Contacts of the strand formed by residues 157 - 162 (chain G) in PDB entry 2HU4
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 157 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E LYS* 4.0 24.2 + - + +
104E ASN* 3.9 12.5 + - - +
134G LEU* 3.6 1.2 - - - -
135G THR* 2.8 48.4 + - - +
155G HIS 3.5 13.3 + - - +
156G ARG* 1.3 80.9 - - - +
158G LEU* 1.3 62.0 + - - +
159G MET* 3.5 17.7 + - - +
173G PHE* 3.8 12.5 - - + -
175G SER 3.5 10.1 - - - -
176G VAL* 4.3 6.5 - - + -
177G ALA 3.5 5.6 + - - +
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Residues in contact with LEU 158 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121G PHE* 4.5 5.2 - - + -
132G PHE* 4.0 17.5 - - + -
133G PHE 3.4 30.3 - - - +
134G LEU* 4.0 11.8 - - + +
157G THR* 1.3 69.3 - - - +
159G MET* 1.3 61.9 + - - +
173G PHE* 4.5 0.2 - - - -
174G GLU* 2.9 42.9 + - + +
175G SER* 2.7 26.6 + - - +
177G ALA* 4.2 5.9 - - + +
180G ALA* 3.6 29.4 - - + -
181G SER 4.4 7.9 - - - +
182G ALA* 5.0 0.7 - - + -
191G THR* 4.3 20.4 - - + -
192G ILE 4.5 3.6 - - - +
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Residues in contact with MET 159 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164E GLY 4.6 6.7 - - - +
165E GLU* 4.6 10.1 - - + -
115G PHE* 3.8 30.7 - - + -
132G PHE* 3.4 3.3 - - - +
133G PHE* 3.0 51.2 + - + +
135G THR* 4.0 4.7 - - + -
157G THR* 3.5 21.0 + - - +
158G LEU* 1.3 79.7 - - - +
160G SER* 1.3 62.1 + - - +
169G PRO* 5.4 1.8 - - + -
171G SER* 3.7 30.7 - - - +
172G ARG 3.2 11.2 - - - +
173G PHE* 3.9 26.2 - - + +
174G GLU* 3.9 3.4 - - - -
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Residues in contact with SER 160 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130G ARG* 2.7 33.5 + - - -
131G THR 3.1 14.6 - - - -
132G PHE* 3.7 17.7 - - - -
133G PHE* 3.9 4.3 - - - -
159G MET* 1.3 76.9 - - - +
161G CYS* 1.3 61.7 + - - +
171G SER* 3.2 3.7 - - - -
172G ARG* 2.6 40.1 + - - +
174G GLU* 2.7 24.7 + - - -
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Residues in contact with CYS 161 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130G ARG* 3.6 8.6 - - - +
131G THR* 2.8 34.6 + - - -
133G PHE* 3.9 18.4 - - - -
160G SER* 1.3 77.8 - - - +
162G PRO* 1.3 75.9 - - - +
165G GLU 3.6 23.8 - - - -
167G PRO* 4.1 7.9 - - - -
170G ASN* 3.4 33.4 - - - +
171G SER* 4.1 3.8 - - - +
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Residues in contact with PRO 162 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128G GLU* 5.0 6.5 - - - +
129G CYS 4.0 10.8 - - - +
130G ARG* 3.9 16.8 - - - +
131G THR* 4.2 0.3 + - - -
161G CYS* 1.3 94.0 - - + +
163G VAL* 1.3 69.1 + - + +
165G GLU* 3.0 52.3 + - - +
170G ASN* 4.3 6.7 - - + +
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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