Contacts of the strand formed by residues 115 - 124 (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 PHE 115 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108E ILE* 3.5 29.4 - - + -
105G SER* 5.6 0.5 + - - -
113G ASP 4.2 0.2 + - - -
114G VAL* 1.3 83.5 - - - +
116G VAL* 1.3 61.9 + - - +
117G ILE* 3.5 26.0 + - + +
133G PHE* 4.4 2.7 - + - -
135G THR* 3.8 26.5 - - + -
137G GLY* 5.1 1.6 - - - -
138G ALA 3.4 17.7 - - - -
139G LEU* 4.1 6.7 - - + +
140G LEU* 4.2 2.9 - - - +
159G MET* 3.8 28.0 - - + -
167G PRO* 2.8 15.7 + - - +
168G SER* 3.5 19.7 - - - -
169G PRO* 3.3 37.7 - - + -
171G SER* 3.9 8.3 - - - -
440G SER* 4.2 2.6 + - - -
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Residues in contact with VAL 116 (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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114G VAL 3.6 1.6 + - - -
115G PHE* 1.3 73.3 - - - +
117G ILE* 1.3 64.9 + - - +
135G THR* 3.5 1.9 - - - -
136G GLN* 3.2 32.6 + - + -
138G ALA* 3.2 38.3 + - + +
139G LEU* 4.1 2.5 - - - +
140G LEU* 4.2 15.7 - - + +
145G SER* 4.4 9.0 - - - +
148G THR* 3.8 17.5 - - + +
438G TRP* 5.3 0.2 - - + -
439G THR 3.2 28.3 - - - +
440G SER* 3.4 12.6 - - - +
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Residues in contact with ILE 117 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G ASP* 6.0 1.6 - - - +
105G SER* 5.4 0.4 - - - +
115G PHE* 3.7 22.2 - - + +
116G VAL* 1.3 82.2 - - - +
118G ARG* 1.3 66.5 + - - +
120G PRO* 3.9 20.9 - - + -
131G THR* 6.5 0.2 - - + -
133G PHE* 3.6 45.8 - - + -
134G LEU 3.5 9.6 - - - +
135G THR* 4.0 5.2 - - - -
136G GLN* 5.1 2.2 - - - -
156G ARG* 4.8 0.9 - - - -
167G PRO* 4.5 13.9 - - + -
439G THR 4.2 0.6 - - - +
440G SER* 2.9 33.9 + - - +
441G GLY 3.1 29.1 + - - +
442G SER* 5.8 0.7 - - - -
443G SER* 6.5 0.2 - - - -
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Residues in contact with ARG 118 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117G ILE* 1.3 82.9 - - - +
119G GLU* 1.3 109.8 + - - +
120G PRO* 3.4 5.0 - - - +
134G LEU 3.2 19.8 + - - +
136G GLN* 5.2 5.2 - - + +
148G THR 5.2 1.6 - - - +
151G ASP* 5.0 2.0 + - - -
156G ARG* 3.2 10.8 - - - +
371G ARG* 4.9 0.2 - - - +
406G TYR* 3.6 20.4 - - - -
425G GLU* 2.5 42.9 + - - -
427G ILE* 3.6 17.2 - - - +
439G THR* 4.1 30.4 - - + +
440G SER* 4.4 7.6 - - - -
441G GLY 5.1 0.2 - - - +
806G G39 3.6 28.9 + - - +
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Residues in contact with GLU 119 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118G ARG* 1.3 103.6 + - - +
120G PRO* 1.3 66.8 - - - +
121G PHE* 3.9 10.4 - - - -
133G PHE* 3.7 9.5 - - - -
134G LEU* 3.4 27.4 + - + +
151G ASP* 4.4 0.9 - - - +
156G ARG* 2.7 29.0 + - - -
227G GLU* 4.3 24.0 - - + +
406G TYR* 4.4 21.5 - - + -
423G TRP* 6.0 0.2 - - - -
425G GLU* 3.0 14.1 + - - -
806G G39 3.0 30.0 + - - +
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Residues in contact with PRO 120 (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 ILE* 3.9 22.4 - - + -
118G ARG* 3.4 3.6 - - - -
119G GLU* 1.3 93.3 - - - +
121G PHE* 1.3 66.3 + - - +
131G THR* 4.6 8.5 - - + -
132G PHE 3.3 12.3 - - - +
133G PHE* 4.0 3.4 - - + -
227G GLU 4.2 0.5 - - - +
423G TRP* 3.3 21.1 - - + -
425G GLU* 3.2 38.6 - - + +
441G GLY* 5.8 0.4 - - - -
442G SER 4.8 2.5 - - - +
443G SER* 4.7 15.3 - - - -
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Residues in contact with PHE 121 (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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119G GLU 3.9 8.5 - - - -
120G PRO* 1.3 78.4 - - - +
122G ILE* 1.3 70.6 + - - +
123G SER* 4.6 0.7 - - - -
131G THR* 3.4 4.0 - - - +
132G PHE* 2.8 71.5 + + + +
133G PHE* 5.4 0.2 - - - -
134G LEU* 6.2 0.9 - - + -
158G LEU* 4.5 10.5 - - + -
180G ALA* 4.7 2.7 - - + -
181G SER* 4.0 11.7 - - - -
182G ALA* 3.8 24.2 - - + -
227G GLU* 3.4 24.2 - - - +
228G SER* 3.5 11.2 - - - -
229G GLU* 3.4 28.7 - - + -
423G TRP* 3.5 24.5 - - + +
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Residues in contact with ILE 122 (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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100G TYR* 5.3 0.7 - - + -
101G SER* 4.4 4.0 - - - +
121G PHE* 1.3 82.4 - - - +
123G SER* 1.3 80.7 + - - +
124G CYS* 4.5 3.4 - - - -
129G CYS* 4.6 0.2 - - + -
130G ARG 3.2 13.2 - - - +
131G THR* 4.2 9.4 - - + +
163G VAL* 3.7 26.9 - - + -
229G GLU* 3.5 10.2 + - - +
409G SER 4.7 0.3 - - - +
410G PHE* 3.5 52.5 - - + +
423G TRP* 3.5 16.9 - - + -
443G SER* 6.1 3.4 - - - +
444G ILE 5.4 0.4 - - - +
445G SER* 3.5 35.0 - - - +
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Residues in contact with SER 123 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121G PHE* 4.6 0.7 - - - -
122G ILE* 1.3 80.3 - - - +
124G CYS* 1.3 65.1 + - - +
130G ARG* 2.9 27.6 + - - +
132G PHE* 3.9 22.0 - - - -
182G ALA 3.6 8.4 + - - -
183G CYS* 3.7 11.3 - - - +
189G TRP* 3.5 12.5 - - - -
229G GLU* 2.6 33.3 + - - +
410G PHE* 4.9 0.9 - - - -
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Residues in contact with CYS 124 (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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85G LEU* 5.1 5.0 - - - +
122G ILE* 4.5 0.2 - - - -
123G SER* 1.3 78.3 + - - +
125G SER* 1.3 67.7 + - - +
128G GLU 3.3 5.6 - - - +
129G CYS* 2.1 48.5 - - - -
184G HIS* 3.8 14.4 + - - +
189G TRP* 4.0 6.1 - - - -
229G GLU* 4.0 3.7 + - - +
410G PHE* 4.0 17.0 - - - -
411G VAL 3.8 22.9 + - - +
412G HIS* 4.0 12.5 - - - +
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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