 7.4 - - - +
206A THR* 4.4 0.7 - - - -
235A THR* 3.9 20.2 - - + -
237A VAL* 4.0 13.6 - - + +
242A VAL* 1.3 72.6 - - - +
244A VAL* 1.3 59.3 + - - +
245A ILE* 3.8 29.4 - - + -
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Residues in contact with VAL 244 (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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165A ASN* 4.3 13.5 - - - +
166A VAL 3.3 8.7 - - - +
167A THR* 3.4 23.6 - - - +
203A THR 3.8 0.5 - - - +
204A VAL* 3.5 2.6 - - - +
205A SER* 2.9 34.5 + - - +
242A VAL* 4.5 1.8 - - + -
243A LEU* 1.3 72.8 - - - +
245A ILE* 1.3 64.4 + - - +
246A ASN 4.8 0.2 - - - +
219E SER 3.4 28.0 - - - +
220E ARG 4.6 0.4 - - - -
221E PRO* 3.5 36.6 - - + -
1G NAG 4.2 16.4 - - - +
2G NAG 4.8 0.7 - - + -
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Residues in contact with ILE 245 (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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125A PHE* 4.1 15.3 - - + -
127A TRP* 4.2 7.6 - - + -
164A LEU* 3.9 2.3 - - - +
165A ASN* 3.5 2.1 + - - -
166A VAL* 2.9 39.8 + - + +
167A THR* 6.4 0.2 - - - -
180A TRP* 5.9 1.3 - - + -
202A VAL* 4.9 0.7 - - + -
203A THR 3.7 2.2 - - - +
204A VAL* 4.1 23.1 - - + +
243A LEU* 3.8 25.5 + - + -
244A VAL* 1.3 75.5 - - - +
246A ASN* 1.3 63.3 + - - +
251A LEU* 3.9 34.8 - - + -
254A PRO* 3.5 35.2 - - + -
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Residues in contact with ASN 246 (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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163A VAL* 3.9 17.9 - - - +
164A LEU 3.1 10.1 + - - -
165A ASN* 2.9 27.6 + - - +
201A ARG* 3.9 18.2 + - - -
202A VAL* 4.5 0.3 - - - +
203A THR* 2.8 42.6 + - - +
244A VAL 4.0 0.2 - - - -
245A ILE* 1.3 76.3 - - - +
247A SER* 1.3 65.3 + - - +
218E GLY* 4.1 6.8 - - - -
219E SER* 3.6 34.3 + - - +
1G NAG 6.0 0.4 - - - +
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Residues in contact with SER 247 (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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161A TYR* 4.5 1.4 - - - -
162A PRO 3.6 0.9 - - - +
163A VAL* 3.4 2.1 - - - -
164A LEU* 2.7 46.9 + - - +
201A ARG* 2.9 20.0 + - - +
202A VAL* 3.7 4.6 - - - +
246A ASN* 1.3 81.4 + - - +
248A ASN* 1.3 56.6 + - - +
249A GLY 2.9 22.2 + - - -
251A LEU* 3.7 33.1 - - - +
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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