Contacts of the helix formed by residues 114 - 131 (chain G) in PDB entry 1GUL
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 LEU 3.3 7.5 - - - +
113G LYS* 1.3 93.3 - - + -
115G ASP* 1.3 64.5 + - - +
117G GLN* 3.3 33.6 + - + +
118G GLN* 3.9 4.9 + - - +
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Residues in contact with ASP 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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113G LYS* 2.6 10.2 + - + +
114G PRO* 1.3 80.0 - - + +
116G ASP* 1.3 75.1 + - - +
117G GLN 3.2 0.5 + - - -
118G GLN* 3.5 10.9 + - - +
119G LYS* 4.0 6.1 + - - +
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Residues in contact with ASP 116 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112G LEU* 4.1 9.9 - - + -
113G LYS* 2.3 57.6 + - - +
115G ASP* 1.3 81.0 - - - +
117G GLN* 1.3 63.3 + - - -
118G GLN 3.1 2.5 - - - -
119G LYS* 3.9 7.9 - - + +
120G GLU* 2.8 32.7 + - + +
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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
----------------------------------------------------------
109G HIS* 2.8 60.3 + - + +
110G PRO* 3.6 20.2 + - - +
112G LEU* 3.3 26.4 + - + -
113G LYS 3.1 0.4 + - - -
114G PRO* 3.4 30.8 - - + +
115G ASP 3.1 0.6 - - - -
116G ASP* 1.3 80.1 - - - +
118G GLN* 1.3 66.3 + - - +
120G GLU* 3.1 8.1 - - - +
121G VAL* 3.2 5.9 + - - +
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Residues in contact with GLN 118 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118F GLN* 2.7 59.6 + - + +
119F LYS* 5.8 0.4 - - - +
122F VAL* 4.3 9.9 - - - +
109G HIS* 5.7 0.7 - - - -
114G PRO 3.9 3.7 + - - +
115G ASP 3.5 9.2 + - - +
116G ASP 3.1 0.6 - - - -
117G GLN* 1.3 79.2 - - - +
119G LYS* 1.3 66.4 + - - +
120G GLU 3.0 2.1 + - - -
121G VAL* 3.1 36.1 + - - +
122G VAL* 3.3 12.3 + - - +
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Residues in contact with LYS 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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118F GLN* 5.8 0.2 - - - +
170F LYS 5.5 3.4 - - - +
171F ILE* 4.9 2.7 - - - -
172F PRO* 5.1 13.5 - - + -
173F ASN* 3.4 33.6 - - - +
115G ASP* 4.0 3.7 + - - +
116G ASP* 3.4 14.4 + - - +
118G GLN* 1.3 76.3 - - - +
120G GLU* 1.3 68.7 + - + +
122G VAL* 3.1 17.1 + - + +
123G ASN* 2.8 64.6 + - - +
126G GLN* 4.3 0.4 + - - -
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Residues in contact with GLU 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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105G LEU* 5.0 11.8 - - - +
108G MET* 5.4 5.3 - - - +
109G HIS* 3.9 8.7 - - + -
112G LEU* 3.4 24.9 - - + +
116G ASP* 2.8 22.2 - - + +
117G GLN 3.1 7.2 - - - +
119G LYS* 1.3 88.0 + - + +
121G VAL* 1.3 59.5 + - - +
123G ASN* 3.1 17.7 + - - +
124G MET* 2.9 34.6 + - + +
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Residues in contact with VAL 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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122F VAL* 4.1 14.8 - - + -
109G HIS* 3.7 16.6 - - + +
117G GLN 3.4 14.1 - - - +
118G GLN* 3.1 26.3 + - - +
120G GLU* 1.3 74.1 - - - +
122G VAL* 1.3 68.6 + - - +
124G MET* 3.1 10.5 + - + +
125G ALA* 2.9 21.5 + - - +
170G LYS* 4.4 21.5 - - + +
171G ILE* 3.8 26.2 - - + +
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Residues in contact with VAL 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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118F GLN* 4.7 4.3 - - - +
121F VAL* 4.1 20.2 - - + -
122F VAL* 4.0 22.0 - - + -
125F ALA* 4.1 15.7 - - + -
170F LYS 6.0 0.4 - - - +
171F ILE* 3.5 33.2 - - + -
118G GLN 3.3 11.9 + - - +
119G LYS* 3.1 14.3 + - + +
121G VAL* 1.3 80.9 - - - +
123G ASN* 1.3 64.0 + - - +
125G ALA* 3.0 10.0 + - - +
126G GLN* 2.9 27.5 + - - +
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Residues in contact with ASN 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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173F ASN* 3.7 15.4 + - - -
105G LEU* 4.1 14.1 - - - +
119G LYS* 2.8 29.9 + - - +
120G GLU* 3.1 21.5 + - - +
121G VAL 3.1 0.6 - - - -
122G VAL* 1.3 78.0 - - - +
124G MET* 1.3 62.3 + - - +
126G GLN* 3.0 8.0 + - - +
127G LYS* 2.8 54.0 + - - +
