Contacts of the helix formed by residues 123 - 142 (chain N) in PDB entry 3H1J
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 GLU 123 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62N LEU* 5.6 0.4 - - - +
121N ALA* 3.1 14.7 - - + +
122N LEU* 1.3 73.4 - - - +
124N GLU* 1.3 56.8 + - - +
125N SER* 2.7 42.7 + - - +
126N GLN* 2.8 27.3 + - + +
127N ILE* 3.1 9.9 + - - +
179N ARG* 5.3 0.2 - - - +
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Residues in contact with GLU 124 (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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122N LEU 2.7 8.1 + - - -
123N GLU* 1.3 72.7 - - - +
125N SER* 1.3 60.6 + - - +
127N ILE* 4.0 14.4 - - + -
128N GLU* 3.8 28.3 + - - +
179N ARG* 3.9 33.6 - - + +
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Residues in contact with SER 125 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123N GLU* 2.7 29.5 + - - +
124N GLU* 1.3 73.3 - - - +
126N GLN* 1.3 64.8 + - - +
128N GLU* 3.4 14.5 + - - +
129N LYS* 3.7 8.1 + - - +
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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
----------------------------------------------------------
62N LEU* 3.6 23.8 - - + -
65N LYS* 3.6 30.8 - - + +
72N CYS* 4.5 11.4 - - - +
123N GLU* 2.8 19.2 + - + +
125N SER* 1.3 78.4 - - - +
127N ILE* 1.3 56.4 + - - +
129N LYS* 2.6 68.2 + - - +
130N GLU* 2.9 26.5 + - + +
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Residues in contact with ILE 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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58N PHE* 3.6 17.5 - - + -
62N LEU* 3.6 22.0 - - + +
122N LEU* 3.7 15.5 - - + +
123N GLU 3.1 11.2 + - - +
124N GLU* 3.9 14.4 - - + +
126N GLN* 1.3 78.3 - - - +
128N GLU* 1.3 64.1 + - - +
129N LYS 3.0 0.2 + - - -
130N GLU* 3.2 2.4 + - - +
131N ARG* 2.9 53.3 + - - +
177N LEU 5.2 0.9 - - - +
179N ARG* 3.6 39.9 - - + +
182N LEU* 3.8 13.9 - - + -
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Residues in contact with GLU 128 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124N GLU* 3.8 23.7 - - - +
125N SER* 3.4 9.2 + - - +
126N GLN 3.2 1.0 - - - -
127N ILE* 1.3 81.3 - - - +
129N LYS* 1.3 61.1 + - - +
131N ARG* 2.7 56.9 + - - +
132N GLY* 3.7 3.6 + - - -
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Residues in contact with LYS 129 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125N SER 3.7 4.1 + - - +
126N GLN* 2.6 45.0 + - - +
128N GLU* 1.3 70.0 - - - +
130N GLU* 1.3 73.0 + - - +
131N ARG 3.0 1.3 - - - -
132N GLY* 2.9 15.1 + - - -
133N VAL* 3.1 19.7 + - + +
52V ARG* 5.5 9.7 - - - +
53V GLU* 5.3 8.1 + - - -
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Residues in contact with GLU 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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58N PHE* 3.7 14.6 - - + -
61N HIS* 3.2 41.3 + - + +
62N LEU* 3.5 26.7 - - + -
65N LYS* 4.0 15.2 + - - -
126N GLN* 2.9 32.4 + - + +
127N ILE 3.7 5.4 - - - +
129N LYS* 1.3 86.0 - - - +
131N ARG* 1.3 56.8 + - - +
133N VAL* 3.4 12.5 - - - +
134N ILE* 2.8 37.4 + - - +
53V GLU* 4.8 5.1 - - - +
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Residues in contact with ARG 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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58N PHE* 3.5 18.3 - - + -
127N ILE* 2.9 31.0 + - - +
128N GLU* 2.7 48.3 + - - +
129N LYS 3.0 0.2 - - - -
130N GLU* 1.3 77.4 - - - +
132N GLY* 1.3 62.3 + - - +
135N LEU* 3.2 32.6 + - + +
174N ILE* 2.6 53.0 + - + +
175N LYS* 3.5 25.8 + - - +
176N HIS* 4.8 0.4 - - - -
177N LEU 3.1 29.9 + - - +
178N THR* 5.1 1.2 - - - +
179N ARG 5.7 0.2 - - - +
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Residues in contact with GLY 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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128N GLU 3.7 4.5 + - - -
129N LYS 2.9 9.2 + - - -
131N ARG* 1.3 79.4 - - - +
133N VAL* 1.3 62.3 + - - +
135N LEU* 3.7 12.2 - - - +
136N GLN* 3.2 20.6 + - - +
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Residues in contact with VAL 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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61N HIS* 4.0 7.4 - - + +
129N LYS* 3.1 24.0 + - + +
130N GLU* 2.9 23.7 + - - +
132N GLY* 1.3 75.6 - - - +
134N ILE* 1.3 68.6 + - - +
136N GLN* 2.9 8.9 + - - +
137N GLU* 2.9 32.8 + - + +
51V CYS* 4.3 9.6 - - + -
53V GLU* 3.6 47.3 - - + +
