Contacts of the helix formed by residues 123 - 141 (chain M) in PDB entry 6GYK
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 ASP 123 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91M ASN* 3.8 21.2 + - - -
121M LYS* 3.2 39.8 + - - +
122M LYS* 1.3 81.1 + - - +
124M ASN* 1.3 64.9 + - - +
125M GLU 3.2 2.7 - - - +
126M VAL* 3.4 25.4 + - + +
127M GLN* 3.7 12.8 + - - +
158M HIS* 5.4 3.3 + - - -
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Residues in contact with ASN 124 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118M VAL* 3.1 54.3 + - - +
119M MET* 5.0 6.5 - - - -
121M LYS* 3.8 16.2 + - - -
122M LYS* 3.4 2.7 - - - +
123M ASP* 1.3 79.0 - - - +
125M GLU* 1.3 62.4 + - + +
127M GLN* 3.1 35.5 + - - +
128M ALA* 3.3 13.7 + - - +
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Residues in contact with GLU 125 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122M LYS* 4.8 18.3 - - - +
123M ASP 3.2 0.8 - - - -
124M ASN* 1.3 80.1 - - + +
126M VAL* 1.3 61.0 + - + +
128M ALA* 4.7 3.6 - - - +
129M ALA* 2.9 33.3 + - - +
154M TYR* 3.8 10.1 + - - +
158M HIS* 5.0 10.3 - - + -
159M ASP* 5.2 9.5 - - - +
168M MET* 5.3 9.5 - - + +
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Residues in contact with VAL 126 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122M LYS 5.0 0.2 - - - +
123M ASP* 3.4 24.9 + - + +
124M ASN 3.3 0.6 - - - -
125M GLU* 1.3 76.2 - - - +
127M GLN* 1.3 59.0 + - - +
129M ALA* 4.5 2.7 - - - -
130M PHE* 2.9 57.0 + - + +
154M TYR* 4.6 5.6 - - + -
155M LYS* 3.4 29.2 - - - +
158M HIS* 3.5 33.2 - - + +
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Residues in contact with GLN 127 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118M VAL* 5.3 2.0 - - - +
121M LYS* 5.1 4.8 + - - +
123M ASP 3.7 6.8 + - - +
124M ASN* 3.1 46.8 + - - +
126M VAL* 1.3 78.7 - - - +
128M ALA* 1.3 59.6 + - + +
130M PHE* 3.8 4.8 - - - +
131M ALA* 2.9 28.8 + - - +
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Residues in contact with ALA 128 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124M ASN 3.3 14.0 + - - +
125M GLU* 4.4 3.6 - - - +
127M GLN* 1.3 79.9 - - + +
129M ALA* 1.3 60.9 + - - +
131M ALA* 3.1 7.3 + - - +
132M LYS* 2.9 32.7 + - - +
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Residues in contact with ALA 129 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125M GLU 2.9 22.8 + - - +
126M VAL 4.1 0.2 - - - +
128M ALA* 1.3 77.6 - - - +
130M PHE* 1.3 59.4 + - - +
132M LYS* 3.5 4.2 + - - +
133M ILE* 2.9 38.4 + - + +
154M TYR* 3.4 35.7 - - + +
168M MET* 4.4 11.0 - - + -
172M MET* 5.2 5.6 - - - -
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Residues in contact with PHE 130 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87M LEU* 4.6 10.5 - - + -
126M VAL* 2.9 38.5 + - + +
127M GLN* 4.0 5.2 - - - +
129M ALA* 1.3 79.2 - - - +
131M ALA* 1.3 52.2 + - - +
133M ILE* 4.3 5.8 - - + -
134M THR* 2.3 39.4 + - - -
151M LYS* 3.4 69.3 - - + +
154M TYR* 3.5 28.0 - + + -
155M LYS* 3.9 21.8 - - + -
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Residues in contact with ALA 131 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127M GLN 2.9 18.8 + - - +
128M ALA* 3.1 9.4 + - - +
130M PHE* 1.3 77.1 - - - +
132M LYS* 1.3 61.2 + - - +
134M THR* 3.2 7.2 + - - +
135M MET* 2.9 28.4 + - - +
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Residues in contact with LYS 132 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434B ARG* 4.7 18.6 - - - +
128M ALA 2.9 16.3 + - - +
129M ALA* 4.1 2.0 - - - +
131M ALA* 1.3 73.6 - - - +
133M ILE* 1.3 61.3 + - - +
135M MET* 3.0 14.3 + - + +
136M LEU* 2.9 41.0 + - + +
168M MET* 6.1 3.0 - - - +
172M MET* 3.6 30.4 - - + -
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Residues in contact with ILE 133 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129M ALA* 2.9 24.2 + - + +
