Contacts of the strand formed by residues 4236 - 4249 (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 ASN4236 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288A GLY* 5.2 3.9 - - - -
289A ALA* 4.0 18.5 + - - +
4232D LYS* 3.2 6.1 - - - +
4233D GLU* 2.7 50.6 + - + +
4235D GLU* 1.3 83.7 - - - +
4237D VAL* 1.3 63.6 + - - +
4238D VAL* 3.7 4.7 - - + +
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Residues in contact with VAL4237 (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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4227D ARG* 4.0 9.9 - - - +
4230D ALA* 4.0 18.4 - - + -
4231D VAL 3.7 3.1 - - - +
4232D LYS* 4.2 16.6 - - + -
4235D GLU 3.9 3.8 + - - +
4236D ASN* 1.3 74.5 - - - +
4238D VAL* 1.3 61.4 + - - +
4239D GLY 3.9 17.0 - - - +
4264D TYR* 3.7 18.4 - - + +
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Residues in contact with VAL4238 (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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4231D VAL* 2.9 31.5 + - + +
4232D LYS 4.7 0.2 - - - -
4233D GLU* 3.9 31.9 - - + -
4236D ASN* 3.6 4.6 + - + -
4237D VAL* 1.3 73.2 - - - +
4239D GLY* 1.3 57.4 + - - +
4263D LEU* 3.8 12.6 - - + +
4264D TYR* 3.1 32.8 + - + +
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Residues in contact with GLY4239 (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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4227D ARG* 4.0 0.2 + - - -
4230D ALA* 3.7 4.5 - - - -
4231D VAL* 2.7 40.5 + - - +
4237D VAL* 3.9 3.3 - - - +
4238D VAL* 1.3 81.1 - - - +
4240D SER* 1.3 57.8 + - - -
4262D ILE 3.1 12.6 - - - -
4263D LEU* 4.1 2.7 - - - -
4264D TYR* 3.5 19.9 + - - -
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Residues in contact with SER4240 (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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4069D SER 4.9 2.4 + - - -
4070D SER 5.7 1.6 - - - -
4227D ARG* 3.0 29.0 + - - +
4229D GLY 3.7 4.3 - - - -
4231D VAL* 4.0 2.9 - - - -
4239D GLY* 1.3 71.4 - - - -
4241D GLU* 1.3 62.3 + - - +
4242D THR* 3.3 10.0 + - - -
4261D GLN* 3.6 0.9 - - - -
4262D ILE* 2.7 45.3 + - - -
4264D TYR* 2.7 29.1 + - - -
4502D ADP 4.0 8.4 + - - -
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Residues in contact with GLU4241 (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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4227D ARG* 3.6 4.0 - - - -
4228D ILE* 2.8 43.5 + - + -
4229D GLY* 2.8 32.2 + - - +
4230D ALA 4.4 3.1 - - - +
4231D VAL* 3.4 14.0 - - + +
4240D SER* 1.3 70.8 - - - +
4242D THR* 1.3 60.8 + - - +
4259D GLU* 5.6 2.9 - - + +
4260D PHE* 3.8 10.8 + - - +
4261D GLN* 3.2 38.3 + - - +
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Residues in contact with THR4242 (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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4070D SER 4.2 6.2 + - - +
4225D ILE* 3.7 28.7 - - + -
4226D ARG 3.5 6.2 + - - +
4227D ARG* 4.8 1.0 - - - -
4228D ILE* 4.4 4.1 - - - +
4240D SER* 3.3 18.2 + - - -
4241D GLU* 1.3 75.0 + - - +
4243D ARG* 1.3 65.0 + - - +
4258D ALA 3.9 0.2 - - - +
4259D GLU* 3.2 6.4 - - - +
4260D PHE* 2.7 73.9 + - + +
4262D ILE* 3.6 14.0 - - + +
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Residues in contact with ARG4243 (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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4224D ASP 3.6 1.9 - - - +