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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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54N GLY 5.6 0.2 - - - +
57N TYR* 3.5 27.8 - - + -
58N PHE* 3.4 59.2 - - + +
61N HIS* 3.6 21.1 - - + +
130N GLU 2.8 23.1 + - - +
131N ARG 4.0 2.5 - - - +
133N VAL* 1.3 71.3 - - - +
135N LEU* 1.3 65.9 + - - +
136N GLN 2.9 0.5 + - - -
137N GLU* 2.9 12.2 + - - +
138N LEU* 2.9 24.1 + - + +
174N ILE* 3.3 28.5 - - + -
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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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131N ARG* 3.2 24.7 + - + +
132N GLY* 3.7 12.6 - - - +
133N VAL 3.2 0.6 - - - -
134N ILE* 1.3 78.9 - - - +
136N GLN* 1.3 61.6 + - - +
138N LEU* 3.6 8.9 + - + +
139N LYS* 3.4 25.3 + - - +
171N THR* 4.1 26.2 - - + +
174N ILE* 3.5 28.7 - - + -
175N LYS* 3.9 22.4 - - + -
1R VAL* 5.9 0.2 - - - +
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Residues in contact with GLN 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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132N GLY 3.2 11.0 + - - +
133N VAL 2.9 9.9 + - - +
135N LEU* 1.3 75.7 - - - +
137N GLU* 1.3 57.6 + - - +
138N LEU 2.9 1.1 - - - -
139N LYS* 2.5 43.6 + - - +
140N GLU* 3.1 24.9 + - - +
50V LEU* 2.9 47.5 - - - +
51V CYS* 3.4 37.0 - - + +
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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
----------------------------------------------------------
57N TYR* 2.9 30.1 + - + +
61N HIS* 3.0 23.8 + - - -
133N VAL* 2.9 22.3 + - + +
134N ILE* 3.3 5.7 - - - +
136N GLN* 1.3 75.2 - - - +
138N LEU* 1.3 57.6 + - + +
140N GLU* 3.2 13.4 + - - +
141N MET* 2.8 41.5 + - + +
287O ARG* 3.0 22.2 + - - -
51V CYS* 4.2 2.9 - - - -
53V GLU* 3.4 18.5 - - - +
54V SER* 4.0 15.7 + - - +
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Residues in contact with LEU 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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57N TYR* 5.3 0.9 - - + -
134N ILE* 2.9 18.3 + - + +
135N LEU* 3.7 12.1 - - + +
136N GLN 2.7 4.0 + - - -
137N GLU* 1.3 72.4 - - - +
139N LYS* 1.3 66.5 + - - +
140N GLU 2.8 1.9 + - - -
141N MET* 3.1 6.5 + - + +
142N ASP* 2.9 26.6 + - - +
168N GLU* 3.4 37.2 - - + -
169N GLY 4.2 8.7 - - - +
171N THR* 4.3 20.0 - - - +
174N ILE* 3.5 26.9 - - + -
1R VAL* 4.5 9.0 - - + -
2R HIS* 6.2 0.2 - - + -
3R ASN* 4.0 27.2 + - - +
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Residues in contact with LYS 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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135N LEU* 3.4 17.0 - - - +
136N GLN* 2.5 32.6 + - - +
138N LEU* 1.3 73.3 - - - +
140N GLU* 1.3 61.8 + - + +
142N ASP* 3.6 12.4 - - - +
143N ASN* 3.5 16.2 + - - -
241Q LYS* 4.9 9.9 + - - -
1R VAL* 4.7 18.3 - - + +
50V LEU* 5.0 5.8 - - + -
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Residues in contact with GLU 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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136N GLN* 3.1 26.5 + - - +
137N GLU* 3.5 9.9 - - - +
138N LEU 2.8 1.6 + - - -
139N LYS* 1.3 73.3 - - - +
141N MET* 1.3 54.9 + - + +
142N ASP 2.9 3.8 - - - -
143N ASN* 2.7 39.1 + - - +
144N ASP 4.0 0.2 + - - -
47V ARG* 4.0 7.7 + - - -
48V PRO* 2.6 36.0 - - + +
49V LEU* 3.2 12.8 - - - +
50V LEU* 3.5 7.4 + - + -
51V CYS* 3.4 19.2 - - - -
54V SER* 3.0 33.7 + - - -
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Residues in contact with MET 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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57N TYR* 4.1 14.1 - - + +
137N GLU* 2.8 32.0 + - + +
138N LEU* 4.0 6.1 - - + +
140N GLU* 1.3 72.5 - - + +
142N ASP* 1.3 61.1 + - - +
143N ASN 3.1 0.4 - - - -
144N ASP* 3.1 28.1 + - - +
147N ASN* 4.0 23.1 + - + +
148N VAL* 4.1 2.8 - - - +
168N GLU* 3.5 43.7 - - - +
2R HIS* 4.6 8.3 - - + -
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Residues in contact with ASP 142 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138N LEU 2.9 16.9 + - - +
139N LYS* 3.6 10.8 - - - +
140N GLU 2.8 0.4 + - - -
141N MET* 1.3 76.8 - - - +
143N ASN* 1.3 62.1 + - - +
144N ASP 3.1 1.1 + - - -
145N MET* 3.7 6.2 - - - +
148N VAL* 3.2 22.1 - - - +
1R VAL* 3.6 16.2 - - + +
2R HIS* 2.4 57.8 + - - +
3R ASN* 4.1 0.4 + - - +
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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
------------------------------------------------------------
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