Contacts of the helix formed by residues 114 - 124 (chain G) in PDB entry 1W88
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 PRO 114 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112G GLY 3.3 10.0 - - - +
113G LEU* 1.3 88.1 - - + +
115G LEU* 1.3 64.8 - - - +
116G TYR* 3.2 28.0 - - + -
117G GLN* 2.9 39.4 + - + +
118G ALA 3.2 8.0 + - - -
132G PRO* 3.7 14.4 - - + -
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Residues in contact with LEU 115 (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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55G TYR* 3.9 18.2 - - + +
59G LEU* 3.6 20.9 - - + -
109G ILE* 3.5 37.4 - - + +
113G LEU 3.3 3.9 + - - -
114G PRO* 1.3 71.8 - - - +
116G TYR* 1.3 57.3 + - - +
118G ALA* 3.1 6.6 + - - +
119G PHE* 3.1 36.7 + - + -
324G GLU* 4.2 2.9 - - + +
325G ILE* 3.8 32.1 - - + +
328G ALA* 3.7 22.0 - - + -
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Residues in contact with TYR 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 PRO* 3.2 27.5 - - + -
115G LEU* 1.3 80.5 - - - +
117G GLN* 1.3 77.7 + - + +
119G PHE* 3.5 4.6 + - - +
120G LEU* 3.0 39.7 + - + +
127G HIS* 3.3 32.5 + + - -
328G ALA* 3.1 38.3 - - - +
331G LYS* 3.8 51.8 - - + -
332G ALA* 4.1 1.2 - - - +
335G THR* 4.7 4.0 - - - -
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Residues in contact with GLN 117 (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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113G LEU* 3.9 15.4 - - + +
114G PRO* 2.9 33.8 + - + +
116G TYR* 1.3 106.5 + - + +
118G ALA* 1.3 65.0 + - - +
120G LEU* 3.5 2.2 + - - -
121G PHE* 3.1 16.8 + - - +
127G HIS* 2.8 34.4 + - + +
128G GLY* 3.2 24.2 + - - +
130G GLN* 3.1 30.2 + - - +
131G ILE 4.3 0.2 - - - +
132G PRO* 3.9 7.1 - - - +
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Residues in contact with ALA 118 (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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105G VAL* 3.6 30.1 - - + +
109G ILE* 3.7 22.9 - - + -
113G LEU* 3.8 12.0 - - + +
114G PRO 3.2 4.8 + - - -
115G LEU* 3.1 12.2 + - + +
117G GLN* 1.3 76.4 - - - +
119G PHE* 1.3 63.4 + - + +
121G PHE* 3.2 19.5 + - - +
122G SER* 3.2 12.0 + - - -
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Residues in contact with PHE 119 (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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59G LEU* 3.8 31.4 - - + -
63G SER* 4.0 13.7 - - - -
66G LEU* 4.8 2.9 - - + -
72G LEU* 3.7 28.3 - - + +
109G ILE* 6.1 0.2 - - + -
115G LEU* 3.1 20.7 + - + -
116G TYR 3.8 6.1 - - - +
117G GLN 3.4 0.4 - - - -
118G ALA* 1.3 76.2 - - + +
120G LEU* 1.3 65.1 + - - +
122G SER* 3.3 6.8 + - - -
123G ARG* 3.1 27.6 + - - +
325G ILE* 3.7 26.9 - - + -
328G ALA* 3.7 32.1 - - + -
329G ILE* 3.7 23.6 - - + -
332G ALA* 4.4 9.4 - - + -
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Residues in contact with LEU 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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116G TYR* 3.0 28.1 + - + +
117G GLN* 3.8 1.1 - - - +
119G PHE* 1.3 73.6 - - - +
121G PHE* 1.3 64.3 + - - +
123G ARG* 3.4 13.5 + - - +
124G GLY 3.1 16.6 + - - -
125G HIS* 3.1 31.4 + - + +
127G HIS* 3.8 27.6 - - + -
128G GLY* 3.6 22.9 - - - +
332G ALA* 3.5 32.8 - - + +
335G THR* 3.6 25.6 - - + +
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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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74G PHE* 4.2 28.6 - + - +
102G TYR* 4.5 1.8 - - - -
105G VAL* 4.3 15.7 - - + -
117G GLN 3.1 13.9 + - - +
118G ALA* 3.3 13.9 - - - +
119G PHE 3.2 0.4 - - - -
120G LEU* 1.3 73.1 - - - +
122G SER* 1.3 72.1 + - - +
124G GLY* 3.0 14.4 + - - -
125G HIS 4.8 2.5 - - - -
128G GLY* 3.9 4.4 - - - +
129G ASN* 3.5 31.9 - - - +
140G PRO* 3.6 48.5 - - + -
142G ILE* 4.1 24.9 - - + -
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Residues in contact with SER 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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72G LEU* 3.4 22.2 - - - +
73G GLY* 3.2 17.2 + - - -
74G PHE* 3.0 52.6 + - - +
75G TYR* 4.7 3.5 - - - +
118G ALA 3.2 7.4 + - - -
119G PHE* 3.3 11.6 + - - -
121G PHE* 1.3 87.9 - - - +
123G ARG* 1.3 59.7 + - - +
124G GLY 3.4 0.3 + - - -
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Residues in contact with ARG 123 (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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301F ALA* 3.6 16.1 - - - +
302F GLN* 4.0 10.4 + - + +
71G ARG* 3.0 36.3 + - - +
72G LEU* 4.4 4.8 - - - +
73G GLY* 4.1 14.3 - - - +
119G PHE 3.1 14.6 + - - +
120G LEU* 3.7 18.8 - - - +
121G PHE 3.2 0.4 - - - -
122G SER* 1.3 77.3 - - - +
124G GLY* 1.3 63.2 + - - +
125G HIS* 5.2 3.1 - - + -
329G ILE* 4.4 15.0 + - - +
332G ALA* 3.6 16.4 + - - +
333G ASP* 2.5 48.5 + - - +
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Residues in contact with GLY 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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300F PHE* 3.3 21.1 - - - +
301F ALA* 4.1 14.1 - - - -
302F GLN* 3.3 16.0 + - - +
120G LEU 3.1 0.6 + - - -
121G PHE 3.0 16.0 + - - -
122G SER 3.3 0.6 + - - -
123G ARG* 1.3 75.9 - - - +
125G HIS* 1.3 57.8 + - - +
338G GLN* 3.2 14.7 + - - -
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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