Contacts of the helix formed by residues 109 - 120 (chain G) in PDB entry 1U8R
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 SER 109 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78G LYS* 4.1 0.9 - - - +
107G VAL 3.3 2.3 + - - -
108G MET* 1.3 77.2 - - - +
110G GLU* 1.3 65.0 + - - +
111G ASP* 3.6 9.3 + - - +
112G VAL* 3.2 21.2 + - - +
113G GLU* 3.3 19.4 + - - +
92H LEU* 5.7 0.2 - - - +
100H GLU* 2.7 31.8 + - - -
103H ARG* 3.8 8.7 - - - +
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Residues in contact with GLU 110 (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 ALA* 5.9 0.5 - - - +
77G ARG* 3.4 29.5 + - - +
78G LYS* 4.1 5.5 + - - +
108G MET 4.0 0.4 + - - -
109G SER* 1.3 73.9 - - - +
111G ASP* 1.3 65.5 + - - +
113G GLU* 3.3 21.7 - - - +
114G ARG* 3.3 40.0 + - - +
137G GLU 5.4 3.1 - - - +
138G LEU* 4.1 8.5 - - + -
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Residues in contact with ASP 111 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109G SER* 3.1 9.1 - - - +
110G GLU* 1.3 75.0 - - - +
112G VAL* 1.3 68.0 + - - +
113G GLU 2.9 2.2 + - - -
114G ARG* 2.9 39.9 + - - +
115G ARG* 3.1 13.8 + - + +
92H LEU* 4.4 15.5 - - + -
96H GLU* 3.5 18.2 - - - +
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Residues in contact with VAL 112 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108G MET* 4.1 4.9 - - + -
109G SER* 3.2 22.7 + - - +
111G ASP* 1.3 76.5 - - - +
113G GLU* 1.3 57.5 + - - +
115G ARG* 3.4 7.3 + - - +
116G LEU* 2.8 47.9 + - + +
86H LEU* 4.3 2.7 - - + -
90H ILE* 4.3 11.2 - - + -
92H LEU* 3.6 26.2 - - + -
100H GLU* 3.4 25.1 - - + +
104H TRP* 3.9 20.4 - - + -
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Residues in contact with GLU 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77G ARG* 2.6 55.9 + - - +
78G LYS* 2.6 39.1 + - + +
81G LEU* 3.6 11.4 - - + +
108G MET* 3.8 20.9 - - + -
109G SER 3.3 12.3 + - - +
110G GLU* 3.3 12.8 - - - +
111G ASP 3.0 0.2 - - - -
112G VAL* 1.3 77.8 - - - +
114G ARG* 1.3 64.8 + - - +
116G LEU* 2.9 16.6 + - - +
117G VAL* 2.9 17.5 + - - +
138G LEU* 4.0 7.9 - - + -
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Residues in contact with ARG 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110G GLU* 3.7 35.1 + - - +
111G ASP* 2.9 34.1 + - - +
113G GLU* 1.3 77.9 - - - +
115G ARG* 1.3 59.7 + - + +
117G VAL* 2.9 32.6 + - - +
118G LYS* 3.3 10.3 + - - +
138G LEU* 2.9 60.8 + - + +
139G GLY* 5.5 7.4 - - - +
140G VAL* 5.8 2.5 - - + -
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Residues in contact with ARG 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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111G ASP 3.1 10.1 + - - +
112G VAL* 3.8 7.9 - - - +
114G ARG* 1.3 81.2 - - + +
116G LEU* 1.3 61.4 + - - +
118G LYS* 3.2 20.2 + - - +
119G VAL* 3.0 41.1 + - - +
89H VAL 5.4 0.2 + - - -
90H ILE* 2.7 36.8 + - + +
91H GLY* 2.9 31.8 + - - -
92H LEU* 3.8 14.4 - - + +
93H PRO* 4.5 6.7 - - - -
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Residues in contact with LEU 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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81G LEU* 4.7 15.0 - - + +
82G ALA* 5.2 0.4 - - - +
85G LEU* 3.6 51.8 - - + -
108G MET* 3.4 34.8 - - + -
112G VAL* 2.8 24.7 + - + +
113G GLU* 3.2 10.8 - - - +
115G ARG* 1.3 76.5 - - - +
117G VAL* 1.3 62.2 + - - +
119G VAL* 4.4 7.2 - - + -
120G LEU* 3.0 43.7 + - + +
90H ILE* 4.0 11.4 - - + -
104H TRP* 5.7 0.4 - - + -
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Residues in contact with VAL 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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81G LEU* 4.3 12.3 - - + -
113G GLU 2.9 15.6 + - - +
114G ARG* 2.9 17.8 + - - +
116G LEU* 1.3 77.9 - - - +
118G LYS* 1.3 59.6 - - - +
120G LEU 3.6 0.2 + - - -
121G ASN 3.3 3.6 + - - -
122G ASN* 2.8 58.3 + - + +
123G PRO* 3.6 8.8 - - + +
135G LEU* 4.1 25.1 - - + -
138G LEU* 4.3 8.5 - - + -
140G VAL* 4.2 23.3 - - + -
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Residues in contact with LYS 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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114G ARG 3.3 9.1 + - - +
115G ARG* 3.2 27.2 + - - +
117G VAL* 1.3 78.8 - - - +
119G VAL* 1.3 62.6 + - - +
120G LEU 3.5 0.3 + - - -
121G ASN* 3.5 17.3 + - - +
122G ASN* 4.0 23.1 - - - +
140G VAL* 4.2 20.5 - - - +
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Residues in contact with VAL 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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85G LEU* 5.5 1.3 - - + -
89G VAL* 4.7 11.9 - - + +
115G ARG* 3.0 27.0 + - - +
116G LEU* 3.3 12.8 + - + +
118G LYS* 1.3 78.1 - - - +
120G LEU* 1.3 70.2 + - + +
121G ASN* 3.9 4.4 + - - -
89H VAL* 4.0 21.5 - - + +
90H ILE* 3.4 26.5 - - - +
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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
----------------------------------------------------------
81G LEU* 4.0 9.0 - - + +
84G ARG* 3.4 35.3 - - + -
85G LEU* 3.9 12.3 - - + +
88G ASP* 4.4 14.6 - - + +
89G VAL* 3.9 26.5 - - + -
116G LEU* 3.0 29.5 + - + +
119G VAL* 1.3 85.8 - - + +
121G ASN* 1.3 72.8 + - - +
123G PRO* 3.6 25.0 - - + +
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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