Contacts of the helix formed by residues 414 - 425 (chain 3) in PDB entry 5U8T
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 ALA 414 (chain 3).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3713 ILE* 4.4 17.7 - - + -
4073 MET* 5.2 0.2 - - - -
4123 SER 3.3 0.8 - - - -
4133 THR* 1.3 81.2 - - - +
4153 LYS* 1.3 51.9 + - - +
4173 GLN* 4.0 7.2 - - + -
4183 LEU* 2.6 37.3 + - + +
10013 ANP 3.0 61.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 415 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4073 MET* 3.5 33.9 - - + -
4093 GLY 2.3 36.8 + - - +
4103 ASP 2.7 12.1 + - - -
4133 THR* 3.2 17.4 - - - -
4143 ALA* 1.3 76.1 - - - +
4163 SER* 1.3 65.1 + - - +
4183 LEU* 3.3 3.5 + - - +
4193 LEU* 2.9 34.9 + - - +
4743 GLU* 5.9 0.7 - - - +
5153 ALA* 3.9 24.0 - - + -
5163 ALA 4.8 6.1 - - - +
5173 ASN* 2.5 24.3 + - - +
10013 ANP 2.7 43.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 416 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4153 LYS* 1.3 72.6 - - - +
4173 GLN* 1.3 59.6 + - - -
4193 LEU* 2.9 22.9 + - - +
4203 ARG* 3.0 17.3 + - - +
4733 ASP* 2.6 29.8 + - - -
4743 GLU* 4.8 0.2 + - - -
10013 ANP 2.4 38.8 + - - -
4995 GLN* 3.2 29.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 417 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3713 ILE* 5.2 1.8 - - + +
4143 ALA* 4.0 9.9 - - + +
4153 LYS 3.4 0.2 - - - -
4163 SER* 1.3 79.4 - - - +
4183 LEU* 1.3 62.0 + - - +
4203 ARG* 3.0 29.9 + - - +
4213 PHE* 3.5 6.4 + - - +
10013 ANP 3.1 42.1 + - + +
4035 GLY 4.7 0.4 + - - -
4045 MET* 3.3 44.9 - - + +
4055 ARG* 3.3 27.2 + - - +
4065 LEU* 3.5 11.7 - - - +
4995 GLN* 3.9 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 418 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3673 LEU* 6.3 0.7 - - + -
3683 ALA* 4.8 3.1 - - + -
3713 ILE* 3.7 27.1 - - + +
3743 HIS* 6.1 1.1 - - + -
3773 ILE* 4.1 20.0 - - + -
3783 LYS* 4.8 16.2 - - + +
3813 ILE* 4.3 20.2 - - + -
4073 MET* 3.5 28.9 - - + -
4133 THR 6.1 0.2 - - - +
4143 ALA* 2.6 25.0 + - + +
4153 LYS 3.3 4.9 - - - +
4173 GLN* 1.3 72.5 - - - +
4193 LEU* 1.3 66.5 + - + +
4213 PHE* 3.2 23.8 + - + +
4223 VAL* 3.6 7.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 419 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4073 MET* 5.3 6.1 - - - -
4153 LYS* 2.9 23.2 + - - +
4163 SER* 2.9 12.6 + - - +
4183 LEU* 1.3 82.9 - - + +
4203 ARG* 1.3 57.7 + - - +
4213 PHE 3.1 0.2 - - - -
4223 VAL* 2.8 29.7 + - + +
4233 LEU* 2.9 8.8 + - - +
4313 ALA* 5.8 2.7 - - + -
4713 CYS* 4.0 16.5 - - + -
4723 ILE 3.7 41.7 - - - +
4733 ASP* 4.1 11.4 - - - +
5133 ILE* 4.2 24.0 - - + +
5143 ALA 5.1 0.4 - - - -
5153 ALA* 4.8 11.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 420 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4163 SER* 3.0 19.0 + - - +
