Contacts of the helix formed by residues 2301 - 2312 (chain D) in PDB entry 3CMT
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 GLY2301 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2233A GLU* 5.3 4.3 - - - -
2289D ALA* 2.8 23.6 + - - +
2291D TYR* 3.5 10.1 - - - -
2300D GLN* 1.3 73.9 - - - +
2302D LYS* 1.3 66.5 + - - -
2303D ALA* 3.1 4.9 - - - -
2304D ASN 3.0 14.4 + - - -
2305D ALA 3.3 7.1 + - - -
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Residues in contact with LYS2302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2233A GLU* 4.1 32.4 + - - +
2234A GLY* 5.7 4.9 - - - +
2261D GLN* 5.3 15.1 - - - +
2269D ASN* 5.0 3.4 - - - +
2272D GLY* 2.9 40.2 + - - -
2275D VAL* 4.2 10.1 - - + -
2276D ASP* 3.2 32.6 + - - +
2291D TYR* 3.3 24.3 + - - +
2301D GLY* 1.3 70.9 - - - -
2303D ALA* 1.3 57.8 + - - +
2305D ALA* 3.4 3.3 + - - +
2306D THR* 2.8 39.1 + - - +
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Residues in contact with ALA2303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2300A GLN 5.8 1.8 - - - +
2303A ALA* 4.8 18.2 - - + -
2304A ASN* 5.1 6.5 - - - +
2300D GLN 5.6 0.2 - - - +
2301D GLY* 3.0 2.6 + - - -
2302D LYS* 1.3 78.5 - - - +
2304D ASN* 1.3 64.3 + - - +
2306D THR* 3.5 7.0 - - - -
2307D ALA* 3.3 19.2 + - - +
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Residues in contact with ASN2304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2300A GLN* 6.0 1.0 - - - +
2303A ALA* 6.0 0.3 - - - +
2304A ASN* 2.3 49.0 + - - +
2298D ILE 4.1 1.2 - - - +
2299D GLY* 4.0 5.8 - - - -
2300D GLN* 2.9 36.6 + - - +
2301D GLY 3.0 2.6 + - - -
2303D ALA* 1.3 77.3 - - - +
2305D ALA* 1.3 61.5 + - - +
2307D ALA* 3.1 12.3 + - - +
2308D TRP* 2.9 28.1 + - - +
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Residues in contact with ALA2305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2275D VAL* 3.9 17.2 - - + +
2291D TYR* 3.8 40.4 - - + -
2298D ILE* 4.1 19.4 - - + +
2299D GLY* 4.2 2.7 - - - -
2301D GLY 3.3 3.0 + - - -
2302D LYS 3.8 6.3 - - - +
2304D ASN* 1.3 78.2 - - - +
2306D THR* 1.3 62.0 - - - +
2308D TRP* 3.3 4.7 + - - +
2309D LEU* 3.2 25.6 + - - +
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Residues in contact with THR2306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2269D ASN* 3.7 14.8 + - - +
2271D TYR* 3.6 11.0 - - + +
2272D GLY* 3.6 35.1 - - - +
2275D VAL* 3.9 11.5 - - - +
2302D LYS* 2.8 27.2 + - - +
2303D ALA* 3.5 7.6 - - - -
2305D ALA* 1.3 76.1 - - - +
2307D ALA* 1.3 61.7 + - - +
2309D LEU* 3.2 5.8 + - - +
2310D LYS* 3.2 32.5 + - - +
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Residues in contact with ALA2307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2300A GLN* 5.2 12.1 - - - +
2303D ALA 3.3 9.8 + - - +
2304D ASN* 3.1 18.2 + - - +
2306D THR* 1.3 78.4 - - - +
2308D TRP* 1.3 59.9 + - - +
2310D LYS* 3.4 15.7 + - + +
2311D ASP* 3.1 30.0 + - - +
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Residues in contact with TRP2308 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2293D TYR* 4.6 9.0 - + + -
2296D GLU* 3.8 26.6 + - - -
2297D LYS 5.1 1.2 + - - -
2298D ILE* 3.2 66.9 - - + +
2304D ASN 2.9 7.8 + - - +
2305D ALA 3.5 7.9 - - - +
2307D ALA* 1.3 78.3 - - - +
2309D LEU* 1.3 81.1 + - + +
2311D ASP* 3.1 6.4 + - + +
2312D ASN* 2.8 69.0 + - + +
2315D THR* 4.0 25.1 - - + -
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Residues in contact with LEU2309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2271D TYR* 3.8 22.3 - - + +
2274D LEU* 4.0 23.3 - - + -
2275D VAL* 3.7 31.9 - - + +
2284D ILE* 4.7 8.1 - - + -
2298D ILE* 5.0 3.4 - - + -
2305D ALA 3.2 5.8 + - - +
2306D THR 3.2 7.9 + - - +
2308D TRP* 1.3 97.3 - - + +
2310D LYS* 1.3 65.4 + - - +
2312D ASN 3.3 18.8 - - - +
2313D PRO* 3.7 1.9 - - - +
2316D ALA* 3.8 25.9 - - - +
2319D ILE* 3.9 23.6 - - + -
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Residues in contact with LYS2310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2266D GLU* 3.2 29.8 + - - +
2269D ASN* 5.7 1.9 + - - -
2271D TYR* 3.5 36.2 + - + -
2306D THR* 3.2 25.2 + - - +
2307D ALA* 3.4 15.7 - - + +
2309D LEU* 1.3 77.2 - - - +
2311D ASP* 1.3 65.9 - - - +
2312D ASN 3.5 0.2 + - - -
2313D PRO* 3.6 15.2 - - - +
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Residues in contact with ASP2311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2307D ALA* 3.1 15.3 + - - +
2308D TRP* 3.1 14.1 + - + +
2310D LYS* 1.3 84.7 - - - +
2312D ASN* 1.3 65.3 + - - +
2313D PRO* 3.2 9.7 - - - +
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Residues in contact with ASN2312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2308D TRP* 2.8 54.6 + - + +
2309D LEU* 3.3 8.5 - - - +
2310D LYS 3.3 0.4 - - - -
2311D ASP* 1.3 86.8 - - - +
2313D PRO* 1.3 64.6 - - - +
2314D GLU* 3.2 6.8 + - + -
2315D THR* 3.2 20.9 + - - +
2316D ALA* 3.0 17.7 + - - +
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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