Contacts of the strand formed by residues 164 - 170 (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 LEU 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A TRP* 3.7 25.1 - - + -
128A THR 4.1 13.2 - - - +
130A VAL* 3.9 14.4 - - + -
154A LEU* 3.7 27.4 - - + -
161A TYR* 3.8 25.8 - - + +
162A PRO* 3.0 31.0 + - + +
163A VAL* 1.3 73.2 - - - +
165A ASN* 1.3 59.7 + - - +
166A VAL* 4.1 1.8 - - + -
245A ILE 4.1 1.1 - - - +
246A ASN* 3.1 9.3 - - - -
247A SER* 2.7 41.3 + - - +
251A LEU* 4.3 8.7 - - + -
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Residues in contact with ASN 165 (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* 3.6 7.9 + - + +
164A LEU* 1.3 77.1 - - - +
166A VAL* 1.3 64.2 + - - +
244A VAL* 4.3 3.4 - - - +
245A ILE 3.5 4.5 - - - -
246A ASN* 2.9 26.9 + - - +
219E SER* 3.3 9.9 - - - -
1G NAG 1.5 71.3 + - - +
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Residues in contact with VAL 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A PHE* 4.2 16.2 - - + -
126A THR* 3.9 24.5 - - - +
127A TRP* 3.5 44.9 - - + -
128A THR* 5.9 0.9 - - - +
164A LEU* 5.2 1.1 - - + -
165A ASN* 1.3 84.0 - - - +
167A THR* 1.3 63.3 + - - +
244A VAL* 3.3 7.3 - - - +
245A ILE* 2.9 42.6 + - + +
1G NAG 4.8 1.6 - - - -
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Residues in contact with THR 167 (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* 4.8 2.3 - - - -
166A VAL* 1.3 80.4 - - - +
168A MET* 1.3 70.0 + - - +
169A PRO* 4.3 7.1 - - + +
242A VAL* 3.1 26.5 - - - +
243A LEU 3.1 7.8 + - - -
244A VAL* 3.4 7.1 - - - +
1G NAG 3.3 31.7 - - - +
2G NAG 4.1 2.5 - - + +
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Residues in contact with MET 168 (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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123A GLU* 3.4 46.4 - - + +
124A GLY 3.8 20.4 - - - +
125A PHE* 3.5 42.0 - - + -
167A THR* 1.3 81.3 + - - +
169A PRO* 1.3 73.1 - - - +
170A ASN 3.9 0.2 + - - -
178A TYR* 3.5 11.2 + - - +
237A VAL* 5.1 1.4 - - - +
242A VAL* 4.1 0.4 - - - -
243A LEU* 2.9 36.8 + - + +
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Residues in contact with PRO 169 (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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123A GLU* 4.7 0.2 - - - +
167A THR* 4.2 7.6 - - + +
168A MET* 1.3 95.9 - - - +
170A ASN* 1.3 61.7 + - - +
171A ASN* 3.4 29.6 + - + +
176A LYS* 3.2 19.7 + - - -
178A TYR* 5.3 0.2 - - - -
241A ASP 3.6 8.5 - - - +
242A VAL* 4.0 13.7 - - + -
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Residues in contact with ASN 170 (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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169A PRO* 1.3 74.5 - - - +
171A ASN* 1.3 59.4 + - - +
172A ASP* 3.1 23.6 - - - +
174A PHE 2.8 24.9 + - - +
176A LYS* 3.3 19.9 - - + +
237A VAL* 2.9 30.9 + - + -
238A LYS 3.1 22.6 + - - +
239A PRO* 3.5 3.8 - - - +
240A GLY* 2.7 27.4 + - - -
241A ASP 2.8 14.5 + - - +
242A VAL* 4.6 0.2 - - - +
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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