Contacts of the helix formed by residues 114 - 131 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112F LEU 3.3 7.7 - - - +
113F LYS* 1.3 95.3 - - + -
115F ASP* 1.3 64.2 + - + +
116F ASP 3.3 0.2 - - - -
117F GLN* 3.3 32.3 + - + +
118F GLN* 3.9 5.2 + - - +
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Residues in contact with ASP 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F LYS* 2.6 10.1 + - + +
114F PRO* 1.3 78.5 - - + +
116F ASP* 1.3 76.0 + - - +
117F GLN 3.2 0.7 + - - -
118F GLN* 3.5 11.4 + - - +
119F LYS* 4.0 6.6 + - - +
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Residues in contact with ASP 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112F LEU* 4.1 9.2 - - + -
113F LYS* 2.3 57.9 + - - +
115F ASP* 1.3 81.5 - - - +
117F GLN* 1.3 63.7 + - - -
118F GLN 3.1 2.7 - - - -
119F LYS* 3.4 8.3 + - + +
120F GLU* 2.8 31.5 + - + +
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Residues in contact with GLN 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109F HIS* 2.8 59.3 + - + +
110F PRO* 3.6 19.6 + - - +
112F LEU* 3.3 26.6 + - + -
114F PRO* 3.4 30.1 - - + +
115F ASP 3.1 0.8 - - - -
116F ASP* 1.3 79.8 - - - +
118F GLN* 1.3 65.8 + - - +
120F GLU* 3.1 8.5 - - - +
121F VAL* 3.2 5.7 + - - +
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Residues in contact with GLN 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109F HIS* 5.7 0.5 - - - -
114F PRO 3.9 3.9 + - - +
115F ASP 3.5 8.5 + - - +
116F ASP 3.1 0.6 - - - -
117F GLN* 1.3 79.7 - - - +
119F LYS* 1.3 68.3 + - - +
120F GLU 3.0 2.4 + - - -
121F VAL* 3.1 35.5 + - - +
122F VAL* 3.3 12.3 + - - +
118G GLN* 2.7 63.2 + - + +
119G LYS* 5.8 0.2 - - - +
122G VAL* 4.7 3.8 - - - +
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Residues in contact with LYS 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115F ASP 4.0 3.6 + - - +
116F ASP* 3.4 14.5 + - + +
118F GLN* 1.3 76.7 - - - +
120F GLU* 1.3 67.7 + - + +
122F VAL* 3.1 17.0 + - + +
123F ASN* 2.8 66.6 + - - +
126F GLN* 4.3 0.6 + - - -
118G GLN* 5.8 0.2 - - - +
170G LYS 6.1 1.1 - - - +
171G ILE* 5.5 1.1 - - - -
172G PRO* 5.6 9.2 - - + -
173G ASN* 4.1 25.1 - - - +
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Residues in contact with GLU 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105F LEU* 5.0 11.3 - - - +
108F MET* 5.4 5.6 - - - +
109F HIS* 3.9 8.1 - - + -
112F LEU* 3.4 24.7 - - + -
116F ASP* 2.8 22.9 - - + +
117F GLN 3.1 7.4 - - - +
119F LYS* 1.3 88.0 + - + +
121F VAL* 1.3 60.6 + - - +
123F ASN* 3.1 18.2 + - - +
124F MET* 2.9 35.6 + - + +
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Residues in contact with VAL 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109F HIS* 3.7 17.9 - - + +
117F GLN 3.4 14.1 - - - +
118F GLN* 3.1 26.1 + - - +
120F GLU* 1.3 75.0 - - - +
122F VAL* 1.3 68.6 + - - +
124F MET* 3.1 10.3 + - + +
125F ALA* 2.9 21.5 + - - +
170F LYS* 4.4 21.1 - - + +
171F ILE* 3.8 26.2 - - + +
122G VAL* 4.1 13.7 - - + -
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Residues in contact with VAL 122 (chain F).
