Contacts of the helix formed by residues 135 - 151 (chain M) in PDB entry 7KHI
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 CYS 135 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114M CYS* 3.4 7.7 - - + +
117M CYS* 3.8 6.1 - - - -
119M VAL* 3.9 17.0 - - + -
120M GLU 5.5 0.7 - - - +
121M ILE* 4.2 12.6 - - + -
125M ARG* 4.0 2.5 - - - +
134M LEU* 1.3 77.0 - - - +
136M ILE* 1.3 61.0 + - + +
137M ASP* 3.1 9.3 + - - -
138M CYS* 3.1 15.1 + - - -
139M LYS* 2.7 34.4 + - - +
201M ZN 2.2 37.9 - - - -
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Residues in contact with ILE 136 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671D GLY* 3.7 32.1 - - - +
672D LEU* 4.4 3.6 - - - -
673D VAL* 5.1 5.2 - - - +
674D THR* 5.3 8.5 - - - +
121M ILE* 5.8 0.7 - - + -
122M GLY* 5.8 4.5 - - - +
125M ARG* 3.7 34.7 - - + +
134M LEU 4.0 0.6 + - - -
135M CYS* 1.3 75.8 - - + +
137M ASP* 1.3 65.0 + - - +
139M LYS* 3.3 7.2 + - + +
140M THR* 2.9 40.4 + - - +
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Residues in contact with ASP 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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268C ARG* 6.4 1.6 - - - -
270C THR* 2.5 35.1 + - - +
271C ALA* 5.3 4.9 - - - +
135M CYS* 3.2 8.8 - - - -
136M ILE* 1.3 85.2 - - - +
138M CYS* 1.3 63.8 + - - +
140M THR* 3.1 5.5 + - - -
141M LEU* 3.0 35.3 + - + +
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Residues in contact with CYS 138 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268C ARG* 3.9 19.7 - - - +
114M CYS* 4.1 3.8 - - - -
116M SER* 3.6 28.3 - - - +
117M CYS* 3.6 7.2 - - - -
134M LEU* 4.2 8.1 - - + -
135M CYS* 3.1 6.2 + - - +
137M ASP* 1.3 79.5 - - - +
139M LYS* 1.3 63.9 + - - +
141M LEU* 3.9 6.3 - - - +
142M ALA* 2.9 27.2 + - - +
201M ZN 2.2 36.3 - - - -
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Residues in contact with LYS 139 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674D THR* 3.8 20.0 - - + +
677D GLU* 2.1 43.3 + - - +
125M ARG* 3.8 13.0 - - - +
129M ARG* 4.6 4.4 - - - +
132M ALA* 6.2 0.6 - - - +
133M ASP 6.1 1.1 - - - +
134M LEU* 4.1 24.1 - - + +
135M CYS 2.7 22.9 + - - +
136M ILE* 3.5 9.4 - - + +
138M CYS* 1.3 73.9 - - - +
140M THR* 1.3 56.4 + - - +
142M ALA* 3.7 2.9 - - + +
143M GLU* 2.8 33.2 + - - +
202M G4P 3.7 33.1 + - - -
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Residues in contact with THR 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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674D THR* 4.0 17.2 + - - +
136M ILE* 2.9 26.4 + - - +
137M ASP* 3.1 5.6 + - - -
139M LYS* 1.3 76.8 - - - +
141M LEU* 1.3 72.1 + - + +
143M GLU* 3.1 7.8 + - - +
144M ILE* 2.9 40.5 + - + +
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Residues in contact with LEU 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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247C ARG* 5.0 16.6 - - + -
248C GLY* 4.2 22.9 - - - +
268C ARG* 5.9 7.2 - - - +
341C LEU* 4.0 27.6 - - + -
137M ASP* 3.0 36.2 + - + +
138M CYS* 3.9 6.1 - - - +
140M THR* 1.3 84.5 - - + +
142M ALA* 1.3 63.5 + - - +
144M ILE* 3.2 10.4 + - + +
145M ARG* 3.0 31.0 + - - +
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Residues in contact with ALA 142 (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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134M LEU* 4.4 15.5 - - + -
138M CYS 2.9 18.5 + - - +
139M LYS* 3.8 4.5 - - + +
141M LEU* 1.3 77.0 - - - +
143M GLU* 1.3 57.6 + - - +
145M ARG* 3.3 11.9 + - - +
146M GLU* 2.8 33.0 + - - +
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Residues in contact with GLU 143 (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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674D THR* 2.9 42.0 + - - +
675D ALA* 4.0 14.6 - - - +
676D GLY* 3.8 9.9 + - - -