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Residues in contact with MET 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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102G LEU* 4.4 2.3 - - + +
105G LEU* 3.8 44.6 - - + +
106G LEU* 3.8 29.2 - - + -
109G HIS* 3.6 33.9 - - + +
120G GLU* 2.9 18.5 + - + +
121G VAL* 3.5 14.8 - - - +
123G ASN* 1.3 72.5 - - - +
125G ALA* 1.3 65.1 + - - +
127G LYS* 3.7 0.7 - - - +
128G ALA* 2.8 28.0 + - - +
167G LEU* 3.9 22.4 - - + -
170G LYS* 4.5 11.4 - - + -
171G ILE* 4.5 3.6 - - + -
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Residues in contact with ALA 125 (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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122F VAL* 4.5 13.5 - - + +
125F ALA* 5.7 2.2 - - + -
126F GLN* 4.6 14.4 - - + -
121G VAL 2.9 9.4 + - - +
122G VAL* 3.2 12.8 - - + +
124G MET* 1.3 83.2 - - - +
126G GLN* 1.3 66.7 + - + +
128G ALA* 3.5 0.3 - - - +
129G ILE* 2.9 30.7 + - + +
171G ILE* 3.7 19.9 - - + +
174G ILE* 4.1 9.0 - - + -
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Residues in contact with GLN 126 (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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125F ALA* 4.7 7.0 - - + -
129F ILE* 4.3 20.9 - - + +
171F ILE* 3.5 23.1 - - - +
173F ASN* 3.2 42.0 + - - +
174F ILE* 3.7 16.1 + - - +
176F SER* 4.0 7.5 + - - -
119G LYS* 4.3 1.6 + - - -
122G VAL* 2.9 24.9 + - + +
123G ASN* 3.6 9.6 - - - +
125G ALA* 1.3 78.5 - - + +
127G LYS* 1.3 61.1 + - + +
129G ILE* 4.5 4.3 - - - -
130G ILE* 2.8 49.1 + - + +
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Residues in contact with LYS 127 (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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173F ASN* 5.9 0.6 - - - +
176F SER* 5.4 7.5 + - - -
102G LEU* 4.2 13.5 - - + -
105G LEU* 4.2 8.7 - - + -
123G ASN* 2.8 48.7 + - - +
124G MET 3.7 3.1 - - - +
126G GLN* 1.3 77.2 - - - +
128G ALA* 1.3 59.8 + - - +
130G ILE* 4.8 4.2 - - - +
131G ARG* 2.6 69.6 + - - +
132G TYR* 3.2 15.5 + - + -
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Residues in contact with ALA 128 (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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102G LEU* 4.2 14.1 - - + +
124G MET 2.8 17.4 + - - +
125G ALA 3.5 3.4 - - - +
127G LYS* 1.3 80.9 - - - +
129G ILE* 1.3 62.1 + - - +
132G TYR* 3.3 1.9 + - - -
133G PHE* 2.8 50.2 + - + +
167G LEU* 4.3 9.4 - - + -
174G ILE* 3.9 20.4 - - + -
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Residues in contact with ILE 129 (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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126F GLN* 4.9 16.4 - - + +
129F ILE* 4.5 7.2 - - + -
130F ILE* 3.8 33.2 - - + -
125G ALA* 2.9 22.1 + - - +
126G GLN* 3.7 5.2 - - - +
128G ALA* 1.3 83.3 - - + +
130G ILE* 1.3 66.9 + - + +
133G PHE* 4.4 1.1 - - + -
134G PRO* 2.9 22.7 - - - +
174G ILE* 3.8 36.3 - - + +
178G PHE* 3.7 21.1 - - + -
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Residues in contact with ILE 130 (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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129F ILE* 3.7 33.7 - - + -
176F SER* 5.1 2.9 - - - +
177F ALA* 3.9 31.6 - - + -
178F PHE* 5.0 1.3 - - + -
126G GLN* 2.8 35.1 + - + +
127G LYS* 4.8 4.3 - - - +
129G ILE* 1.3 83.8 - - + +
131G ARG* 1.3 73.6 + - + +
134G PRO* 3.7 12.4 - - - +
53H GLN* 5.4 4.4 - - + +
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Residues in contact with ARG 131 (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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177F ALA* 5.9 3.6 - - - +
127G LYS* 2.6 51.6 + - - +
130G ILE* 1.3 86.3 - - + +
132G TYR* 1.3 82.8 + - + +
134G PRO* 4.5 0.9 - - - -
135G VAL* 3.6 19.1 - - - +
45H GLN* 4.5 3.6 - - - +
51H LEU 4.8 0.2 - - - +
52H PHE* 3.3 28.5 - - - +
53H GLN* 3.6 29.8 - - - +
54H GLN* 4.2 13.1 - - - +
301H IBG 2.9 37.2 + - - -
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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
------------------------------------------------------------
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