Contacts of the helix formed by residues 4044 - 4051 (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 SER4044 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4042D THR* 3.0 19.1 + - - -
4043D GLY* 1.3 78.6 - - - +
4045D LEU* 1.3 61.3 + - - +
4047D LEU* 3.1 26.7 + - - +
4048D ASP* 3.1 15.7 + - - -
4260D PHE* 3.3 25.1 - - - -
4268D ILE* 4.0 12.5 - - - +
4270D PHE* 4.4 0.9 - - - -
4273D GLU* 2.4 28.0 + - - -
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Residues in contact with LEU4045 (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* 1.3 69.4 - - - +
4046D SER* 1.3 59.4 + - - +
4048D ASP* 3.1 7.9 + - - +
4049D ILE* 3.0 41.4 + - + +
4270D PHE* 3.7 20.0 - - + +
4273D GLU* 2.7 19.4 + - + +
4274D LEU* 3.7 41.7 - - + +
4277D LEU* 4.0 21.3 - - + -
4320D GLU* 3.9 25.6 - - + +
4323D VAL* 4.3 7.2 - - + -
4324D ARG* 4.1 24.7 - - + +
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Residues in contact with SER4046 (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* 3.4 1.4 + - - -
4045D LEU* 1.3 74.7 - - - +
4047D LEU* 1.3 54.3 + - - +
4049D ILE* 3.4 13.6 + - - +
4050D ALA* 2.9 27.4 + - - +
4257D GLN 4.7 0.9 - - - +
4258D ALA* 3.3 21.2 - - - +
4259D GLU 3.5 17.1 + - - -
4260D PHE* 4.1 0.7 - - - -
4273D GLU* 2.6 31.0 + - - +
4277D LEU* 4.3 15.5 - - - -
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Residues in contact with LEU4047 (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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4042D THR* 3.5 30.7 - - + +
4044D SER* 3.1 21.0 + - - +
4046D SER* 1.3 74.0 + - - +
4048D ASP* 1.3 56.2 + - - +
4049D ILE 3.1 1.8 - - - -
4050D ALA* 3.0 4.0 + - + -
4051D LEU* 2.7 51.2 + - + +
4075D LEU* 4.0 25.6 - - + -
4223D LEU* 4.5 15.5 - - + -
4244D VAL* 4.3 22.4 - - + +
4246D VAL* 4.3 13.5 - - + -
4258D ALA* 3.6 13.0 - - + -
4260D PHE* 4.8 1.1 - - + -
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Residues in contact with ASP4048 (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* 3.0 19.6 + - - -
4042D THR* 2.9 32.2 + - - +
4044D SER 3.1 17.9 + - - +
4045D LEU* 3.1 9.4 + - + +
4047D LEU* 1.3 76.1 - - - +
4049D ILE* 1.3 61.9 + - + +
4051D LEU* 3.6 2.6 + - - +
4052D GLY 3.6 4.0 + - - -
4054D GLY* 3.1 48.0 + - - +
4055D GLY* 3.4 8.1 - - - +
4270D PHE* 5.5 0.7 - - - -
4324D ARG* 2.8 27.9 + - - +
4328D LEU* 3.6 2.2 - - + +
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Residues in contact with ILE4049 (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* 3.0 34.3 + - + +
4046D SER* 3.6 8.1 - - - +
4048D ASP* 1.3 75.5 - - + +
4050D ALA* 1.3 66.0 + - - +
4052D GLY* 2.9 16.6 + - - -
4256D LYS* 4.2 9.1 + - + +
4277D LEU* 3.8 35.0 - - + -
4323D VAL* 4.2 11.9 - - + +
4324D ARG* 5.8 2.5 - - + -
4327D LEU* 4.1 36.3 - - + +
4328D LEU* 4.1 14.4 - - + +
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Residues in contact with ALA4050 (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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4046D SER 2.9 17.2 + - - +
4047D LEU* 3.5 9.2 - - + +
4049D ILE* 1.3 75.9 - - - +
4051D LEU* 1.3 61.7 + - - +
4052D GLY 3.2 1.2 + - - -
4246D VAL* 4.1 15.2 - - + +
4253D ALA 4.4 5.7 - - - +
4256D LYS* 3.4 38.6 - - + +
4257D GLN 3.9 27.8 - - - +
4258D ALA* 4.2 1.6 - - + -
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Residues in contact with LEU4051 (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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4042D THR* 3.5 31.6 - - + -
4047D LEU* 2.7 31.9 + - + +
4048D ASP* 3.7 7.6 - - - +
4049D ILE 3.1 0.2 - - - -
4050D ALA* 1.3 71.2 - - - +
4052D GLY* 1.3 55.8 + - - +
4053D ALA 2.8 10.0 + - - -
4055D GLY* 3.6 31.0 - - - +
4056D LEU* 4.0 7.6 - - + +
4221D VAL* 3.6 39.3 - - + -
4223D LEU* 4.3 9.0 - - + -
4246D VAL* 4.4 8.5 - - + -
4249D ASN* 3.2 22.5 + - - +
4251D ILE* 4.1 6.3 - - + +
4252D ALA* 3.3 3.8 - - - +
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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