4225D ILE* 3.5 0.9 - - - -
4226D ARG* 2.9 39.9 + - + +
4228D ILE* 3.6 39.8 - - + +
4242D THR* 1.3 75.1 - - - +
4244D VAL* 1.3 68.2 + - - +
4245D LYS* 4.1 22.3 - - - +
4257D GLN* 3.3 31.3 + - - +
4258D ALA 3.3 4.9 - - - +
4259D GLU* 2.4 43.7 + - + -
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Residues in contact with VAL4244 (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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4047D LEU* 4.3 19.0 - - + +
4075D LEU* 4.3 6.3 - - + -
4223D LEU* 3.7 36.1 - - + -
4224D ASP 3.3 7.6 - - - +
4225D ILE* 3.8 22.2 - - + -
4243D ARG* 1.3 76.3 - - - +
4245D LYS* 1.3 66.6 + - - +
4246D VAL* 4.1 1.2 + - - +
4257D GLN* 3.3 5.4 - - - +
4258D ALA* 2.8 36.7 + - + +
4260D PHE* 3.7 30.7 - - + -
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Residues in contact with LYS4245 (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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4223D LEU* 3.4 4.7 - - - -
4224D ASP* 2.8 51.8 + - + +
4226D ARG* 5.9 5.5 - - - +
4243D ARG* 4.1 18.6 - - - +
4244D VAL* 1.3 73.0 - - - +
4246D VAL* 1.3 62.6 + - - +
4247D VAL* 3.3 12.4 + - + -
4255D PHE* 6.1 5.4 - - + +
4256D LYS 4.0 2.9 - - - +
4257D GLN* 3.4 33.9 - - + +
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Residues in contact with VAL4246 (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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4047D LEU* 4.3 9.6 - - + -
4050D ALA* 4.1 28.5 - - + +
4051D LEU* 4.4 7.0 - - + +
4222D ARG 3.7 4.3 - - - +
4223D LEU* 4.0 18.4 - - + -
4244D VAL 5.2 1.1 - - - +
4245D LYS* 1.3 70.5 - - - +
4247D VAL* 1.3 60.0 + - - +
4248D LYS 3.6 20.0 - - - +
4249D ASN* 3.9 25.8 - - + +
4254D PRO* 4.5 2.9 - - + -
4255D PHE* 2.7 37.4 + - - +
4256D LYS 3.0 21.7 + - - +
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Residues in contact with VAL4247 (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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3069D SER* 6.1 0.2 - - - -
4065D TYR* 3.5 26.5 - - - +
4222D ARG* 2.8 30.7 + - + +
4224D ASP* 3.6 24.2 - - + +
4245D LYS* 3.9 13.2 - - + +
4246D VAL* 1.3 73.4 - - - +
4248D LYS* 1.3 60.5 + - + +
4254D PRO* 4.5 1.7 - - - +
4255D PHE* 3.5 31.6 - - + -
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Residues in contact with LYS4248 (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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3068D GLU* 3.9 5.6 - - + +
3069D SER* 3.2 27.1 - - - +
3501D ALF 2.6 38.9 - - - -
4216D LYS 2.7 29.2 + - - +
4217D PHE 2.8 15.4 + - - -
4219D ALA 3.0 20.5 + - - +
4220D SER 4.8 0.9 - - - +
4221D VAL* 3.2 5.1 - - - -
4222D ARG* 2.9 46.7 + - + +
4246D VAL* 3.6 8.8 - - - +
4247D VAL* 1.3 81.8 - - + +
4249D ASN* 1.3 66.5 + - - +
4250D LYS* 4.5 7.0 - - - -
4254D PRO* 4.4 2.5 - - - -
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Residues in contact with ASN4249 (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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3069D SER* 5.4 0.2 - - - -
3502D ADP 3.0 28.8 + - - -
4051D LEU* 3.2 28.7 + - - +
4220D SER 3.5 2.2 - - - -
4221D VAL* 3.7 9.1 - - - +
4246D VAL* 3.9 12.5 - - + +
4248D LYS* 1.3 80.8 - - - +
4250D LYS* 1.3 59.8 + - - +
4251D ILE* 3.0 29.0 + - - +
4252D ALA 3.1 31.4 + - - +
4253D ALA 3.3 13.1 + - - -
4254D PRO* 3.8 19.5 - - + +
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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