Contacts of the helix formed by residues 121 - 142 (chain N) in PDB entry 6CET
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 MET 121 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118N PHE 4.1 3.6 + - - +
119N VAL 3.1 0.4 - - - -
120N SER* 1.3 79.0 - - - +
122N GLU* 1.3 65.2 + - + +
123N GLU* 3.3 35.0 - - + +
124N SER* 2.7 25.6 + - - +
125N LYS* 3.4 12.0 + - - +
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Residues in contact with GLU 122 (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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25N TYR* 3.5 21.6 + - - +
121N MET* 1.3 77.3 - - + +
123N GLU* 1.3 64.4 + - - +
125N LYS* 3.0 15.4 + - + +
126N GLN* 2.9 39.5 + - - +
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Residues in contact with GLU 123 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121N MET* 3.8 38.3 - - + +
122N GLU* 1.3 84.9 + - - +
124N SER* 1.3 75.7 + - - +
126N GLN* 3.2 12.1 + - - +
127N LYS* 2.9 28.1 + - - +
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Residues in contact with SER 124 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118N PHE* 2.7 60.0 + - - -
119N VAL* 3.6 6.8 - - - -
121N MET* 2.7 18.9 + - - -
123N GLU* 1.3 94.2 - - - +
125N LYS* 1.3 56.4 + - - +
127N LYS* 3.1 8.1 + - - +
128N LEU* 2.9 26.9 + - - +
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Residues in contact with LYS 125 (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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12N PHE* 5.1 13.2 - - + -
14N GLU* 4.2 21.5 - - - +
16N HIS* 6.0 2.2 - - - -
23N ILE* 5.9 4.5 - - + -
25N TYR* 3.5 40.3 - - + +
118N PHE* 5.4 0.4 - - - -
119N VAL* 2.4 53.8 + - + -
120N SER 4.4 0.6 - - - -
121N MET* 3.4 18.5 + - - +
122N GLU* 3.0 13.6 + - + +
124N SER* 1.3 83.5 + - - +
126N GLN* 1.3 60.8 + - - +
128N LEU* 3.3 23.4 + - + +
129N VAL* 3.6 6.4 - - - +
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Residues in contact with GLN 126 (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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25N TYR* 5.2 1.6 - - - -
122N GLU* 2.9 28.0 + - - +
123N GLU* 3.5 14.9 - - - +
124N SER 3.2 0.2 - - - -
125N LYS* 1.3 75.0 - - - +
127N LYS* 1.3 67.7 + - - +
128N LEU 3.1 0.2 - - - -
129N VAL* 3.3 24.7 + - + +
130N PRO* 3.9 5.5 - - - +
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Residues in contact with LYS 127 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118N PHE* 4.6 16.2 - - + -
123N GLU* 2.9 14.5 + - - +
124N SER* 3.1 10.5 + - - +
126N GLN* 1.3 81.1 + - - +
128N LEU* 1.3 61.0 + - - +
129N VAL 3.2 2.3 + - - -
130N PRO* 3.3 14.4 - - - +
131N ILE* 4.0 20.9 - - + +
149N ILE* 4.0 23.0 + - - +
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Residues in contact with LEU 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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12N PHE* 5.0 18.6 - - + -
25N TYR* 4.9 6.7 - - + -
109N LEU* 4.6 21.8 - - + -
118N PHE* 4.6 13.9 - - + -
119N VAL* 6.0 2.5 - - + -
124N SER 2.9 12.2 + - - +
125N LYS* 3.3 20.2 - - + +
126N GLN 3.1 0.6 - - - -
127N LYS* 1.3 77.1 - - - +
129N VAL* 1.3 57.9 + - - +
131N ILE* 3.4 38.6 - - + +
132N MET* 3.2 44.3 - - + +
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Residues in contact with VAL 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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25N TYR* 4.5 13.7 - - + -
26N GLN 5.8 1.6 - - - +
27N VAL* 4.9 9.2 - - + -
125N LYS 3.6 12.1 - - - +
126N GLN* 3.5 20.9 - - + +
127N LYS 3.2 2.0 - - - -
128N LEU* 1.3 73.8 - - - +
130N PRO* 1.4 64.8 - - + +
131N ILE 3.1 1.8 - - - -
132N MET* 2.9 34.7 + - + +
133N THR* 3.1 17.5 + - + +
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Residues in contact with PRO 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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126N GLN* 3.9 8.1 - - - +
127N LYS* 3.3 16.4 - - - +
129N VAL* 1.4 90.9 - - + +
131N ILE* 1.3 58.0 + - - +
133N THR* 2.6 30.2 + - + +
134N ILE* 2.9 27.5 + - + +
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Residues in contact with ILE 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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118N PHE* 5.6 3.6 - - + -
127N LYS* 4.0 22.7 - - + +
128N LEU* 3.4 43.1 - - + +
130N PRO* 1.3 78.0 - - - +
132N MET* 1.3 58.0 + - - +
134N ILE* 3.9 7.6 - - + +
135N LEU* 2.9 53.6 + - + +
147N LEU* 5.3 6.3 - - + -
149N ILE* 4.1 35.7 - - + -
155N ILE* 4.8 3.8 - - + -
