Contacts of the helix formed by residues 127 - 141 (chain M) in PDB entry 5KZ5
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 ALA 127 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126M GLY* 1.4 70.4 - - - -
128M THR* 1.3 66.1 + - + +
129M GLU 3.5 0.2 - - - -
130M SER* 3.8 1.8 - - - -
131M ASN* 3.1 31.4 + - - +
207M ASN* 5.0 7.2 - - - +
232M ASP* 3.9 6.1 - - - +
234M ALA* 3.7 29.4 - - + -
235M GLN* 5.0 4.7 - - - +
253M SER* 3.7 12.6 - - - +
254M ILE 4.9 0.4 - - - -
255M SER* 3.6 9.7 + - - +
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Residues in contact with THR 128 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4521 ILE* 3.6 27.2 - - + +
4531 LYS* 5.2 0.2 + - - -
4541 TRP* 4.3 1.5 - - - -
118L TYR* 4.9 6.8 + - - -
126M GLY 3.5 0.2 - - - -
127M ALA* 1.3 78.5 - - + +
129M GLU* 1.4 70.4 + - - +
131M ASN* 3.4 5.5 + - - +
132M ASN* 3.1 33.0 + - - -
156M HIS* 5.8 6.1 - - + -
158M CYS* 4.0 31.0 - - + -
159M VAL* 4.9 5.3 - - + +
207M ASN* 6.2 1.6 - - - +
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Residues in contact with GLU 129 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4541 TRP* 4.1 16.0 - - + -
4571 HIS* 4.2 23.1 - - + +
117L PRO* 3.9 13.4 - - + +
118L TYR* 3.4 28.7 + - - -
124M THR* 3.8 25.9 - - + +
125M SER* 3.7 12.3 - - - +
126M GLY* 3.2 26.4 + - - +
128M THR* 1.4 90.4 + - - +
130M SER* 1.3 61.3 + - - +
132M ASN* 3.9 4.9 - - - +
133M ILE* 3.2 29.5 + - - +
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Residues in contact with SER 130 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124M THR* 3.1 26.2 + - - +
126M GLY 3.2 7.3 + - - -
127M ALA 3.5 4.9 + - - -
128M THR 3.3 0.4 - - - -
129M GLU* 1.3 76.9 - - - +
131M ASN* 1.3 63.0 + - - +
133M ILE* 3.2 21.9 - - - +
134M ALA* 3.4 12.6 + - - +
230M HIS* 4.3 0.9 + - - -
253M SER* 3.3 28.5 - - - -
254M ILE 4.5 0.3 + - - -
267M ALA 3.2 17.1 + - - -
268M ILE* 3.7 9.3 - - - +
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Residues in contact with ASN 131 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127M ALA* 3.1 15.3 + - - +
128M THR* 3.4 4.4 + - - +
130M SER* 1.3 74.8 - - - +
132M ASN* 1.4 57.6 + - - +
134M ALA* 3.6 0.5 + - - +
135M ILE* 3.0 42.0 + - + +
155M GLU* 5.2 1.0 + - - -
159M VAL* 3.6 34.2 - - + +
203M MET* 3.8 23.8 - - - +
207M ASN* 4.2 6.3 - - - +
230M HIS* 3.3 16.5 - - - -
232M ASP* 3.3 7.4 + - - +
253M SER* 3.2 27.2 + - - -
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Residues in contact with ASN 132 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4501 LYS* 4.1 6.6 - - - +
4541 TRP* 3.7 28.0 - - + -
4571 HIS* 4.7 6.2 - - + +
128M THR* 3.1 28.2 + - - +
129M GLU* 3.9 8.5 - - + +
130M SER 3.5 0.2 - - - -
131M ASN* 1.4 74.0 - - - +
133M ILE* 1.4 61.8 + - - +
135M ILE* 5.1 0.2 - - - -
136M LYS* 3.2 41.8 + - + +
158M CYS 4.5 1.2 + - - -
159M VAL* 4.4 13.8 - - - +
162M SER* 3.3 36.1 + - - -
281M LEU* 6.3 2.9 - - + -
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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
----------------------------------------------------------
122M ILE* 5.7 0.7 - - + -
129M GLU 3.2 13.7 + - - +
130M SER* 3.2 16.2 - - - +
132M ASN* 1.4 78.2 - - - +
134M ALA* 1.4 62.3 + - - +
136M LYS* 5.0 0.4 - - - +
137M GLY* 3.5 9.0 + - - -
268M ILE* 3.8 24.2 - - + -
277M ARG* 3.9 19.3 - - - +
278M VAL* 3.5 29.3 - - + +
279M GLU 5.2 0.9 - - - +
280M ALA* 4.6 1.3 - - - -
281M LEU* 3.7 47.0 - - + +
282M GLN* 4.2 11.9 - - + +
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Residues in contact with ALA 134 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130M SER 3.4 12.7 + - - +