139M LYS* 2.8 19.8 + - + +
140M THR* 3.1 6.9 + - - +
142M ALA* 1.3 76.7 - - - +
144M ILE* 1.3 66.3 + - + +
146M GLU* 3.6 12.3 - - - +
147M LYS* 2.9 31.9 + - + +
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Residues in contact with ILE 144 (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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341C LEU* 4.7 15.9 - - + -
140M THR* 2.9 29.7 + - + +
141M LEU* 3.2 13.4 + - + +
143M GLU* 1.3 84.9 - - + +
145M ARG* 1.3 67.1 + - - +
147M LYS* 3.3 17.9 + - + +
148M GLN* 2.9 28.7 + - + +
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Residues in contact with ARG 145 (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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340C ASP* 3.1 52.1 + - - +
341C LEU* 3.4 23.5 - - + +
141M LEU* 3.0 19.6 + - - +
142M ALA* 3.7 12.6 - - - +
144M ILE* 1.3 75.5 - - - +
146M GLU* 1.3 57.7 + - - +
148M GLN* 3.3 8.1 + - - +
149M MET* 2.9 31.2 + - - +
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Residues in contact with GLU 146 (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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142M ALA* 2.8 21.3 + - - +
143M GLU* 3.6 11.7 - - - +
145M ARG* 1.3 71.0 - - - +
147M LYS* 1.3 69.0 + - - +
148M GLN 3.0 0.2 + - - -
149M MET* 3.1 14.1 + - + +
150M ALA* 2.8 30.1 + - + +
202M G4P 4.7 14.0 + - - +
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Residues in contact with LYS 147 (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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438C GLY* 3.4 28.7 + - - -
440C GLY 5.0 5.7 + - - -
441C GLU* 5.6 10.0 + - - +
143M GLU* 2.9 23.0 + - + +
144M ILE* 4.0 18.8 - - + +
146M GLU* 1.3 75.1 - - - +
148M GLN* 1.3 64.1 + - - +
150M ALA* 4.3 5.6 - - - -
151M GLY* 3.0 27.8 + - - +
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Residues in contact with GLN 148 (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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170C VAL* 3.7 1.4 - - - +
172C TYR* 3.2 27.4 + - - +
340C ASP 5.7 0.7 - - - +
341C LEU* 5.3 10.2 - - + +
346C TYR* 4.7 1.6 + - - -
435C ILE 5.0 0.6 + - - +
436C ARG* 2.9 46.6 + - - +
437C ASN* 3.5 24.0 + - - +
438C GLY* 4.2 9.0 - - - -
144M ILE* 2.9 22.8 + - + +
145M ARG* 3.7 8.6 - - - +
147M LYS* 1.3 84.2 - - + +
149M MET* 1.3 69.6 + - - +
150M ALA 3.4 0.2 + - - -
151M GLY* 3.5 3.4 - - - +
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Residues in contact with MET 149 (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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167C SER 5.2 2.7 - - - +
168C GLY* 4.2 21.8 - - - -
169C LYS* 4.7 9.2 - - - +
170C VAL* 2.7 37.9 - - + +
145M ARG 2.9 17.2 + - - +
146M GLU* 3.9 11.4 - - + +
148M GLN* 1.3 83.1 + - - +
150M ALA* 1.3 56.8 + - + +
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Residues in contact with ALA 150 (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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161C LYS* 3.7 12.1 - - - +
170C VAL* 3.1 17.8 - - - +
146M GLU* 2.8 23.3 + - + +
147M LYS* 4.0 4.7 - - - +
149M MET* 1.3 80.8 - - + +
151M GLY* 1.3 67.0 + - - +
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Residues in contact with GLY 151 (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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159C SER* 3.7 16.5 + - - -
161C LYS* 3.6 25.4 - - - +
170C VAL* 4.8 0.2 - - - -
172C TYR* 2.3 37.2 + - - -
435C ILE* 6.1 0.5 - - - +
442C VAL* 4.4 10.9 - - - +
147M LYS* 3.0 19.1 + - - +
148M GLN* 3.5 5.7 - - - +
150M ALA* 1.3 80.1 - - - +
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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
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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