Contacts of the helix formed by residues 302 - 307 (chain A) in PDB entry 1CM8
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 302 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A LEU* 4.0 8.9 - - + +
141A LEU* 4.0 12.3 - - + -
142A ARG* 3.6 31.9 - - - +
145A HIS* 4.3 10.5 + - + +
209A ILE* 3.6 19.2 - - + +
301A THR* 1.3 72.9 - - - +
303A GLY* 1.3 62.8 + - - +
305A ALA* 3.3 5.4 - - - +
306A LEU* 3.0 31.0 + - - +
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Residues in contact with GLY 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A ARG* 4.0 22.7 - - - +
301A THR* 3.2 5.8 + - - -
302A ALA* 1.3 80.9 - - - +
304A GLU* 1.3 61.1 + - - +
306A LEU* 3.2 6.8 + - - +
307A ALA* 3.1 20.3 + - - +
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Residues in contact with GLU 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A GLN 5.6 0.5 - - - +
299A ARG 5.1 1.1 - - - +
300A VAL* 3.4 29.3 - - + +
301A THR* 3.1 34.2 + - - +
303A GLY* 1.3 74.4 - - - +
305A ALA* 1.3 64.5 + - - +
307A ALA* 2.9 20.4 + - - +
308A HIS* 3.2 9.9 + - - +
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Residues in contact with ALA 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A LEU* 3.7 24.2 - - + -
209A ILE* 5.0 0.7 - - + -
287A LEU* 4.1 10.8 - - + +
291A MET* 4.9 2.2 - - - -
300A VAL* 3.8 20.6 - - + +
301A THR 2.5 21.2 + - - +
302A ALA* 3.3 10.8 - - - +
304A GLU* 1.3 71.2 - - - +
306A LEU* 1.3 61.5 + - - +
308A HIS* 3.1 21.2 + - - +
311A PHE* 3.2 12.6 - - - -
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Residues in contact with LEU 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A TYR* 3.4 42.6 - - + +
138A LEU* 3.5 35.7 - - + +
139A LYS* 3.9 5.8 - - + -
142A ARG* 3.1 46.4 - - + +
302A ALA 3.0 18.2 + - - +
303A GLY 3.2 6.5 + - - +
305A ALA* 1.3 75.3 - - - +
307A ALA* 1.3 60.5 + - - +
308A HIS 3.1 1.8 + - - +
311A PHE* 3.6 24.1 - - + +
315A HIS* 5.1 6.6 - - - +
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Residues in contact with ALA 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A GLY 3.1 11.0 + - - +
304A GLU* 2.9 15.5 + - - +
306A LEU* 1.3 76.4 - - - +
308A HIS* 1.3 61.9 + - - +
309A PRO* 3.8 2.8 - - - +
1309B PRO* 5.3 4.0 - - - +
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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