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Residues in contact with MET 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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10N ILE* 4.3 20.2 - - + +
11N PHE* 5.8 2.0 - - - +
12N PHE* 5.0 9.6 - - + +
25N TYR* 4.6 17.5 - - + -
26N GLN 5.9 1.1 - - - +
27N VAL* 3.6 31.0 - - + -
85N LEU* 5.8 5.8 - - - -
128N LEU* 3.2 51.5 + - + +
129N VAL* 2.9 26.4 + - + +
131N ILE* 1.3 80.2 - - - +
133N THR* 1.3 58.2 + - - +
135N LEU* 4.1 6.8 - - + +
136N LEU* 2.9 32.6 + - - +
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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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27N VAL* 4.4 15.3 - - + -
129N VAL* 3.1 18.1 + - + +
130N PRO* 2.6 27.9 + - + +
132N MET* 1.3 76.5 - - - +
134N ILE* 1.3 66.2 + - - +
136N LEU* 3.8 5.6 - - - +
137N GLU* 3.0 25.3 + - - +
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Residues in contact with ILE 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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130N PRO* 2.9 24.3 + - + +
131N ILE* 3.9 4.9 - - + +
133N THR* 1.3 83.6 + - - +
135N LEU* 1.3 62.9 + - + +
137N GLU* 3.4 3.3 + - - +
138N GLU* 2.9 48.1 + - + +
145N CYS* 6.2 0.9 - - + -
147N LEU* 4.4 38.8 - - + -
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Residues in contact with LEU 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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10N ILE* 4.6 9.2 - - + -
105N LEU* 4.4 22.9 - - + -
131N ILE* 2.9 38.0 + - + +
132N MET* 4.1 6.3 - - + +
134N ILE* 1.3 81.4 - - + +
136N LEU* 1.3 57.3 + - - +
138N GLU 4.4 0.2 - - - +
139N LEU* 2.9 44.3 + - + +
145N CYS* 3.6 28.7 - - + -
147N LEU* 5.6 2.2 - - + -
155N ILE* 3.8 27.6 - - + -
157N LEU* 4.7 5.6 - - + -
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Residues in contact with LEU 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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7N ILE* 3.8 19.4 - - + +
8N GLU* 3.7 20.0 - - - +
10N ILE* 3.8 28.8 - - + +
27N VAL* 4.1 21.8 - - + +
28N PRO 3.7 30.3 - - - +
132N MET 2.9 17.9 + - - +
133N THR* 3.9 4.9 - - - +
135N LEU* 1.3 76.6 - - - +
137N GLU* 1.3 59.3 + - - +
140N ASN* 3.2 29.3 + - - +
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Residues in contact with GLU 137 (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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133N THR 3.0 17.2 + - - +
134N ILE* 4.0 3.6 - - - +
136N LEU* 1.3 79.2 - - - +
138N GLU* 1.3 80.4 + - + +
140N ASN* 3.2 8.8 + - - +
141N ALA* 2.9 30.5 + - - +
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Residues in contact with GLU 138 (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 ILE* 2.9 33.6 + - + +
137N GLU* 1.3 89.7 - - - +
139N LEU* 1.3 64.6 + - - +
140N ASN 3.3 0.2 - - - -
141N ALA* 3.4 19.0 + - - +
142N SER* 3.4 8.3 + - - -
143N GLY* 3.2 16.8 + - - -
144N ARG 3.8 16.0 + - - +
145N CYS* 3.7 22.0 - - + -
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Residues in contact with LEU 139 (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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7N ILE* 4.1 22.2 - - + -
10N ILE* 6.2 1.1 - - + -
87N PHE* 4.9 9.6 - - + -
98N LEU* 5.3 9.4 - - + -
101N ILE* 4.8 17.9 - - + -
105N LEU* 6.4 2.2 - - + -
135N LEU* 2.9 35.4 + - + +
136N LEU 4.8 0.2 - - - +
138N GLU* 1.3 77.7 - - - +
140N ASN* 1.3 59.5 + - - +
143N GLY* 3.2 26.4 + - - +
145N CYS* 3.7 20.6 - - - -
157N LEU* 5.1 10.1 - - + -
159N VAL* 3.7 30.3 - - + +
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Residues in contact with ASN 140 (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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5N CYS 4.9 5.5 - - - +
6N ARG* 4.3 21.1 + - - +
7N ILE* 3.5 39.6 + - - +
8N GLU* 5.8 0.2 - - - +
136N LEU* 3.2 22.4 + - - +
137N GLU* 3.2 9.5 + - - +
139N LEU* 1.3 76.0 - - - +
141N ALA* 1.3 66.0 + - - +
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Residues in contact with ALA 141 (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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137N GLU* 2.9 27.0 + - - +
138N GLU* 3.7 25.6 - - - +
139N LEU 3.3 0.6 - - - -
140N ASN* 1.3 81.4 - - - +
142N SER* 1.3 63.8 + - - +
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Residues in contact with SER 142 (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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138N GLU* 3.4 6.8 + - - -
141N ALA* 1.3 80.7 - - - +
143N GLY* 1.3 64.6 + - - +
144N ARG* 3.3 37.9 + - - +
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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