4173 GLN* 3.0 27.7 + - - +
4193 LEU* 1.3 79.7 - - - +
4213 PHE* 1.3 56.7 + - - +
4233 LEU* 3.1 49.7 - - + +
4243 ASN* 4.0 2.4 + - - +
4313 ALA* 6.0 5.1 - - - +
4333 THR* 5.3 4.8 - - - +
4733 ASP* 6.3 0.6 - - - -
4035 GLY* 5.4 14.4 + - - +
4045 MET* 5.9 2.2 - - + +
4055 ARG* 5.9 2.4 - - - +
4955 GLU* 3.6 8.3 + - - -
4995 GLN* 3.6 27.3 + - + +
5015 THR* 2.7 40.2 + - - +
5035 SER* 5.7 0.8 - - - -
5125 VAL* 4.3 12.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 421 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3673 LEU* 2.9 65.5 - - + +
3683 ALA* 6.0 0.4 - - - -
3693 PRO* 5.1 0.2 - - + -
3713 ILE* 6.1 0.2 - - + -
3813 ILE* 5.7 5.4 - - + -
3853 LEU* 5.5 3.8 - - + -
4173 GLN 3.5 5.8 + - - +
4183 LEU* 3.2 20.5 + - + +
4193 LEU 3.1 0.8 - - - -
4203 ARG* 1.3 73.6 - - - +
4223 VAL* 1.3 68.3 + - + +
4233 LEU 2.9 8.1 + - - -
4243 ASN* 3.3 11.5 + - - +
4253 THR* 3.5 46.5 + - + +
6533 ILE* 3.8 15.5 - - + -
6563 LEU* 4.9 0.9 - - + -
4025 ASP* 3.1 28.0 - - + +
4035 GLY 6.3 0.9 - - - +
4045 MET* 5.5 7.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 422 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3813 ILE* 4.0 26.7 - - + -
3843 MET* 4.5 9.6 - - + -
3853 LEU* 4.8 3.6 - - + -
4183 LEU* 3.7 14.8 - - + +
4193 LEU* 2.8 14.2 + - + +
4213 PHE* 1.3 81.7 - - + +
4233 LEU* 1.3 62.5 + - - +
4253 THR* 5.1 1.3 - - - -
4263 ALA* 3.4 26.2 - - + +
4283 LEU 4.1 3.8 - - - +
4293 ALA 4.9 3.3 - - - +
4693 VAL* 3.7 30.8 - - + +
4713 CYS* 4.0 15.9 - - - -
5133 ILE* 5.9 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 423 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2913 ARG* 5.6 5.9 + - - +
4193 LEU 2.9 5.5 + - - +
4203 ARG* 3.1 50.5 - - + +
4213 PHE 2.9 1.4 - - - -
4223 VAL* 1.3 81.1 - - - +
4243 ASN* 1.3 86.6 + - - +
4283 LEU* 4.6 9.0 + - - +
4293 ALA 5.1 6.3 - - - +
4313 ALA* 5.6 13.7 - - + -
4035 GLY* 6.1 2.5 - - - -
5125 VAL* 5.9 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 424 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2913 ARG* 4.6 12.0 + - - -
3303 HIS* 6.2 0.3 - - - -
4203 ARG 4.0 2.8 + - - +
4213 PHE 3.3 5.1 + - - +
4233 LEU* 1.3 99.4 - - + +
4253 THR* 1.3 68.7 + - + +
4263 ALA 3.2 3.0 + - - -
4273 SER* 3.9 6.9 + - - -
6573 ARG* 4.7 6.9 + - - +
4025 ASP* 6.5 0.4 - - + -
4035 GLY* 5.0 15.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 425 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3853 LEU* 4.7 10.0 - - - +
4213 PHE* 3.5 39.0 + - + +
4223 VAL* 5.1 1.0 - - - -
4243 ASN* 1.3 76.8 - - + +
4263 ALA* 1.3 63.1 + - - +
4273 SER* 3.0 10.0 + - - -
6533 ILE* 3.4 33.0 - - + -
6563 LEU* 5.1 5.5 - - - +
6573 ARG* 3.6 43.3 + - - +
4025 ASP* 5.9 1.6 - - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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