Contacts of the helix formed by residues 263 - 283 (chain 2) 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 CYS 263 (chain 2).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2592 PHE 3.3 7.6 + - - +
2622 LYS* 1.3 113.1 - - - +
2642 PRO* 1.3 66.7 - - - +
2652 GLU* 3.0 4.6 + - + +
2662 GLU* 2.8 40.4 - - - +
2672 MET* 3.8 4.9 + - - +
3152 SER* 3.8 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 264 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2592 PHE 3.3 1.0 - - - -
2602 LEU* 3.1 29.6 - - + +
2632 CYS* 1.3 85.8 - - - +
2652 GLU* 1.3 66.0 + - - +
2672 MET* 2.9 27.4 + - + +
2682 LEU* 3.3 20.2 + - + +
3152 SER 3.1 15.9 - - - +
3162 SER* 3.6 2.5 - - - -
3172 LEU* 3.2 41.7 - - + +
4292 ILE* 3.8 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 265 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2632 CYS* 3.0 4.4 - - + -
2642 PRO* 1.3 83.9 - - - +
2662 GLU* 1.3 74.1 + - + +
2682 LEU* 4.0 10.2 + - - +
2692 LYS* 4.2 19.4 + - - +
3152 SER* 5.0 8.1 - - - +
4292 ILE* 3.3 31.4 - - + +
4312 LYS* 5.5 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 266 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2632 CYS* 2.8 48.3 - - - +
2652 GLU* 1.3 83.5 - - + +
2672 MET* 1.3 68.1 + - - +
2682 LEU 3.1 2.9 - - - -
2692 LYS* 2.9 38.2 + - + +
2702 ILE* 3.7 7.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 267 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2072 ILE* 6.4 0.2 - - + -
2112 LEU* 5.2 9.8 - - + +
2492 LEU* 6.2 0.7 - - - -
2562 LEU* 3.7 23.3 - - + +
2592 PHE* 3.3 52.0 - - + +
2602 LEU* 3.4 27.8 - - + +
2632 CYS 3.9 6.7 - - - +
2642 PRO* 2.9 13.9 + - + +
2662 GLU* 1.3 86.9 - - - +
2682 LEU* 1.3 69.2 + - + +
2702 ILE* 3.8 3.1 + - - +
2712 PHE* 3.2 22.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 268 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2602 LEU* 4.6 2.0 - - + -
2642 PRO* 3.3 24.7 + - + +
2652 GLU* 4.3 6.1 - - - +
2662 GLU 3.1 0.2 - - - -
2672 MET* 1.3 95.7 - - + +
2692 LYS* 1.3 55.6 + - - +
2712 PHE* 3.3 20.2 - - + -
2722 ASP* 2.8 40.6 + - - +
2952 VAL* 4.5 9.2 - - + -
2972 ILE* 4.1 28.5 - - + -
3172 LEU* 5.1 3.8 - - + -
4292 ILE* 6.2 2.5 - - + -
4542 ASN* 3.1 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 269 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2652 GLU* 4.2 15.7 + - - +
2662 GLU* 2.9 35.7 + - + +
2682 LEU* 1.3 78.7 - - - +
2702 ILE* 1.3 61.2 + - + +
2722 ASP* 2.7 19.6 - - - +
2732 LEU* 3.1 21.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 270 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2042 SER* 5.3 11.2 - - - +
2052 ARG* 5.7 2.9 - - - +
2082 ALA* 3.8 29.8 - - + -
2112 LEU* 5.5 2.5 - - + -
2662 GLU 3.7 7.6 + - - +
2672 MET 4.5 2.9 - - - +
2682 LEU 3.3 0.2 - - - -
2692 LYS* 1.3 83.0 - - + +
2712 PHE* 1.3 66.0 + - - +
2732 LEU* 2.9 16.0 + - + +
2742 VAL* 2.9 34.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 271 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2112 LEU* 4.4 31.1 - - + +
2142 PHE* 5.1 12.8 - + - -
2152 LEU* 3.5 36.2 - - + +
2442 VAL* 3.9 23.6 - - + -
2672 MET* 3.2 25.2 + - + +
2682 LEU* 3.0 20.3 + - + +
2702 ILE* 1.3 74.8 - - - +
2722 ASP* 1.3 67.5 + - - +
2742 VAL* 2.9 21.8 + - - +
2752 ALA 3.1 8.3 + - - -
2952 VAL* 3.3 44.2 - - + -
2972 ILE* 5.4 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 272 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2682 LEU* 2.8 16.9 + - - +
2692 LYS* 2.7 23.1 - - - +
2712 PHE* 1.3 79.2 - - + +
2732 LEU* 1.3 77.7 + - - +
2742 VAL 3.0 0.2 - - - -
2752 ALA* 2.9 11.7 + - + +
2762 MET* 2.9 29.3 + - - +
2922 GLU* 3.0 16.3 - - - +
2932 ILE* 2.7 31.7 - - + +
2942 HIS* 3.4 18.1 - - - +
2952 VAL* 4.0 13.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 273 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2692 LYS* 3.1 26.2 - - + +
2702 ILE* 2.9 21.7 + - + +
2722 ASP* 1.3 87.5 + - - +
2742 VAL* 1.3 58.8 + - + +
