Contacts of the strand formed by residues 52 - 60 (chain A) in PDB entry 3A98
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 HIS 52 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LEU* 3.0 23.0 + - + +
50A ILE 3.2 0.6 - - - -
51A LYS* 1.3 101.1 + - + +
53A LYS* 1.3 53.5 + - - +
54A MSE 3.0 5.6 - - - -
55A LEU* 2.8 54.3 + - + +
680D ASP* 2.8 32.9 + - - +
683D ARG* 5.8 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A TYR* 3.4 55.3 - - + +
49A LEU 3.4 4.7 - - - -
50A ILE* 2.9 36.7 + - - +
52A HIS* 1.3 72.5 - - - +
54A MSE 1.3 76.9 + - + +
55A LEU 3.2 1.7 - - - -
56A GLN* 4.5 3.6 - - - +
727B ASN* 4.6 10.5 - - - +
659D LYS* 6.3 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A HIS 2.9 1.4 + - - -
53A LYS* 1.3 92.4 - - + +
55A LEU* 1.3 60.3 + - - +
56A GLN* 3.3 5.5 + - - +
727B ASN* 3.8 38.1 - - + +
659D LYS* 4.4 24.2 - - + +
660D HIS* 4.2 24.9 - - + +
663D CYS* 4.1 12.6 - - - -
680D ASP* 3.6 23.1 - - + +
681D LEU* 3.8 32.3 - - + +
684D ASN* 3.2 24.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 3.8 15.9 - - + +
48A TYR* 3.1 19.2 - - - +
49A LEU* 3.2 32.4 + - + -
52A HIS* 2.8 36.5 + - + +
54A MSE 1.3 76.4 - - - +
56A GLN* 1.3 57.1 - - - +
680D ASP* 3.6 33.2 - - + +
683D ARG* 4.1 27.4 - - + +
684D ASN* 3.9 12.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ALA* 5.9 2.6 - - - +
25A PRO 4.7 1.0 - - - +
26A GLN 5.5 0.2 - - - -
27A LEU* 4.2 10.4 - - - +
38A GLN* 2.7 31.9 + - - +
46A ARG* 4.1 22.3 - - - +
47A GLY* 3.1 15.0 - - - +
48A TYR* 3.9 9.2 - - + +
53A LYS 4.5 2.5 - - - +
54A MSE 3.3 9.4 + - - +
55A LEU* 1.3 75.4 - - - +
57A GLY* 1.3 62.9 + - - +
725B ASP 3.7 14.6 + - - -
726B CYS* 3.1 13.1 - - + +
727B ASN* 2.6 35.4 + - - +
684D ASN* 3.6 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A PRO* 3.2 14.1 - - - -
27A LEU* 3.8 10.1 - - - +
46A ARG* 4.1 6.1 - - - -
47A GLY 2.9 31.5 + - - +
56A GLN* 1.3 81.0 - - - +
58A ILE* 1.3 66.2 + - - -
59A PHE* 3.6 5.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A TRP* 3.8 20.6 - - + -
19A PHE* 4.0 0.9 - - - -
25A PRO* 2.8 24.4 + - + +
26A GLN* 3.3 22.3 - - + +
27A LEU 2.8 25.7 + - - +
44A TRP* 3.7 20.6 - - + -
45A TYR 3.1 10.1 - - - +
46A ARG* 4.0 11.9 - - + -
57A GLY* 1.3 75.5 - - - -
59A PHE* 1.3 66.0 + - - +
717B PRO* 3.9 28.0 - - + -
720B TYR* 4.2 13.5 - - + +
722B PHE* 4.1 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PHE* 4.1 1.1 - - + -
27A LEU* 3.9 26.2 - - + +
29A LEU* 3.6 20.0 - - + -
35A VAL* 3.8 25.8 - - + -
37A ILE* 4.3 4.3 - - + -
44A TRP* 3.3 7.5 - - - -
45A TYR* 2.9 49.4 + + + +
46A ARG 4.3 0.4 - - - -
47A GLY* 3.7 25.6 - - - -
57A GLY 3.6 16.6 - - - -
58A ILE* 1.3 80.0 - - - +
60A PRO* 1.3 74.1 - - + +
64A ILE* 3.6 37.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PHE* 3.5 42.2 - - + -
43A ASP 3.5 7.0 - - - +
44A TRP* 3.5 16.4 - - + -
45A TYR* 4.8 0.2 - - - -
59A PHE* 1.3 90.3 - - + +
61A LYS* 1.3 67.0 + - - +
62A SER* 3.6 7.9 - - - +
63A PHE* 3.1 32.2 + - + +
64A ILE* 3.8 11.8 - - - +
713B ILE* 4.9 0.4 - - + -
714B PRO* 3.7 19.3 - - + -
----------------------------------------------------------
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