Contacts of the helix formed by residues 445 - 458 (chain B) in PDB entry 1L8A
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 SER 445 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B PHE* 3.6 3.7 - - - +
442B PRO* 2.6 48.0 + - - +
443B GLU 3.3 0.8 + - - -
444B GLY* 1.3 76.8 - - - +
446B GLU* 1.3 65.5 + - - +
447B GLU* 3.8 11.2 + - - -
448B HIS* 3.1 17.8 + - - +
449B THR* 3.0 25.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 446 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ASN* 4.5 6.4 + - - -
77B LEU* 3.7 26.3 - - + +
80B ARG* 3.8 19.6 + - - +
444B GLY 3.7 1.6 + - - -
445B SER* 1.3 73.0 - - - +
447B GLU* 1.3 68.4 + - - +
449B THR* 3.9 6.1 - - - -
450B TYR* 3.1 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 447 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LEU* 3.4 20.0 - - + -
80B ARG* 2.6 44.6 + - + -
81B ILE* 3.5 19.2 - - + +
441B PHE* 3.4 41.0 - - + -
445B SER* 3.8 9.9 - - - -
446B GLU* 1.3 80.8 + - - +
448B HIS* 1.3 58.6 + - - +
450B TYR 3.3 0.3 + - - -
451B LEU* 2.9 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 448 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B LEU 5.2 4.9 - - - -
441B PHE* 3.3 26.8 - - + +
442B PRO 3.3 8.3 - - - +
443B GLU* 3.5 35.9 - - + +
444B GLY 3.9 4.2 + - - -
445B SER* 3.1 22.7 + - - +
447B GLU* 1.3 77.5 - - - +
449B THR* 1.3 68.3 + - - +
451B LEU* 3.4 6.1 + - + +
452B HIS* 3.0 63.7 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 449 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B GLY* 4.2 13.9 + - - -
445B SER 3.0 16.2 + - - -
446B GLU* 3.9 6.2 - - - -
448B HIS* 1.3 83.3 + - - +
450B TYR* 1.3 57.8 + - - +
452B HIS* 4.0 2.4 - - - +
453B ALA* 2.8 38.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 450 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLY* 3.4 6.3 - - - -
74B ASN* 3.0 30.8 + - + -
77B LEU* 3.6 23.6 - - + -
78B GLU* 2.5 44.3 + - + -
81B ILE* 3.9 15.3 - - + -
122B ASN* 3.9 7.4 - - - -
123B HIS* 4.0 0.2 + - - -
446B GLU 3.1 16.9 + - - +
447B GLU 3.8 2.9 - - - +
449B THR* 1.3 75.8 - - - +
451B LEU* 1.3 68.0 + - - +
453B ALA* 4.2 4.9 - - + -
454B GLN* 3.0 67.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 451 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ILE* 4.1 26.2 - - + -
85B ILE* 5.3 0.2 - - + -
122B ASN* 5.2 4.5 - - - +
150B ARG* 3.8 28.9 - - + +
153B LEU* 3.4 40.2 - - + +
154B GLU* 4.0 18.6 - - + +
441B PHE* 5.5 4.0 - - + -
447B GLU 2.9 18.6 + - - +
448B HIS* 3.6 7.2 - - + +
450B TYR* 1.3 80.3 - - - +
452B HIS* 1.3 81.0 + - + +
454B GLN* 3.7 3.5 + - - +
455B ARG* 3.4 23.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 452 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B LEU 4.4 1.3 - - - -
154B GLU* 3.3 26.6 + - - -
448B HIS* 3.0 59.6 + + + +
449B THR* 4.2 3.1 - - - +
451B LEU* 1.3 90.4 - - + +
453B ALA* 1.3 61.3 + - - +
455B ARG* 3.3 3.8 + - - +
456B GLN* 2.8 37.2 + - + +
461B TYR* 2.7 36.1 - + - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 453 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B THR* 2.8 27.1 + - + +
450B TYR* 3.7 7.2 - - + +
452B HIS* 1.3 77.0 - - - +
454B GLN* 1.3 69.4 + - - +
456B GLN* 3.8 6.0 - - - +
457B LYS* 3.1 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 454 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B PHE 4.7 0.9 - - - +
122B ASN* 3.0 42.7 - - - +
123B HIS* 3.7 16.1 + - - -
450B TYR* 3.0 61.6 + - + +
451B LEU 4.0 2.9 - - - +
453B ALA* 1.3 81.3 - - - +
455B ARG* 1.3 62.8 + - + +
457B LYS* 2.8 43.3 + - - +
458B LEU* 3.3 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 455 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B PHE* 2.7 50.4 + - - +
125B PHE* 2.9 37.3 + - - +
127B ALA* 3.7 4.6 - - - +
150B ARG* 5.0 3.8 - - - +
154B GLU* 3.7 23.3 - - + +
451B LEU* 3.4 14.7 + - + +
452B HIS 3.3 5.2 + - - +
454B GLN* 1.3 77.4 - - - +
456B GLN* 1.3 60.4 + - - +
458B LEU* 2.9 36.0 + - - +
459B HIS 3.2 0.5 + - - -
460B GLY* 2.7 52.2 + - - +
461B TYR* 3.6 25.9 - - + +
462B LEU* 3.1 24.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 456 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B HIS* 2.8 23.0 + - + +
453B ALA* 3.8 7.0 - - - +
455B ARG* 1.3 76.4 - - - +
457B LYS* 1.3 63.0 + - - +
459B HIS* 3.0 16.6 + - - -
460B GLY* 4.0 12.2 + - - +
461B TYR* 3.2 37.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 457 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B ALA* 3.1 25.9 + - - +
454B GLN* 2.8 45.3 + - - +
455B ARG 3.2 0.2 - - - -
456B GLN* 1.3 76.9 - - + +
458B LEU* 1.3 63.3 + - + +
459B HIS* 3.3 6.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 458 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B PHE 3.7 9.2 - - - +
122B ASN 3.8 13.9 - - - +
123B HIS* 3.8 9.2 - - - +
124B PHE 3.6 35.2 - - - +
125B PHE 3.1 11.2 - - - +
126B ARG* 3.4 12.6 - - + -
127B ALA 2.9 25.5 + - - -
454B GLN 3.3 13.1 + - - +
455B ARG* 2.9 36.3 + - - +
457B LYS* 1.3 83.2 - - + +
459B HIS* 1.3 61.3 + - - +
460B GLY 3.4 1.0 + - - -
----------------------------------------------------------
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