Contacts of the helix formed by residues 2269 - 2281 (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 ASN2269 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2260D PHE* 5.0 1.2 - - - +
2261D GLN* 2.7 48.0 + - + +
2263D LEU* 4.0 23.1 - - + +
2266D GLU* 5.3 4.9 - - - +
2267D GLY 3.4 1.4 + - - -
2268D ILE* 1.3 73.8 - - - +
2270D PHE* 1.3 61.4 + - - +
2271D TYR* 3.7 2.1 + - - +
2272D GLY* 2.9 28.9 + - - -
2273D GLU* 3.3 22.3 + - - +
2302D LYS* 5.0 3.6 - - - +
2306D THR* 3.7 14.8 + - - +
2310D LYS* 5.7 2.3 + - - -
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Residues in contact with PHE2270 (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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2041D SER* 5.2 7.0 - - - -
2043D GLY* 3.3 27.4 - - - +
2044D SER 4.4 1.3 - - - -
2045D LEU* 3.6 36.7 - - + +
2048D ASP* 5.4 1.1 - - - -
2268D ILE* 2.8 10.8 + - - +
2269D ASN* 1.3 70.4 + - - +
2271D TYR* 1.3 92.9 + + + +
2273D GLU* 3.2 13.7 + - - +
2274D LEU* 3.0 32.0 + - + +
2317D LYS* 4.9 7.4 - - - -
2320D GLU* 3.7 36.1 - - + -
2324D ARG* 5.5 0.9 - - - -
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Residues in contact with TYR2271 (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 1.6 + - - +
2270D PHE* 1.3 97.4 - + + +
2272D GLY* 1.3 64.8 + - - +
2274D LEU* 3.5 11.8 - - + +
2275D VAL* 3.0 28.2 + - - +
2306D THR* 3.6 24.2 - - + +
2309D LEU* 3.8 27.6 + - + +
2310D LYS* 3.5 39.1 + - + -
2313D PRO* 4.9 10.6 - - - +
2316D ALA* 3.7 24.6 - - + +
2317D LYS* 5.2 7.8 + - - -
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Residues in contact with GLY2272 (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* 2.9 28.4 + - - -
2271D TYR* 1.3 77.5 - - - +
2273D GLU* 1.3 61.4 + - - +
2275D VAL* 3.3 3.9 + - - +
2276D ASP* 3.2 13.7 + - - -
2302D LYS* 2.9 33.3 + - - -
2306D THR* 3.6 11.1 - - - +
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Residues in contact with GLU2273 (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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2044D SER* 2.4 33.8 + - - -
2045D LEU* 2.9 30.3 + - + -
2046D SER* 2.6 23.9 + - - +
2259D GLU 4.6 2.9 - - - +
2260D PHE* 3.6 21.0 - - + +
2268D ILE* 3.8 1.7 - - - +
2269D ASN 3.3 9.9 + - - +
2270D PHE* 3.2 21.4 + - - +
2272D GLY* 1.3 73.3 - - - +
2274D LEU* 1.3 55.2 + - - +
2276D ASP* 3.1 6.9 + - - -
2277D LEU* 2.8 47.5 + - + +
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Residues in contact with LEU2274 (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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2045D LEU* 3.6 26.9 - - + +
2270D PHE* 3.0 17.1 + - + +
2271D TYR* 3.2 20.1 + - + +
2273D GLU* 1.3 79.7 - - - +
2275D VAL* 1.3 56.6 + - - +
2278D GLY* 2.8 28.1 + - - -
2284D ILE* 4.3 2.1 - - - +
2309D LEU* 4.0 18.8 - - + -
2316D ALA* 3.7 38.4 - - + +
2319D ILE* 4.3 11.8 - - + +
2320D GLU* 3.7 31.4 - - + +
2323D VAL* 4.6 3.6 - - + -
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Residues in contact with VAL2275 (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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2271D TYR 3.0 17.8 + - - +
