Contacts of the helix formed by residues 121 - 127 (chain M) in PDB entry 3QUM
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 SER 121 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122K TYR* 3.4 13.7 - - - +
123K PRO* 4.0 33.7 + - - -
124K LEU* 5.6 1.6 - - - +
214K ASP 5.8 0.9 - - - -
120M PRO* 1.3 72.9 - - - +
122M SER* 1.3 55.6 + - - +
123M GLU* 2.5 22.8 + - - -
124M GLN* 2.8 44.0 + - - +
125M LEU* 3.1 15.0 + - - +
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Residues in contact with SER 122 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213K ARG* 2.7 41.6 + - - -
214K ASP* 4.2 5.1 + - - +
120M PRO 3.9 1.4 + - - -
121M SER* 1.3 70.2 - - - +
123M GLU* 1.3 56.8 + - - +
125M LEU* 3.9 15.6 - - - +
126M THR* 3.6 21.3 + - - -
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Residues in contact with GLU 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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121K VAL 3.8 7.0 - - - +
122K TYR* 3.8 17.7 - - + -
123K PRO* 4.2 10.1 - - + +
208K LYS* 3.1 39.3 + - - +
121M SER* 2.5 13.9 + - - +
122M SER* 1.3 79.5 - - - +
124M GLN* 1.3 63.6 + - - +
125M LEU 3.2 1.1 - - - -
126M THR* 3.8 5.8 + - - +
127M SER* 3.4 19.4 + - - -
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Residues in contact with GLN 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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122K TYR* 3.6 36.2 - - + +
141K LEU* 4.7 6.9 - - - +
143K LYS* 4.4 15.0 - - - +
120M PRO* 3.7 9.7 - - + +
121M SER* 2.8 22.2 + - - +
123M GLU* 1.3 77.4 - - - +
125M LEU* 1.3 61.1 + - - +
127M SER* 3.2 8.9 + - - -
129M GLY* 2.7 35.4 + - - +
130M ALA* 4.0 5.7 - - - +
131M SER* 3.1 54.9 + - - +
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Residues in contact with LEU 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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214K ASP* 5.3 4.0 - - - +
120M PRO* 4.1 18.6 - - + +
121M SER 3.1 33.1 + - - +
122M SER* 3.9 11.9 - - - +
124M GLN* 1.3 77.0 - - - +
126M THR* 1.3 55.2 + - - +
128M GLY* 2.6 30.7 + - - -
129M GLY 3.1 14.8 + - - +
130M ALA* 3.5 20.6 - - + -
183M LYS* 3.9 33.5 + - + +
186M TYR* 5.2 5.4 - - + -
187M GLU* 5.5 1.6 - - - +
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Residues in contact with THR 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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122M SER 3.6 15.9 + - - -
123M GLU* 3.8 6.6 + - - +
124M GLN 3.4 0.2 - - - -
125M LEU* 1.3 73.5 - - - +
127M SER* 1.3 58.9 + - - +
128M GLY* 2.7 12.3 + - - -
183M LYS* 5.7 0.4 - - - +
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Residues in contact with SER 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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120K PRO* 6.1 0.2 - - - +
122K TYR* 3.7 20.2 + - - -
123M GLU 3.4 12.0 + - - -
124M GLN* 3.2 9.3 + - - -
125M LEU 3.1 1.2 - - - -
126M THR* 1.3 77.4 - - - +
128M GLY* 1.3 54.0 + - - +
129M GLY* 3.1 9.6 + - - -
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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
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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