Contacts of the helix formed by residues 4301 - 4312 (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 GLY4301 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4289D ALA* 2.8 23.0 + - - +
4291D TYR* 3.5 10.0 - - - -
4300D GLN* 1.3 74.9 - - - +
4302D LYS* 1.3 67.7 + - - -
4303D ALA* 3.1 4.7 - - - -
4304D ASN 3.0 14.2 + - - -
4305D ALA 3.3 7.1 + - - -
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Residues in contact with LYS4302 (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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4261D GLN* 5.8 8.9 - - - +
4269D ASN* 5.0 5.0 - - - +
4272D GLY* 2.9 41.2 + - - -
4275D VAL* 4.2 9.9 - - + -
4276D ASP* 3.2 32.1 + - - +
4291D TYR* 3.3 25.1 + - - +
4301D GLY* 1.3 70.5 - - - -
4303D ALA* 1.3 58.1 + - - +
4305D ALA* 3.8 2.7 - - - +
4306D THR* 2.7 38.9 + - - +
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Residues in contact with ALA4303 (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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4300D GLN 5.6 0.7 - - - +
4301D GLY* 3.0 2.4 + - - +
4302D LYS* 1.3 79.1 - - - +
4304D ASN* 1.3 64.8 + - - +
4306D THR* 3.5 6.8 + - - -
4307D ALA* 3.3 19.6 + - - +
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Residues in contact with ASN4304 (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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4298D ILE 4.1 0.9 - - - +
4299D GLY* 4.0 5.4 - - - -
4300D GLN* 2.9 38.2 + - - +
4301D GLY 3.0 2.8 + - - -
4303D ALA* 1.3 79.8 - - - +
4305D ALA* 1.3 61.1 + - - +
4307D ALA* 3.1 11.0 + - - +
4308D TRP* 2.9 28.4 + - - +
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Residues in contact with ALA4305 (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* 4.0 17.2 - - + +
4291D TYR* 3.8 39.7 - - + -
4298D ILE* 4.1 20.2 - - + +
4299D GLY* 4.2 2.1 - - - -
4301D GLY 3.3 3.4 + - - -
4302D LYS 3.8 7.0 - - - +
4304D ASN* 1.3 77.5 - - - +
4306D THR* 1.3 61.5 + - - +
4308D TRP* 3.3 4.2 + - - +
4309D LEU* 3.3 25.6 + - - +
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Residues in contact with THR4306 (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 15.1 + - - +
4271D TYR* 3.6 12.1 - - + +
4272D GLY* 3.6 34.7 - - - +
4275D VAL* 3.9 11.6 - - - +
4302D LYS* 2.7 26.8 + - - +
4303D ALA* 3.5 7.5 - - - -
4305D ALA* 1.3 76.5 - - - +
4307D ALA* 1.3 60.7 + - - +
4309D LEU* 3.2 5.6 + - - +
4310D LYS* 3.2 31.8 + - - +
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Residues in contact with ALA4307 (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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4303D ALA 3.3 10.9 + - - +
4304D ASN* 3.1 18.0 + - - +
4306D THR* 1.3 79.0 - - - +
4308D TRP* 1.3 61.9 + - - +
4310D LYS* 3.5 14.6 + - + +
4311D ASP* 3.1 30.5 + - - +
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Residues in contact with TRP4308 (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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4293D TYR* 4.7 8.1 - + + -
4296D GLU* 3.8 27.2 + - - -
4297D LYS 5.0 0.8 + - - -
4298D ILE* 3.2 65.8 - - + +
4304D ASN 2.9 8.1 + - - +
4305D ALA 3.5 7.9 - - - +
4306D THR 3.2 0.2 - - - -
4307D ALA* 1.3 78.3 - - - +
4309D LEU* 1.3 82.5 + - + +
4311D ASP* 3.1 7.0 + - + -
4312D ASN* 2.8 65.6 + - + +
4315D THR* 4.0 26.9 - - + -
4319D ILE* 5.3 0.4 - - + -
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Residues in contact with LEU4309 (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* 3.8 22.7 - - + +
4274D LEU* 4.0 23.3 - - + -
4275D VAL* 3.7 31.4 - - + +
4284D ILE* 4.7 7.9 - - + -
4298D ILE* 5.0 3.8 - - + -
4305D ALA 3.3 6.2 + - - +
4306D THR 3.2 7.9 + - - +
4308D TRP* 1.3 93.9 - - + +
4310D LYS* 1.3 64.7 + - - +
4312D ASN 3.3 19.6 - - - +
4313D PRO* 3.7 1.6 - - - +
4316D ALA* 3.8 26.5 - - + +
4319D ILE* 3.9 25.4 - - + -
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Residues in contact with LYS4310 (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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4266D GLU* 3.2 28.6 + - - +
4269D ASN* 5.7 2.5 + - - -
4271D TYR* 3.5 37.6 + - + -
4306D THR* 3.2 26.1 + - - +
4307D ALA* 3.5 16.8 - - + +
4309D LEU* 1.3 75.9 - - - +
4311D ASP* 1.3 63.6 + - - +
4313D PRO* 3.6 15.2 - - - +
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Residues in contact with ASP4311 (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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4307D ALA* 3.1 15.0 + - - +
4308D TRP* 3.1 14.4 + - + +
4310D LYS* 1.3 85.1 - - - +
4312D ASN* 1.3 66.1 + - - +
4313D PRO* 3.2 8.9 - - - +
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Residues in contact with ASN4312 (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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4308D TRP* 2.8 56.9 + - + +
4309D LEU* 3.3 8.5 - - - +
4310D LYS 3.4 0.2 - - - -
4311D ASP* 1.3 86.7 - - - +
4313D PRO* 1.4 60.3 - - - +
4314D GLU* 3.2 6.0 + - + -
4315D THR* 3.2 21.1 + - - +
4316D ALA* 3.0 22.7 + - - +
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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