131M ASN 3.8 1.1 - - - +
133M ILE* 1.4 79.2 - - - +
135M ILE* 1.4 63.3 + - - +
138M VAL* 3.2 31.0 + - - +
230M HIS* 3.3 38.4 - - + +
251M LEU* 3.5 22.2 - - + -
268M ILE* 4.6 5.4 - - + -
278M VAL* 3.5 1.6 - - - +
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Residues in contact with ILE 135 (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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131M ASN* 3.0 26.2 + - + +
132M ASN 4.4 0.7 - - - +
134M ALA* 1.4 75.3 - - - +
136M LYS* 1.3 83.2 + - + +
139M ALA* 3.2 23.7 + - + +
149M LEU* 6.4 0.2 - - + -
151M THR* 5.3 2.0 - - + -
155M GLU* 3.3 26.5 - - - +
159M VAL* 3.7 16.8 - - + -
163M CYS* 4.4 9.2 - - - -
199M LEU* 3.7 30.5 - - + +
201M SER* 3.6 15.5 - - - +
230M HIS* 3.8 22.9 - - + +
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Residues in contact with LYS 136 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132M ASN* 3.2 35.3 + - - +
133M ILE* 5.0 0.4 - - - +
135M ILE* 1.3 88.3 - - + +
137M GLY* 1.3 64.8 + - - +
139M ALA* 3.4 6.3 + - - +
140M ARG* 3.1 47.4 + - - +
149M LEU* 6.2 1.8 - - - +
159M VAL* 5.8 1.1 - - - -
162M SER* 3.4 39.9 + - - -
163M CYS* 3.4 34.2 - - - +
166M LEU* 3.7 27.2 - - + +
312T GLN* 5.5 0.4 - - - +
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Residues in contact with GLY 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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133M ILE 3.5 8.4 + - - -
135M ILE 3.4 0.6 - - - -
136M LYS* 1.3 77.0 - - - +
138M VAL* 1.4 59.4 + - - +
140M ARG* 4.0 4.5 + - - +
141M PHE* 3.1 27.7 + - - +
278M VAL* 3.5 28.2 - - - +
279M GLU* 4.9 5.6 + - - +
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Residues in contact with VAL 138 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134M ALA 3.2 19.9 + - - +
135M ILE 4.1 2.5 - - - +
137M GLY* 1.4 72.4 - - - +
139M ALA* 1.4 63.5 + - - +
141M PHE* 4.3 4.7 - - - -
142M TYR* 3.1 25.9 + - + +
198M SER 3.5 19.1 - - - +
199M LEU* 3.9 14.1 - - + -
228M TYR* 4.0 31.4 - - + +
230M HIS* 5.9 1.8 - - + -
251M LEU* 3.7 24.2 - - + -
277M ARG 3.9 10.3 - - - +
278M VAL* 3.7 12.1 - - + -
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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
----------------------------------------------------------
135M ILE* 3.2 18.9 + - + +
136M LYS* 3.5 9.0 - - - +
137M GLY 3.3 0.2 - - - -
138M VAL* 1.4 80.4 - - - +
140M ARG* 1.4 64.8 + - - +
143M ARG* 3.3 11.1 + - - +
149M LEU* 3.4 40.7 - - + +
166M LEU* 6.2 1.1 - - + -
171M PHE* 4.3 3.1 - - + -
198M SER* 3.3 22.9 + - - -
199M LEU* 4.5 5.2 - - + -
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Residues in contact with ARG 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 LYS* 3.1 40.1 + - - +
137M GLY* 4.6 4.0 - - - +
139M ALA* 1.4 79.3 - - - +
141M PHE* 1.4 65.7 + - - +
143M ARG* 3.3 28.5 + - - +
166M LEU* 3.6 21.0 - - - +
169M GLU* 3.7 11.0 + - - +
171M PHE* 3.8 28.9 - - + -
312T GLN* 3.5 29.3 - - - +
315T MET* 5.4 3.4 - - - +
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Residues in contact with PHE 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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137M GLY 3.1 20.5 + - - +
138M VAL 3.4 3.6 + - - +
140M ARG* 1.4 78.7 - - - +
142M TYR* 1.3 59.5 + + - +
143M ARG 3.6 0.2 + - - -
144M SER 5.1 1.2 + - - -
228M TYR* 3.9 27.6 - + - -
275M ARG* 5.0 16.4 - - + -
276M VAL* 5.3 4.3 - - - -
277M ARG 3.7 22.4 - - - +
278M VAL* 5.2 4.3 - - - -
279M GLU* 4.0 32.1 - - + +
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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