Contacts of the strand formed by residues 53 - 62 (chain E) in PDB entry 2HAK
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 TYR 53 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E HIS* 3.3 6.9 + - - -
50E ILE* 3.0 46.0 + - + +
51E GLY 3.1 3.2 + - - -
52E ASN* 1.3 83.1 - - + +
54E ARG* 1.3 59.9 + - - +
55E LEU* 3.2 8.0 + - + +
70E ALA* 4.4 11.0 - - + -
71E ARG 3.5 2.7 - - - +
72E HIS* 3.4 39.2 - + + -
73E VAL* 4.4 1.8 - - - -
79E VAL* 3.6 20.2 - - + -
81E VAL* 4.6 2.7 - - + -
116E PHE* 5.0 0.2 - - - +
117E GLU* 2.2 44.1 + - - +
119E ILE* 4.0 9.9 - - + -
128E VAL* 3.4 36.3 - - + +
356E ALA* 3.6 8.8 - - - +
360E LEU* 3.7 8.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 54 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E GLN 4.3 17.5 - - - +
48E PRO 3.8 5.6 - - - +
49E HIS* 3.6 27.8 - - + +
53E TYR* 1.3 70.1 - - - +
55E LEU* 1.3 70.9 + - - +
56E GLN* 3.3 36.4 + - - +
70E ALA* 3.2 2.3 - - - +
71E ARG* 3.0 57.6 + - + +
73E VAL* 3.9 10.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E GLN 5.1 0.5 + - - -
48E PRO* 3.1 42.0 + - + +
49E HIS 4.0 14.4 - - - +
50E ILE* 3.8 27.8 - - + -
53E TYR* 4.0 5.6 - - + +
54E ARG* 1.3 77.6 + - - +
56E GLN* 1.3 60.4 + - - +
68E LYS* 4.1 30.7 - - + -
70E ALA* 3.8 18.4 - - + -
81E VAL* 3.9 21.1 - - + -
83E ILE* 5.0 6.7 - - + -
126E TYR* 5.5 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 56 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E ARG* 3.4 37.2 + - - +
55E LEU* 1.3 76.1 - - - +
57E LYS* 1.3 72.0 + - + +
58E THR 3.4 1.2 + - - -
68E LYS* 3.8 13.5 + - - +
69E LEU* 2.7 22.7 + - + +
70E ALA* 2.8 29.7 - - - +
71E ARG* 3.7 9.7 + - - +
78E GLU* 2.3 40.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 57 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56E GLN* 1.3 80.7 - - + +
58E THR* 1.3 65.9 + - - +
59E ILE* 4.0 19.7 - - + -
68E LYS* 3.5 0.7 - - - -
69E LEU* 2.8 49.6 + - + +
131E TYR* 5.9 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 58 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56E GLN 3.4 0.2 + - - -
57E LYS* 1.3 82.0 - - - +
59E ILE* 1.3 63.3 + - - +
60E GLY 3.9 11.8 + - - -
61E LYS* 5.0 6.1 - - + +
66E LYS* 4.5 14.3 - - - +
67E VAL 3.5 8.7 + - - -
68E LYS* 3.0 36.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 59 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E LYS* 4.0 15.3 - - + +
58E THR* 1.3 79.7 - - - +
60E GLY* 1.3 58.1 + - - +
67E VAL* 2.6 41.2 + - + +
68E LYS 4.4 0.2 - - - -
69E LEU* 3.8 31.4 - - + +
80E ALA* 4.6 3.4 - - + -
131E TYR* 3.9 37.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 60 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58E THR* 3.7 7.8 + - - -
59E ILE* 1.3 81.3 - - - +
61E LYS* 1.3 59.8 + - - +
66E LYS* 3.4 2.3 - - - -
67E VAL* 2.6 34.9 + - - +
202E VAL* 3.5 23.1 - - - -
203E GLY* 4.9 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 61 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58E THR* 5.0 5.4 - - - +
60E GLY* 1.3 74.4 - - - +
62E GLY* 1.3 55.6 + - - +
65E ALA 3.5 6.1 - - - -
66E LYS* 4.3 14.4 - - + -
202E VAL* 3.6 4.2 - - - +
203E GLY* 2.7 27.5 + - - +
146F ARG* 2.8 47.8 + - - +
148F LYS* 6.4 0.4 - - - +
271F PHE* 3.6 30.5 - - + -
272F TYR* 3.7 34.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 62 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E LYS* 1.3 76.5 - - - +
63E ASN* 1.3 73.7 + - - +
64E PHE 3.2 3.3 + - - -
65E ALA 2.7 14.1 + - - +
201E THR* 3.8 16.2 - - - -
202E VAL* 4.2 1.6 - - - -
203E GLY 4.5 3.6 - - - -
146F ARG* 4.7 3.6 - - - -
271F PHE* 3.2 16.5 - - - -
272F TYR* 3.6 8.8 - - - -
----------------------------------------------------------
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