130M PHE* 4.2 9.2 - - + +
132M LYS* 1.3 75.2 - - - +
134M THR* 1.3 58.0 + - - +
136M LEU* 3.3 4.5 + - - +
137M CYS* 2.9 32.8 + - + +
147M LYS* 5.4 3.6 - - + +
150M ALA* 4.9 11.2 - - + +
151M LYS* 4.7 16.8 - - + -
154M TYR* 4.5 21.5 - - + -
172M MET* 3.6 37.9 - - + +
175M SER* 3.9 16.6 - - - +
176M ILE* 4.6 16.9 - - + +
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Residues in contact with THR 134 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130M PHE 2.3 26.6 + - - -
131M ALA* 3.3 8.7 - - - +
133M ILE* 1.3 78.9 - - - +
135M MET* 1.3 56.6 + - - +
137M CYS* 4.1 1.5 - - - +
138M ASP* 2.9 52.1 + - - +
147M LYS* 3.4 27.4 - - - +
151M LYS* 3.3 19.1 + - - -
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Residues in contact with MET 135 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B TYR* 5.5 6.1 - - - -
434B ARG* 5.0 14.8 - - - +
446B LEU* 4.4 22.2 - - - +
449B ASN* 4.0 25.6 + - - +
131M ALA 2.9 13.4 + - - +
132M LYS* 3.0 17.9 + - + +
134M THR* 1.3 78.3 - - - +
136M LEU* 1.3 63.9 + - + +
138M ASP* 3.7 5.6 - - - +
139M ALA* 2.9 30.0 + - + +
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Residues in contact with LEU 136 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B LEU* 3.6 35.7 - - + -
132M LYS* 2.9 27.1 + - + +
133M ILE 3.9 3.6 - - - +
135M MET* 1.3 81.1 - - + +
137M CYS* 1.3 60.6 + - - +
139M ALA* 3.0 7.0 + - - +
140M ALA* 2.9 29.2 + - - +
172M MET* 3.6 24.2 - - + -
176M ILE* 4.1 17.7 - - + -
195M LEU* 4.3 10.7 - - + +
196M ILE* 3.6 35.0 - - + -
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Residues in contact with CYS 137 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451B LYS* 5.1 0.2 + - - -
133M ILE* 2.9 21.5 + - + +
134M THR* 4.1 2.7 - - - +
136M LEU* 1.3 76.0 - - - +
138M ASP* 1.3 63.6 + - - +
140M ALA* 3.2 6.5 + - - +
141M GLU 3.2 18.4 + - - -
142M LEU* 3.5 40.8 + - + +
143M PRO 4.1 1.1 - - - -
146M VAL 5.1 0.2 - - - -
147M LYS* 3.7 40.6 - - + -
176M ILE* 4.9 9.1 - - + +
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Residues in contact with ASP 138 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B ASN* 5.7 4.0 - - + +
450B ALA* 5.5 6.2 + - - +
451B LYS* 2.9 57.3 + - + +
134M THR* 2.9 44.3 + - - +
135M MET* 3.9 5.6 - - - +
137M CYS* 1.3 80.9 - - - +
139M ALA* 1.3 59.4 + - - +
141M GLU* 3.8 9.2 + - - +
142M LEU 5.6 0.7 - - - +
147M LYS* 4.7 9.1 + - - +
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Residues in contact with ALA 139 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445B LYS* 3.2 39.0 - - + +
446B LEU* 4.4 8.3 - - + -
448B ILE 6.2 0.2 - - - -
449B ASN* 4.7 8.3 - - - +
135M MET 2.9 18.6 + - - +
136M LEU* 3.0 9.1 + - - +
138M ASP* 1.3 78.5 - - - +
140M ALA* 1.3 57.4 + - - +
141M GLU* 3.4 5.2 + - - +
195M LEU* 5.0 3.8 - - + -
267R GLY* 4.4 12.6 - - - -
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Residues in contact with ALA 140 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136M LEU 2.9 14.1 + - - +
137M CYS* 3.2 7.3 + - - +
139M ALA* 1.3 75.9 - - - +
141M GLU* 1.3 69.9 + - - +
142M LEU* 3.2 27.2 + - + +
176M ILE* 6.4 1.3 - - + -
187M ARG* 4.6 3.5 + - - -
195M LEU* 3.9 8.7 - - + -
267R GLY* 5.0 9.1 - - - -
268R MET* 3.8 30.0 - - + +
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Residues in contact with GLU 141 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B ASN* 4.0 27.9 + - - +
166B PHE* 4.1 20.9 - - + -
169B ARG* 6.2 1.1 - - - -
450B ALA* 5.7 2.1 - - + +
451B LYS* 5.4 9.6 - - - +
137M CYS 3.2 5.3 + - - -
138M ASP 3.8 9.7 + - - +
139M ALA 3.4 8.3 - - - +
140M ALA* 1.3 81.3 - - - +
142M LEU* 1.3 63.2 + - - +
143M PRO* 4.0 2.3 - - - +
187M ARG* 4.8 4.7 + - - -
263R MET* 4.2 12.3 - - - +
266R THR* 3.6 32.8 + - - +
267R GLY* 4.6 5.6 + - - -
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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