Contacts of the helix formed by residues 4269 - 4281 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4261A GLN* 2.5 58.7 + - + +
4263A LEU* 3.8 24.9 - - + +
4266A GLU* 5.5 3.6 - - - +
4267A GLY 3.3 3.4 + - - -
4268A ILE* 1.4 63.9 - - - +
4270A PHE* 1.3 62.1 + - - +
4271A TYR* 3.7 2.6 + - - +
4272A GLY* 2.9 32.5 + - - -
4273A GLU* 3.3 22.7 + - - +
4302A LYS* 5.0 1.8 - - - +
4306A THR* 3.7 14.5 + - - +
4310A LYS* 5.7 2.8 + - - -
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Residues in contact with PHE4270 (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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4043A GLY 4.0 17.3 - - - +
4044A SER 5.3 0.2 - - - -
4045A LEU* 3.9 26.4 - - + +
4268A ILE 2.9 12.6 + - - +
4269A ASN* 1.3 71.0 + - - +
4271A TYR* 1.3 91.6 + + + +
4273A GLU* 3.2 23.7 + - - +
4274A LEU* 3.0 34.0 + - + +
4317A LYS* 4.8 7.4 - - - -
4320A GLU* 3.7 39.0 - - + -
4324A ARG* 5.5 2.5 - - - -
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Residues in contact with TYR4271 (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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4269A ASN* 3.5 1.2 + - - +
4270A PHE* 1.3 98.9 - + + +
4272A GLY* 1.3 66.1 + - - +
4274A LEU* 3.2 12.7 + - + +
4275A VAL* 3.0 28.2 + - - +
4306A THR* 3.6 25.4 - - + +
4309A LEU* 3.8 28.1 + - + +
4310A LYS* 3.5 39.1 + - + -
4313A PRO* 4.8 10.7 - - - +
4316A ALA* 3.7 23.9 - - + +
4317A LYS* 5.3 8.3 + - - -
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Residues in contact with GLY4272 (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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4261A GLN* 6.3 0.2 - - - -
4269A ASN* 2.9 29.3 + - - -
4271A TYR* 1.3 76.6 - - - +
4273A GLU* 1.3 61.4 + - - +
4275A VAL* 3.3 3.6 + - - +
4276A ASP* 3.2 14.0 + - - -
4302A LYS* 2.9 32.2 + - - -
4306A THR* 3.6 10.9 - - - +
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Residues in contact with GLU4273 (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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4044A SER* 2.5 32.7 + - - -
4045A LEU* 3.3 23.1 + - + -
4046A SER* 2.9 20.4 + - - +
4259A GLU 4.6 2.9 - - - +
4260A PHE* 3.6 24.2 - - + +
4268A ILE* 3.8 3.8 - - - +
4269A ASN 3.3 9.4 + - - +
4270A PHE* 3.2 26.0 + - - +
4272A GLY* 1.3 73.7 - - - +
4274A LEU* 1.3 55.2 + - - +
4276A ASP* 3.0 6.2 + - - -
4277A LEU* 2.8 49.4 + - + +
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Residues in contact with LEU4274 (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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4045A LEU* 4.2 17.0 - - + +
4270A PHE* 3.0 18.1 + - + +
4271A TYR* 3.2 19.7 + - + +
4273A GLU* 1.3 80.5 - - - +
4275A VAL* 1.3 57.4 + - - +
4277A LEU* 4.6 2.2 - - - -
4278A GLY* 2.8 28.4 + - - -
4284A ILE* 4.2 1.9 - - - +
4309A LEU* 4.0 17.7 - - + -
4316A ALA* 3.6 37.7 - - + +
4319A ILE* 4.3 14.1 - - + +
4320A GLU* 3.7 32.8 - - + +
4323A VAL* 4.6 5.4 - - + -
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Residues in contact with VAL4275 (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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4271A TYR 3.0 18.0 + - - +
4272A GLY 3.5 7.2 - - - +