2272D GLY 3.6 7.4 - - - +
2274D LEU* 1.3 75.4 - - - +
2276D ASP* 1.3 65.8 + - - +
2278D GLY* 3.1 1.6 + - - -
2279D VAL* 2.8 31.5 + - + +
2284D ILE* 4.1 10.6 - - + +
2291D TYR* 3.7 33.7 - - + -
2298D ILE* 5.7 0.2 - - + -
2302D LYS* 4.2 11.0 - - + -
2305D ALA* 3.9 9.0 - - + -
2306D THR* 3.9 26.9 - - - +
2309D LEU* 3.7 18.2 - - + -
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Residues in contact with ASP2276 (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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2235A GLU* 5.4 7.6 - - - +
2272D GLY 3.2 1.6 + - - +
2273D GLU* 3.1 10.2 + - - +
2275D VAL* 1.3 78.9 - - - +
2277D LEU* 1.3 60.8 + - + +
2279D VAL* 3.5 6.1 + - - +
2280D LYS* 3.0 29.5 + - - +
2291D TYR* 5.2 1.9 + - - -
2302D LYS* 3.2 43.8 + - - +
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Residues in contact with LEU2277 (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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2045D LEU* 4.2 8.5 - - + -
2046D SER* 4.1 25.1 - - - -
2049D ILE* 4.0 18.6 - - + -
2273D GLU* 2.8 38.8 + - + +
2274D LEU 4.0 2.2 - - - +
2276D ASP* 1.3 75.5 - - + +
2278D GLY* 1.3 60.7 + - - +
2280D LYS* 3.4 18.3 + - + +
2281D GLU* 3.0 34.8 + - - +
2323D VAL* 4.0 14.6 - - + -
2327D LEU* 3.8 26.5 - - + -
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Residues in contact with GLY2278 (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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2274D LEU 2.8 19.4 + - - -
2275D VAL 3.6 0.7 - - - -
2277D LEU* 1.3 74.0 - - - +
2279D VAL* 1.3 61.4 + - - +
2281D GLU* 3.3 1.6 + - - -
2282D LYS 3.2 3.3 + - - -
2283D LEU* 2.9 36.9 + - - +
2284D ILE* 3.1 18.8 + - - -
2319D ILE* 4.6 2.2 - - - -
2323D VAL* 4.4 9.6 - - - +
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Residues in contact with VAL2279 (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 2.8 19.2 + - - +
2276D ASP* 3.9 6.5 - - - +
2278D GLY* 1.3 75.3 - - - +
2280D LYS* 1.3 64.2 + - - +
2282D LYS* 3.1 20.8 + - - +
2284D ILE* 3.5 25.2 - - + +
2286D LYS* 4.2 24.5 - - + +
2291D TYR* 3.6 35.2 - - + -
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Residues in contact with LYS2280 (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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3280A LYS* 4.5 28.1 - - + +
3282A LYS* 4.6 2.4 - - - -
2276D ASP 3.0 18.9 + - - +
2277D LEU* 3.6 20.5 - - + +
2278D GLY 3.3 0.2 - - - -
2279D VAL* 1.3 79.5 - - - +
2281D GLU* 1.3 77.6 + - - +
2282D LYS* 3.3 14.0 + - - +
2327D LEU* 5.2 8.9 - - - +
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Residues in contact with GLU2281 (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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3282A LYS* 2.7 37.8 + - - +
2277D LEU 3.0 20.4 + - - +
2278D GLY 3.3 2.7 + - - +
2279D VAL 3.2 0.2 - - - -
2280D LYS* 1.3 95.7 - - + +
2282D LYS* 1.3 71.3 + - - +
2283D LEU* 3.2 16.3 + - + +
2323D VAL* 5.0 4.9 - - + -
2326D LEU* 3.9 28.4 - - + +
2327D LEU* 3.6 45.0 - - + +
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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