Contacts of the strand formed by residues 134 - 140 (chain G) in PDB entry 3HAE
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 134 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122G PRO 4.2 1.0 - - - +
123G PRO* 3.5 15.4 - - - +
127G GLU* 2.8 33.5 + - - +
133G ALA* 1.3 73.9 - - - +
135G LEU* 1.3 68.1 + - - +
136G VAL* 3.5 26.6 - - + +
180G TYR* 3.8 22.7 - - + -
181G LEU 3.3 8.7 - - - +
182G SER* 4.6 5.0 + - - +
130I LEU* 5.6 0.9 - - - +
147I LEU* 4.3 9.5 - - + +
149I LYS* 3.6 27.3 + - - +
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Residues in contact with LEU 135 (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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120G LEU* 4.5 5.2 - - + -
121G PHE 3.3 15.0 - - - +
122G PRO* 4.2 1.6 - - + -
123G PRO* 4.1 10.1 - - + -
133G ALA 4.1 0.2 - - - -
134G THR* 1.3 77.7 - - - +
136G VAL* 1.3 60.5 + - - +
151G TRP* 3.4 20.9 - - + -
180G TYR* 3.6 1.0 - - - -
181G LEU* 3.0 73.9 + - + +
183G LEU* 3.6 28.9 - - + -
188G TRP* 3.9 24.7 - - + -
194G TYR* 4.2 13.5 - - + -
209G VAL* 5.0 3.6 - - + -
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Residues in contact with VAL 136 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119G THR 3.4 2.3 - - - +
120G LEU* 3.0 20.1 - - - +
121G PHE* 3.1 25.1 + - + +
134G THR* 3.5 24.9 - - + +
135G LEU* 1.3 83.0 - - - +
137G CYS* 1.3 63.2 + - - +
138G LEU* 3.6 19.8 - - + +
179G SER 3.8 1.3 - - - -
180G TYR* 3.6 17.7 - - + -
130I LEU* 4.3 22.4 - - + -
147I LEU* 4.5 6.1 - - + -
185I SER* 3.5 23.8 - - - +
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Residues in contact with CYS 137 (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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118G VAL* 3.9 19.5 - - - -
119G THR 3.4 4.7 - - - -
120G LEU* 4.1 1.6 - - + -
136G VAL* 1.3 72.7 - - - +
138G LEU* 1.3 66.5 + - - +
139G ILE* 4.6 4.3 - - + -
149G VAL* 4.7 1.1 - - - -
151G TRP* 3.6 8.9 - - + -
178G SER* 3.1 8.5 - - - -
179G SER* 2.8 48.2 + - - +
196G CYS* 2.1 50.5 - - + -
198G VAL* 4.5 3.6 - - - -
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Residues in contact with LEU 138 (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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117G THR 3.8 1.6 - - - +
118G VAL* 3.4 1.8 - - - -
119G THR* 2.7 46.6 + - + +
121G PHE* 3.8 26.5 - - + -
136G VAL* 3.6 23.1 - - + -
137G CYS* 1.3 86.5 - - - +
139G ILE* 1.3 61.2 + - - +
140G SER* 3.9 2.9 + - - -
177G ALA 4.0 3.1 - - - -
178G SER* 3.8 13.9 - - - +
180G TYR* 4.7 0.7 - - - +
172I PHE* 3.7 23.6 - - + -
185I SER* 3.9 18.4 - - - +
187I VAL* 3.8 26.7 - - + -
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Residues in contact with ILE 139 (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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116G PRO* 3.9 20.2 - - + -
117G THR 3.6 2.2 - - - -
118G VAL* 4.2 7.6 - - + +
137G CYS* 4.6 4.5 - - - -
138G LEU* 1.3 80.5 - - - +
140G SER* 1.3 59.1 + - - +
142G PHE* 3.3 26.8 - - + -
147G VAL* 4.5 5.2 - - + -
149G VAL* 3.9 26.7 - - + -
176G ALA* 3.5 2.8 - - - -
177G ALA* 3.0 38.2 + - + +
178G SER* 4.5 3.8 - - - -
179G SER 5.2 0.7 - - - +
198G VAL* 3.7 43.3 - - + -
172I PHE* 3.8 3.5 - - - -
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Residues in contact with SER 140 (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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116G PRO 3.6 0.2 - - - -
117G THR* 2.6 59.2 + - - +
119G THR* 6.0 1.2 - - - -
138G LEU 4.4 2.8 + - - -
139G ILE* 1.3 73.8 - - - +
141G ASP* 1.3 78.2 + - - +
142G PHE 3.4 3.2 + - - -
175G TYR 4.6 1.1 - - - -
176G ALA* 5.0 1.1 - - - +
170I HIS* 5.2 12.3 - - - -
172I PHE* 4.1 19.7 - - - -
187I VAL* 6.0 1.4 - - - +
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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