2762 MET* 3.5 17.0 - - + +
2772 GLU* 3.1 24.7 - - - +
2922 GLU* 3.9 21.5 - - - +
2932 ILE 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 274 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2082 ALA* 4.5 6.7 - - + +
2112 LEU* 3.9 17.5 - - + -
2122 LYS* 3.5 47.6 - - + -
2152 LEU* 3.6 13.5 - - + -
2702 ILE* 2.9 25.3 + - + +
2712 PHE 2.9 7.2 + - - +
2732 LEU* 1.3 77.7 - - - +
2752 ALA* 1.3 52.9 + - - +
2762 MET 3.1 1.8 - - - -
2772 GLU* 2.9 9.5 + - + +
2782 ALA* 2.6 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 275 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2152 LEU* 3.2 25.2 - - + +
2312 ILE* 5.5 1.1 - - + -
2422 LEU* 4.3 22.7 - - + -
2712 PHE 3.1 5.1 + - - -
2722 ASP* 2.9 17.6 + - + +
2742 VAL* 1.3 74.4 - - - +
2762 MET* 1.3 52.1 + - - +
2782 ALA* 2.9 5.8 + - - +
2792 THR* 2.3 45.1 + - - +
2932 ILE* 6.3 3.4 - - + -
2952 VAL* 4.8 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 276 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2722 ASP 2.9 12.0 + - - +
2732 LEU* 3.5 22.0 - - + +
2752 ALA* 1.3 73.6 - - - +
2772 GLU* 1.3 60.8 + - - +
2792 THR* 2.9 10.0 + - - -
2802 GLU* 2.4 43.7 + - + +
2852 ASP 4.4 5.2 - - - +
2862 TYR* 4.0 36.6 - - + +
2872 ALA* 4.4 4.3 - - + +
2912 SER* 4.2 22.2 - - - +
2922 GLU* 4.7 2.2 - - - -
2932 ILE* 4.4 28.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 277 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2122 LYS* 4.6 20.0 - - - +
2732 LEU* 3.1 20.2 - - - +
2742 VAL* 2.9 11.4 + - + +
2762 MET* 1.3 82.2 - - - +
2782 ALA* 1.3 58.2 + - - +
2802 GLU* 2.9 13.5 + - - +
2812 LEU* 2.9 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 278 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2152 LEU* 4.8 5.8 - - + -
2162 LEU* 3.6 42.5 - - + +
2312 ILE* 3.6 16.8 - - + +
2742 VAL 2.6 17.5 + - - +
2752 ALA* 3.3 12.1 - - - +
2772 GLU* 1.3 72.9 - - - +
2792 THR* 1.3 60.5 + - - +
2812 LEU* 3.3 23.8 - - - +
2822 HIS* 3.7 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 279 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2312 ILE* 3.3 44.6 - - + +
2342 LEU 4.9 5.4 - - - +
2422 LEU* 4.3 7.0 - - + +
2752 ALA 2.3 39.7 + - - -
2762 MET* 3.3 9.3 - - - -
2782 ALA* 1.3 67.3 - - - +
2802 GLU* 1.3 53.0 + - - +
2822 HIS* 2.9 5.4 + - - +
2832 TYR* 2.5 42.1 + - + -
2862 TYR* 4.8 17.9 - - + -
2932 ILE* 6.1 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 280 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2762 MET* 2.4 36.1 + - + +
2772 GLU* 2.9 19.0 + - - +
2792 THR* 1.3 68.0 - - - +
2812 LEU* 1.3 66.2 + - - +
2832 TYR 2.8 5.6 - - - +
2842 PRO* 2.9 47.1 - - + +
2852 ASP* 2.5 42.5 + - - +
2872 ALA* 5.7 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 281 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2162 LEU* 4.4 24.2 - - + -
2772 GLU 2.9 9.4 + - - +
2782 ALA* 3.3 26.9 - - + +
2792 THR 3.3 0.2 - - - -
2802 GLU* 1.3 77.4 - - - +
2822 HIS* 1.3 75.2 + - + +
2842 PRO* 4.6 4.3 - - - +
365E ARG* 5.9 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 282 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2282 GLY* 3.5 26.5 + - - -
2312 ILE* 3.3 19.7 - - + +
2322 ARG* 3.3 30.8 - - + +
2782 ALA 4.0 4.0 - - - +
2792 THR 2.9 9.1 + - - +
2812 LEU* 1.3 93.6 - - + +
2832 TYR* 1.3 98.3 + + - +
2842 PRO* 4.0 0.7 - - - -
361E LYS* 5.7 0.6 - - - -
365E ARG* 3.7 15.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 283 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2312 ILE 3.1 27.8 - - - -
2322 ARG* 2.9 36.7 + - - +
2352 GLY* 3.2 18.6 - - - -
2362 GLU* 3.9 8.1 - - - +
2792 THR* 2.5 20.6 + - + +
2802 GLU* 2.8 14.3 - - - +
2822 HIS* 1.3 102.8 - + - +
2842 PRO* 1.3 55.0 - - - -
2852 ASP* 2.3 26.9 + - - +
2862 TYR* 4.2 12.9 - + + -
361E LYS* 4.0 19.1 - - + +
364E ALA* 3.4 41.1 - - + +
365E ARG* 4.3 7.0 - - - -
----------------------------------------------------------
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