Contacts of the helix formed by residues 122 - 129 (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 GLY 122 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31M TYR* 5.5 1.3 - - - -
120M GLU* 3.8 3.4 + - - -
121M ILE* 1.3 81.1 - - - +
123M ILE* 1.3 66.0 + - - -
124M ARG 3.3 2.5 - - - -
125M ARG* 3.4 9.9 + - - +
126M LEU* 3.2 20.4 + - - +
136M ILE* 5.8 3.8 - - - +
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Residues in contact with ILE 123 (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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23M TYR* 5.0 16.6 - - + -
25M GLU* 3.5 35.7 - - + +
31M TYR* 4.3 13.9 + - + -
32M MET* 5.5 2.2 - - + -
36M GLN* 4.0 24.0 - - + +
39M HIS* 5.9 0.9 - - + -
40M PHE* 3.6 30.3 - - + -
121M ILE 3.5 2.1 + - - -
122M GLY* 1.3 69.6 - - - -
124M ARG* 1.3 75.5 + - + +
126M LEU* 3.0 9.7 + - + +
127M GLU* 2.9 35.4 + - + +
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Residues in contact with ARG 124 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667D GLN* 4.5 4.2 + - - +
672D LEU* 3.7 23.0 - - + +
22M PRO* 4.6 8.3 - - - +
23M TYR 3.9 21.4 + - - -
24M GLN* 5.4 3.2 - - - +
25M GLU* 4.4 20.0 + - - +
122M GLY* 3.3 0.8 - - - -
123M ILE* 1.3 89.8 - - + +
125M ARG* 1.3 57.3 + - - +
127M GLU* 3.3 23.9 + - - +
128M ALA* 2.9 26.7 + - - +
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Residues in contact with ARG 125 (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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672D LEU* 3.0 37.9 + - + +
673D VAL* 4.7 2.0 - - + +
674D THR 5.6 0.6 - - - +
677D GLU* 3.3 26.7 + - - +
121M ILE* 3.7 16.4 - - + +
122M GLY* 3.4 15.0 + - - +
123M ILE 3.2 0.8 - - - -
124M ARG* 1.3 78.2 - - - +
126M LEU* 1.3 58.6 + - - +
128M ALA* 3.1 6.1 + - - +
129M ARG* 2.9 30.5 + - + +
132M ALA* 3.5 28.7 - - + +
133M ASP 5.2 0.2 - - - +
134M LEU 2.2 34.7 + - - +
135M CYS* 4.0 2.8 - - - +
136M ILE* 3.7 30.1 - - + +
139M LYS* 3.8 18.8 - - - +
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Residues in contact with LEU 126 (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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31M TYR* 4.0 7.0 - - - +
32M MET* 3.9 9.9 - - + -
40M PHE* 3.6 18.3 - - + -
111M PHE* 3.5 39.5 - - + -
112M GLY* 3.9 20.6 - - - +
121M ILE* 4.2 10.1 - - + +
122M GLY 3.2 13.6 + - - +
123M ILE* 3.0 11.5 + - + +
125M ARG* 1.3 79.3 - - - +
127M GLU* 1.3 57.2 + - - +
129M ARG 4.2 1.8 - - - -
130M PRO* 2.9 43.3 - - - +
132M ALA* 4.1 25.8 - - + +
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Residues in contact with GLU 127 (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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14M ILE* 5.4 4.9 - - - +
15M LEU* 4.0 26.9 + - + +
22M PRO* 3.8 12.6 - - - +
23M TYR* 2.9 37.6 + - - +
39M HIS* 3.1 20.8 + - - +
40M PHE* 4.0 18.6 - - + -
43M ILE* 5.9 3.0 - - - +
123M ILE* 2.9 21.8 + - + +
124M ARG* 3.7 26.0 + - - +
126M LEU* 1.3 73.9 - - - +
128M ALA* 1.3 65.4 + - - +
130M PRO* 4.4 3.6 - - - +
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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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667D GLN* 3.3 31.0 - - - +
672D LEU* 4.8 1.8 - - + -
673D VAL* 4.4 18.2 - - + -
681D LYS* 2.6 34.8 + - - +
14M ILE* 3.9 2.6 - - - +
124M ARG 2.9 10.8 + - - +
125M ARG* 3.1 12.3 + - - +
127M GLU* 1.3 80.6 - - - +
129M ARG* 1.3 56.0 + - - +
130M PRO* 3.6 5.4 - - - +
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Residues in contact with ARG 129 (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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673D VAL* 5.0 4.3 - - + -
676D GLY 4.7 0.2 - - - -
677D GLU* 3.3 51.2 + - + +
680D ASN* 4.3 5.3 - - - +
681D LYS* 4.5 6.1 - - - +
14M ILE* 5.1 0.7 - - - -
47M TRP* 5.9 2.4 - - + -
98M LYS* 3.3 13.6 - - - +
125M ARG* 2.9 14.7 + - - +
126M LEU* 3.5 2.5 - - - -
128M ALA* 1.3 75.4 - - + +
130M PRO* 1.3 55.5 - - - +
131M THR* 2.7 38.0 + - + +
132M ALA* 2.8 32.9 + - + +
139M LYS* 4.6 2.9 - - - +
202M G4P 2.5 78.3 + - - -
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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