Contacts of the helix formed by residues 4269 - 4281 (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 ASN4269 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4260D PHE* 5.0 1.7 - - - +
4261D GLN* 2.8 48.0 + - + +
4263D LEU* 4.3 21.0 - - + +
4266D GLU* 5.6 3.0 - - - +
4267D GLY 3.6 0.4 + - - -
4268D ILE* 1.3 73.8 - - - +
4270D PHE* 1.3 61.2 + - - +
4271D TYR* 3.7 1.4 + - - +
4272D GLY* 2.9 28.2 + - - -
4273D GLU* 3.3 21.5 + - - +
4302D LYS* 5.0 4.8 - - - +
4306D THR* 3.7 15.6 + - - +
4310D LYS* 5.7 3.1 + - - -
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Residues in contact with PHE4270 (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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4041D SER* 5.2 7.4 - - - -
4043D GLY* 3.4 27.1 - - - +
4044D SER 4.5 1.1 - - - -
4045D LEU* 3.7 34.7 - - + +
4048D ASP* 5.5 1.1 - - - -
4268D ILE* 3.0 10.6 + - - +
4269D ASN* 1.3 70.4 + - - +
4271D TYR* 1.3 91.1 + + + +
4273D GLU* 3.2 14.0 + - - +
4274D LEU* 3.0 32.8 + - + +
4317D LYS* 4.8 7.4 - - - -
4320D GLU* 3.7 37.5 - - + -
4324D ARG* 5.5 0.4 - - - -
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Residues in contact with TYR4271 (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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4269D ASN* 3.7 1.5 + - - +
4270D PHE* 1.3 94.5 - + + +
4272D GLY* 1.3 66.1 + - - +
4274D LEU* 3.2 14.3 + - + +
4275D VAL* 3.0 28.6 + - - +
4306D THR* 3.6 24.9 - - + +
4309D LEU* 3.8 28.1 + - + +
4310D LYS* 3.5 39.6 + - + -
4313D PRO* 4.8 10.4 - - - +
4316D ALA* 3.7 23.8 - - + +
4317D LYS* 5.3 8.3 + - - -
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Residues in contact with GLY4272 (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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4269D ASN* 2.9 28.2 + - - -
4271D TYR* 1.3 76.3 - - - +
4273D GLU* 1.3 60.3 + - - +
4275D VAL* 3.3 3.7 + - - +
4276D ASP* 3.2 13.9 + - - -
4302D LYS* 2.9 33.1 + - - -
4306D THR* 3.6 11.1 - - - +
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Residues in contact with GLU4273 (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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4044D SER* 2.4 32.0 + - - -
4045D LEU* 2.7 31.6 + - + +
4046D SER* 2.6 26.8 + - - +
4259D GLU 4.8 2.7 - - - +
4260D PHE* 3.8 19.1 - - + +
4268D ILE* 4.0 1.6 - - - +
4269D ASN 3.3 10.4 + - - +
4270D PHE* 3.2 21.0 + - - +
4272D GLY* 1.3 72.8 - - - +
4274D LEU* 1.3 54.3 + - - +
4276D ASP* 3.1 7.1 + - - +
4277D LEU* 2.8 47.1 + - + +
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Residues in contact with LEU4274 (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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4045D LEU* 3.7 21.3 - - + +
4270D PHE* 3.0 20.1 + - + +
4271D TYR* 3.2 19.7 + - + +
4273D GLU* 1.3 75.8 - - - +
4275D VAL* 1.3 56.6 + - - +
4277D LEU 3.8 0.2 - - - -
4278D GLY* 2.8 28.8 + - - -
4284D ILE* 4.2 1.9 - - - +
4309D LEU* 4.0 17.9 - - + -
4316D ALA* 3.7 37.2 - - + +
4319D ILE* 4.3 11.7 - - + -
4320D GLU* 3.7 34.1 - - + +
4323D VAL* 4.6 4.7 - - + -
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Residues in contact with VAL4275 (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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4271D TYR 3.0 17.9 + - - +
4272D GLY 3.5 7.9 - - - +
4273D GLU 3.2 0.2 - - - -
4274D LEU* 1.3 74.6 - - - +
4276D ASP* 1.3 66.7 + - - +
4278D GLY* 3.2 1.2 + - - -
4279D VAL* 2.9 30.9 + - + +
4284D ILE* 4.1 10.8 - - + +
4291D TYR* 3.7 34.3 - - + -
4298D ILE* 5.7 0.4 - - + -
4302D LYS* 4.2 11.0 - - + -
4305D ALA* 4.0 8.1 - - + -
4306D THR* 3.9 27.8 - - - +
4309D LEU* 3.7 18.6 - - + -
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Residues in contact with ASP4276 (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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4272D GLY 3.2 2.0 + - - +
4273D GLU* 3.1 10.9 + - - +
4275D VAL* 1.3 78.6 - - - +
4277D LEU* 1.3 61.5 + - + +
4279D VAL* 3.5 5.4 + - - +
4280D LYS* 3.0 29.5 + - - +
4291D TYR* 5.2 2.1 + - - -
4302D LYS* 3.2 42.2 + - - +
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Residues in contact with LEU4277 (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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4045D LEU* 4.0 9.9 - - + -
4046D SER* 4.3 18.2 - - - -
4049D ILE* 3.8 27.8 - - + -
4273D GLU* 2.8 43.3 + - + +
4274D LEU 4.0 2.0 - - - +
4276D ASP* 1.3 74.7 - - + +
4278D GLY* 1.3 60.0 + - - +
4280D LYS* 3.5 16.4 + - + +
4281D GLU* 3.0 34.8 + - - +
4323D VAL* 4.0 14.8 - - + -
4327D LEU* 3.8 20.2 - - + -
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Residues in contact with GLY4278 (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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4274D LEU 2.8 18.8 + - - -
4275D VAL 3.6 0.7 - - - -
4277D LEU* 1.3 74.1 - - - +
4279D VAL* 1.3 62.4 + - - +
4281D GLU* 3.3 2.3 + - - -
4282D LYS 3.2 3.1 + - - -
4283D LEU* 2.9 37.3 + - - +
4284D ILE* 3.7 19.5 - - - -
4319D ILE* 4.6 2.0 - - - -
4323D VAL* 4.4 9.4 - - - +
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Residues in contact with VAL4279 (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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4275D VAL 2.9 18.8 + - - +
4276D ASP* 3.9 6.3 - - - +
4278D GLY* 1.3 72.8 - - - +
4280D LYS* 1.3 66.2 + - - +
4282D LYS* 3.1 21.1 + - - +
4284D ILE* 3.5 25.5 - - + +
4286D LYS* 4.2 25.4 - - + -
4291D TYR* 3.6 34.5 - - + -
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Residues in contact with LYS4280 (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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1282A LYS* 4.6 19.8 + - - +
4276D ASP 3.0 19.7 + - - +
4277D LEU* 3.6 19.9 - - + +
4279D VAL* 1.3 78.2 - - - +
4281D GLU* 1.3 75.3 + - - +
4282D LYS* 3.3 14.0 + - - +
4327D LEU* 5.2 8.9 - - - +
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Residues in contact with GLU4281 (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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4277D LEU 3.0 20.4 + - - +
4278D GLY 4.1 2.5 - - - +
4279D VAL 3.2 0.2 - - - -
4280D LYS* 1.3 95.0 - - + +
4282D LYS* 1.3 71.6 + - - +
4283D LEU* 3.2 17.0 + - + +
4323D VAL* 5.0 5.2 - - + -
4326D LEU* 3.8 34.9 - - + +
4327D LEU* 3.6 44.2 - - + +
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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