Contacts of the helix formed by residues 2312 - 2328 (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 ASN2312 (chain D).
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Specific contacts
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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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Residues in contact with PRO2313 (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* 4.9 9.6 - - - +
2309D LEU 3.7 7.2 - - - +
2310D LYS 3.6 14.1 - - - +
2311D ASP 3.2 11.9 - - - +
2312D ASN* 1.3 82.7 - - - +
2314D GLU* 1.3 79.4 + - + +
2316D ALA* 3.4 6.2 + - + +
2317D LYS* 3.0 38.1 + - + +
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Residues in contact with GLU2314 (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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2312D ASN* 4.7 2.9 - - + -
2313D PRO* 1.3 99.8 - - + +
2315D THR* 1.3 63.0 + - - +
2317D LYS* 3.5 9.5 + - - +
2318D GLU* 3.3 19.4 + - - +
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Residues in contact with THR2315 (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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2293D TYR* 3.4 37.2 - - + +
2308D TRP* 4.0 17.1 - - + -
2312D ASN* 3.2 26.3 + - - +
2314D GLU* 1.3 76.8 - - - +
2316D ALA* 1.3 65.6 + - - +
2318D GLU* 3.2 12.4 + - - +
2319D ILE* 3.0 26.2 + - + +
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Residues in contact with ALA2316 (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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2270D PHE* 6.3 0.2 - - + -
2271D TYR* 3.7 29.4 - - + +
2274D LEU* 3.7 14.3 - - + +
2309D LEU* 3.8 19.0 - - + +
2312D ASN 3.0 13.7 + - - +
2313D PRO* 3.5 10.5 - - + +
2314D GLU 3.3 0.2 - - - -
2315D THR* 1.3 77.6 - - - +
2317D LYS* 1.3 59.9 + - - +
2319D ILE* 3.2 2.1 + - - -
2320D GLU* 2.8 32.0 + - - +
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Residues in contact with LYS2317 (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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2270D PHE* 4.9 9.7 - - - -
2271D TYR* 5.2 8.1 + - - -
2313D PRO* 3.0 26.5 + - + +
2314D GLU* 3.7 8.5 - - - +
2315D THR 3.3 0.2 - - - -
2316D ALA* 1.3 80.1 - - - +
2318D GLU* 1.3 57.2 + - - +
2320D GLU* 2.9 27.4 + - - +
2321D LYS* 2.9 33.1 + - - +
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Residues in contact with GLU2318 (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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2293D TYR* 2.7 27.2 + - - +
2294D LYS* 3.7 18.3 + - - +
2314D GLU 3.3 10.4 + - - +
2315D THR* 3.2 15.6 + - - +
2317D LYS* 1.3 78.0 - - - +
2319D ILE* 1.3 65.6 + - - +
2321D LYS* 3.4 8.3 + - - +
2322D LYS* 3.3 44.8 + - - +
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Residues in contact with ILE2319 (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* 4.3 13.9 - - + -
2278D GLY* 4.6 2.7 - - - -
2283D LEU* 4.1 23.6 - - + -
2284D ILE* 4.3 19.7 - - + -
2293D TYR* 3.8 46.2 - - + +
2298D ILE* 6.2 0.2 - - + -
2308D TRP* 5.4 0.2 - - + -
2309D LEU* 3.9 24.7 - - + -
2315D THR* 3.0 19.0 + - + +
2316D ALA 3.8 3.1 - - - +
2318D GLU* 1.3 71.7 - - - +
2320D GLU* 1.3 65.8 + - - +
2322D LYS* 3.2 9.0 + - - +
2323D VAL* 2.9 29.7 + - + +
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Residues in contact with GLU2320 (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* 3.7 19.9 - - + +
2270D PHE* 3.7 21.6 - - + -
2274D LEU* 3.7 16.1 - - + +
2316D ALA 2.8 16.6 + - - +
2317D LYS* 2.9 36.4 + - - +
2319D ILE* 1.3 76.8 - - - +
2321D LYS* 1.3 62.3 + - - +
2323D VAL* 3.1 4.2 + - - +
2324D ARG* 2.9 55.8 + - - +
