Contacts of the strand formed by residues 126 - 136 (chain N) in PDB entry 2GTL
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 HIS 126 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114N THR* 3.3 7.6 - - - +
115N SER* 2.8 38.3 + - - -
117N TRP* 2.8 31.9 + + - -
123N ARG* 3.5 25.0 + - + -
124N GLU 2.7 15.4 + - - +
125N ASP* 1.3 73.7 - - - +
127N VAL* 1.3 72.0 + - - +
128N THR* 3.4 23.3 - - - -
153N SER* 3.5 16.7 - - - -
154N GLU 3.7 6.3 - - - +
155N LEU* 3.7 28.0 - - + -
156N GLU 5.4 0.2 - - - +
209N ARG* 5.0 0.2 - - - -
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Residues in contact with VAL 127 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112N SER* 4.8 2.5 - - - -
113N GLY 3.3 18.8 - - - +
114N THR* 4.3 4.0 - - - +
126N HIS* 1.3 90.9 + - - +
128N THR* 1.3 75.2 + - - +
129N ARG* 4.7 18.4 - - + +
153N SER* 3.3 1.4 - - - -
154N GLU* 3.2 54.6 + - + +
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Residues in contact with THR 128 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112N SER* 3.4 3.8 - - - -
113N GLY 2.9 26.4 + - - -
115N SER* 3.5 8.3 - - - -
126N HIS* 3.4 14.2 + - - -
127N VAL* 1.3 77.2 - - - +
129N ARG* 1.3 65.1 + - - +
130N ILE* 4.0 9.4 - - + -
151N VAL* 3.8 22.9 - - + -
152N GLU 3.2 10.5 - - - +
153N SER* 3.3 13.3 + - - +
193N VAL* 5.9 0.2 - - + -
209N ARG* 3.9 10.4 + - - +
221N LEU* 3.6 28.9 - - + +
223N VAL* 5.4 0.3 - - - +
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Residues in contact with ARG 129 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110N VAL* 3.9 23.3 - - + -
111N PHE 3.3 5.6 - - - +
112N SER* 4.1 9.8 - - - +
127N VAL* 4.7 9.1 - - + +
128N THR* 1.3 75.7 - - - +
130N ILE* 1.3 60.3 + - - +
131N THR* 3.6 3.1 + - + +
150N LEU 3.1 14.0 - - - +
152N GLU* 2.7 46.6 + - + +
154N GLU* 3.5 35.3 + - - -
226N GLU* 3.5 26.6 + - - +
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Residues in contact with ILE 130 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110N VAL* 3.5 1.3 - - - +
111N PHE* 2.6 59.7 + - + +
128N THR* 4.1 14.1 - - + -
129N ARG* 1.3 71.6 - - - +
131N THR* 1.3 60.8 + - - +
132N ILE* 4.3 2.7 - - + -
149N ALA* 4.7 3.8 - - + -
150N LEU 3.7 2.7 - - - -
151N VAL* 4.5 14.4 - - + +
179N LEU* 5.1 3.6 - - + -
181N LEU* 3.5 27.8 - - + -
193N VAL* 3.5 33.2 - - + -
195N CYS* 3.8 19.7 - - - -
207N CYS* 4.6 0.9 - - - -
221N LEU* 4.5 10.3 - - + -
223N VAL* 4.6 5.6 - - + -
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Residues in contact with THR 131 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108N GLY* 5.3 2.1 - - - -
109N ASN 3.5 7.0 + - - -
110N VAL* 3.4 25.3 - - + +
129N ARG* 3.7 7.2 - - + +
130N ILE* 1.3 76.6 - - - +
132N ILE* 1.3 66.9 + - - +
133N THR* 3.2 1.9 + - - -
149N ALA* 3.9 2.9 - - - -
150N LEU* 2.7 65.0 + - + +
152N GLU* 4.3 10.3 - - - +
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Residues in contact with ILE 132 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105N VAL* 4.1 13.2 - - + +
106N LYS 3.8 16.8 - - - +
107N ALA* 3.8 14.4 - - - -
108N GLY* 2.9 23.4 + - - -
109N ASN* 3.0 15.4 + - + +
111N PHE* 4.4 20.2 - - + -
130N ILE* 5.2 1.6 - - + -
131N THR* 1.3 73.5 + - - +
133N THR* 1.3 61.0 + - - +
134N ALA 3.6 20.9 - - - +
135N SER* 4.8 0.2 - - - -
147N LEU* 3.5 29.6 - - + -
148N ARG 3.7 2.5 - - - +
149N ALA* 3.7 13.5 - - + -
179N LEU* 4.4 13.7 - - + -
181N LEU* 5.0 2.2 - - + -
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Residues in contact with THR 133 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107N ALA* 3.8 9.6 - - - +
108N GLY 4.7 0.5 + - - -
131N THR* 3.2 2.1 + - - -
132N ILE* 1.3 75.6 - - - +
134N ALA* 1.3 63.8 + - + +
148N ARG* 2.8 24.9 + - + +
149N ALA* 3.1 21.5 - - - -
150N LEU* 3.4 8.5 + - - +
167N ASN* 5.3 2.4 + - - -
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Residues in contact with ALA 134 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107N ALA* 4.2 6.3 - - - -
132N ILE* 3.6 5.1 - - - +
133N THR* 1.3 82.4 - - + +
135N SER* 1.3 64.0 + - - +
136N LYS* 5.7 6.7 - - + +
147N LEU* 3.0 22.5 - - - +
148N ARG* 3.1 27.9 + - + +
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Residues in contact with SER 135 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102N THR* 5.6 4.6 - - - +
105N VAL 4.3 12.8 + - - -
106N LYS* 5.1 0.7 - - - -
107N ALA* 4.1 17.9 + - - +
132N ILE* 4.8 0.4 - - - -
134N ALA* 1.3 80.4 - - - +
136N LYS* 1.3 63.8 + - - +
137N ARG* 5.5 0.3 - - - +
145N ILE* 4.1 14.5 - - - +
146N TRP 3.2 11.2 - - - -
147N LEU* 4.1 7.0 - - - +
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Residues in contact with LYS 136 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134N ALA* 5.7 5.2 - - + +
135N SER* 1.3 76.5 - - - +
137N ARG* 1.3 62.5 + - - +
138N ARG* 4.1 24.0 - - - +
145N ILE* 3.8 2.9 - - - +
146N TRP* 2.9 48.1 + - + +
147N LEU* 6.2 1.0 - - - +
148N ARG* 4.1 30.9 - - - +
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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