4274A LEU* 1.3 75.9 - - - +
4276A ASP* 1.3 65.2 + - - +
4278A GLY* 3.1 1.6 + - - -
4279A VAL* 2.8 31.4 + - + +
4284A ILE* 4.1 9.8 - - + +
4291A TYR* 3.7 34.5 - - + -
4298A ILE* 5.7 0.2 - - + -
4302A LYS* 4.2 11.2 - - + -
4305A ALA* 4.0 7.9 - - + -
4306A THR* 3.9 27.1 - - - +
4309A LEU* 3.7 17.5 - - + -
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Residues in contact with ASP4276 (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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4272A GLY 3.2 2.4 + - - +
4273A GLU* 3.0 9.5 + - - +
4275A VAL* 1.3 78.8 - - - +
4277A LEU* 1.3 61.6 + - + +
4279A VAL* 3.5 5.6 + - - +
4280A LYS* 3.0 30.4 + - - +
4291A TYR* 5.2 2.3 + - - -
4302A LYS* 3.3 43.3 + - - +
235D GLU* 6.1 1.0 - - - +
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Residues in contact with LEU4277 (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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4045A LEU* 4.4 5.2 - - + -
4046A SER* 4.0 26.9 - - - -
4049A ILE* 4.2 11.9 - - + -
4259A GLU 6.0 0.4 - - - +
4273A GLU* 2.8 39.2 + - + +
4274A LEU* 4.0 4.7 - - - +
4276A ASP* 1.3 74.4 - - + +
4278A GLY* 1.3 60.0 + - - +
4280A LYS* 3.7 15.8 - - + +
4281A GLU* 3.0 35.0 + - - +
4323A VAL* 4.0 22.4 - - + -
4327A LEU* 3.8 26.9 - - + -
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Residues in contact with GLY4278 (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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4274A LEU 2.8 18.4 + - - -
4275A VAL 3.5 0.9 - - - -
4277A LEU* 1.3 75.1 - - - +
4279A VAL* 1.3 61.5 + - - +
4281A GLU 3.3 1.9 + - - -
4282A LYS 3.2 3.3 + - - -
4283A LEU* 2.9 35.8 + - - -
4284A ILE* 3.2 18.8 + - - -
4319A ILE* 4.6 2.2 - - - -
4323A VAL* 4.4 9.8 - - - +
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Residues in contact with VAL4279 (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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4275A VAL 2.8 18.6 + - - +
4276A ASP* 3.8 6.3 - - - +
4278A GLY* 1.3 75.3 - - - +
4280A LYS* 1.3 65.8 + - - +
4282A LYS* 3.1 20.4 + - - +
4284A ILE* 3.5 26.5 - - + +
4286A LYS* 4.2 23.6 - - + -
4291A TYR* 3.6 34.1 - - + -
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Residues in contact with LYS4280 (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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4276A ASP 3.0 18.8 + - - +
4277A LEU* 3.7 19.6 - - + +
4278A GLY 3.3 0.2 - - - -
4279A VAL* 1.3 78.2 - - - +
4281A GLU* 1.3 74.7 + - - +
4282A LYS* 3.5 10.1 + - - +
4327A LEU* 5.2 9.5 - - - +
1280D LYS* 4.7 8.8 - - + +
1282D LYS* 4.2 9.7 - - - -
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Residues in contact with GLU4281 (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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4277A LEU 3.0 20.9 + - - +
4278A GLY 3.3 2.4 + - - +
4279A VAL 3.2 0.2 - - - -
4280A LYS* 1.3 95.3 - - + +
4282A LYS* 1.3 70.1 + - - +
4283A LEU* 3.2 17.7 + - + +
4323A VAL* 5.0 4.7 - - + -
4326A LEU* 3.9 31.9 - - + +
4327A LEU* 3.6 43.3 - - + +
1282D LYS* 3.1 31.2 + - - +
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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