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Residues in contact with LYS2321 (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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2317D LYS* 2.9 19.2 + - - +
2318D GLU* 3.7 8.3 - - - +
2320D GLU* 1.3 76.0 - - - +
2322D LYS* 1.3 58.7 + - + +
2324D ARG* 3.5 10.0 + - - +
2325D GLU* 3.0 46.6 + - + +
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Residues in contact with LYS2322 (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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2283D LEU* 3.7 28.0 - - + -
2293D TYR* 4.5 5.7 + - - +
2294D LYS* 5.8 2.0 - - - +
2318D GLU* 3.3 40.7 + - + +
2319D ILE* 3.2 9.4 + - - +
2321D LYS* 1.3 76.5 - - + +
2323D VAL* 1.3 65.9 + - - +
2325D GLU* 3.3 15.3 + - - +
2326D LEU* 2.9 30.8 + - + +
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Residues in contact with VAL2323 (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* 4.2 8.1 - - + -
2049D ILE* 4.0 20.4 - - + -
2274D LEU* 4.6 5.2 - - + -
2277D LEU* 4.0 23.3 - - + +
2278D GLY* 4.4 16.2 - - - +
2281D GLU* 5.0 2.2 - - + -
2283D LEU* 3.8 17.5 - - + -
2319D ILE* 2.9 27.6 + - + +
2320D GLU* 3.6 8.7 - - - +
2322D LYS* 1.3 75.6 - - - +
2324D ARG* 1.3 57.6 + - - +
2326D LEU* 3.2 8.1 + - - +
2327D LEU* 2.9 38.4 + - + +
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Residues in contact with ARG2324 (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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2041D SER* 4.5 7.3 + - - -
2045D LEU* 3.9 17.6 - - + +
2048D ASP* 2.8 36.8 + - - +
2049D ILE* 5.4 3.1 - - + -
2054D GLY* 3.3 31.1 + - - -
2270D PHE* 5.5 1.4 - - - -
2320D GLU* 2.9 48.8 + - - +
2321D LYS* 3.7 8.5 - - - +
2323D VAL* 1.3 76.6 - - - +
2325D GLU* 1.3 58.6 + - - +
2327D LEU* 4.5 1.1 - - - +
2328D LEU* 2.8 60.4 + - + +
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Residues in contact with GLU2325 (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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2321D LYS* 3.0 45.4 + - + +
2322D LYS* 3.6 16.0 - - - +
2324D ARG* 1.3 75.9 - - - +
2326D LEU* 1.3 62.7 + - + +
2328D LEU 4.5 6.8 + - - +
2331D PRO* 5.8 4.4 - - - +
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Residues in contact with LEU2326 (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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3282A LYS* 4.7 9.0 - - - +
2281D GLU* 3.9 41.5 - - + +
2283D LEU* 4.4 19.3 - - + -
2322D LYS* 2.9 23.1 + - + +
2323D VAL* 3.6 4.9 - - - +
2325D GLU* 1.3 79.3 - - + +
2327D LEU* 1.3 67.1 + - + +
2328D LEU 5.3 0.4 - - - +
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Residues in contact with LEU2327 (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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2049D ILE* 3.8 32.1 - - + +
2256D LYS* 5.2 3.6 + - - -
2277D LEU* 3.8 28.7 - - + -
2280D LYS* 5.2 8.5 - - - +
2281D GLU* 3.6 41.3 - - + +
2323D VAL* 2.9 22.0 + - + +
2326D LEU* 1.3 86.1 - - - +
2328D LEU* 1.3 63.4 + - - +
2329D SER* 3.5 4.2 + - - -
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Residues in contact with LEU2328 (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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2048D ASP 3.5 25.6 - - - +
2049D ILE* 3.7 20.0 - - + +
2052D GLY 3.8 10.3 - - - +
2053D ALA 4.6 4.0 - - - +
2054D GLY* 3.7 14.8 - - - +
2324D ARG* 2.8 60.3 + - + +
2325D GLU 4.6 6.1 - - - +
2326D LEU 5.3 0.3 - - - -
2327D LEU* 1.3 71.9 - - - +
2329D SER* 1.3 62.9 + - - +
2331D PRO* 3.8 30.4 - - + +
2332D ASN 5.6 0.9 - - - +
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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