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 3.7 11.4 - - - +
119F LYS* 3.1 15.4 + - + +
121F VAL* 1.3 81.6 - - - +
123F ASN* 1.3 64.7 + - - +
125F ALA* 3.0 10.0 + - - +
126F GLN* 2.9 40.0 + - + +
118G GLN* 4.3 7.6 - - - +
121G VAL* 4.1 18.8 - - + -
122G VAL* 4.0 21.1 - - + -
125G ALA* 4.5 9.6 - - + -
170G LYS 5.9 0.9 - - - +
171G ILE* 3.8 22.9 - - + -
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Residues in contact with ASN 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105F LEU* 4.1 14.3 - - - +
119F LYS* 2.8 31.9 + - - +
120F GLU* 3.5 21.1 + - - +
121F VAL 3.1 0.4 - - - -
122F VAL* 1.3 78.0 - - - +
124F MET* 1.3 62.3 + - - +
126F GLN* 3.0 7.6 + - - +
127F LYS* 2.8 55.0 + - - +
173G ASN* 4.2 10.4 + - - -
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Residues in contact with MET 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102F LEU* 4.4 2.6 - - + +
105F LEU* 3.8 41.5 - - + +
106F LEU* 3.8 31.0 - - + -
109F HIS* 3.6 33.9 - - + +
120F GLU* 2.9 20.0 + - + +
121F VAL* 3.1 15.2 + - - +
123F ASN* 1.3 72.5 - - - +
125F ALA* 1.3 66.6 + - - +
127F LYS* 3.7 1.1 - - - +
128F ALA* 2.8 28.0 + - - +
167F LEU* 3.9 21.3 - - + -
170F LYS* 4.5 11.9 - - + -
171F ILE* 4.5 3.8 - - + -
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Residues in contact with ALA 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121F VAL 2.9 9.9 + - - +
122F VAL* 3.0 11.0 + - + +
124F MET* 1.3 82.3 - - - +
126F GLN* 1.3 65.5 + - + +
128F ALA* 3.5 0.2 - - - +
129F ILE* 2.9 30.9 + - - +
171F ILE* 3.7 19.9 - - + +
174F ILE* 4.1 8.3 - - + -
122G VAL* 4.1 18.8 - - + +
125G ALA* 5.7 2.2 - - + -
126G GLN* 4.7 11.4 - - + -
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Residues in contact with GLN 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119F LYS* 4.3 2.9 + - - -
122F VAL* 2.9 25.5 + - + +
123F ASN* 3.0 10.6 + - - +
125F ALA* 1.3 79.3 - - + +
127F LYS* 1.3 59.9 + - - +
129F ILE* 4.5 4.5 - - - -
130F ILE* 2.8 50.9 + - + +
125G ALA* 4.6 12.8 - - + -
129G ILE* 4.9 10.2 - - + +
171G ILE* 3.5 17.7 - - - +
173G ASN* 3.1 50.1 + - - +
174G ILE* 4.0 12.7 + - - +
176G SER* 4.2 7.1 + - - -
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Residues in contact with LYS 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102F LEU* 4.2 12.8 - - + -
105F LEU* 4.2 8.7 - - + -
123F ASN* 2.8 49.3 + - - +
124F MET* 3.7 4.0 - - - +
126F GLN* 1.3 76.1 - - - +
128F ALA* 1.3 59.2 + - - +
130F ILE* 4.8 4.0 - - - +
131F ARG* 2.6 68.7 + - - +
132F TYR* 3.2 15.3 + - + +
173G ASN* 6.0 1.0 - - - +
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Residues in contact with ALA 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102F LEU* 4.2 14.6 - - + +
124F MET 2.8 17.2 + - - +
125F ALA 3.5 3.4 - - - +
127F LYS* 1.3 80.5 - - - +
129F ILE* 1.3 61.3 + - - +
132F TYR* 3.3 1.8 + - - -
133F PHE* 2.8 49.5 + - + +
167F LEU* 4.3 9.4 - - + -
174F ILE* 3.9 20.6 - - + -
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Residues in contact with ILE 129 (chain F).
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 2.9 22.3 + - - +
126F GLN* 3.7 4.9 - - - +
128F ALA* 1.3 82.8 - - + +
130F ILE* 1.3 68.7 + - + +
133F PHE* 4.4 1.1 - - + -
134F PRO* 2.9 22.0 - - - +
174F ILE* 3.8 35.9 - - + +
178F PHE* 3.7 19.9 - - + -
126G GLN* 4.3 23.6 - - + +
129G ILE* 4.5 8.5 - - + -
130G ILE* 3.7 29.6 - - + -
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Residues in contact with ILE 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E GLN* 5.4 4.9 - - + +
126F GLN* 2.8 34.7 + - + +
127F LYS* 4.8 4.5 - - - +
129F ILE* 1.3 85.1 - - + +
131F ARG* 1.3 73.6 + - + +
132F TYR 3.7 0.2 - - - -
134F PRO* 3.7 12.0 - - - +
129G ILE* 3.8 34.3 - - + -
174G ILE 6.1 0.2 - - - +
176G SER* 5.0 4.9 - - - +
177G ALA* 4.4 28.0 - - + -
178G PHE* 5.4 0.4 - - + -
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Residues in contact with ARG 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E GLN* 4.7 3.2 - - - +
52E PHE* 3.4 30.6 + - - +
53E GLN* 3.8 27.1 - - - +
54E GLN* 4.2 12.8 - - - +
301E IBG 2.8 36.4 + - - -
127F LYS* 2.6 50.7 + - - +
130F ILE* 1.3 86.6 - - + +
132F TYR* 1.3 83.6 + - + +
134F PRO* 4.5 0.9 - - - -
135F VAL* 3.6 19.2 - - - +
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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
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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