Contacts of the strand formed by residues 57 - 60 (chain D) in PDB entry 3HUU
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 57 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C THR* 3.1 20.5 + - - +
57C SER* 3.2 22.4 - - - -
58C THR 3.7 8.1 - - - -
59C ARG* 2.9 23.7 + - - +
20D THR 5.7 0.2 - - - -
21D LEU 2.8 12.2 + - - -
22D THR* 3.9 7.0 - - - -
23D ILE* 2.9 25.5 + - - +
51D CYS* 4.7 2.7 - - - -
56D TYR* 1.3 74.5 - - - +
58D THR* 1.3 64.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 58 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C SER* 3.4 1.7 - - - -
58C THR* 2.8 50.7 + - - +
59C ARG* 5.2 0.2 - - - -
60C MET* 6.4 1.1 - - + -
22D THR* 3.8 4.5 - - - -
23D ILE* 3.2 10.5 + - - -
25D LEU* 3.1 38.9 - - + +
44D LEU* 5.1 2.5 - - + -
47D ILE* 5.5 2.5 - - - -
48D ASN* 4.5 20.6 - - - +
51D CYS* 5.5 6.5 - - - -
57D SER* 1.3 78.4 - - - +
59D ARG* 1.3 70.2 + - - +
60D MET* 6.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 59 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C ASN* 5.4 2.0 - - - -
52C ASN* 3.0 34.6 + - - +
55C GLY* 4.4 11.0 + - - -
56C TYR 3.0 28.5 + - - +
57C SER* 3.8 16.2 - - - -
58C THR* 5.0 2.5 - - - -
22D THR* 4.2 3.2 + - + +
23D ILE 3.2 4.2 + - - +
24D GLY* 4.2 3.1 - - - -
25D LEU* 2.8 24.8 + - - +
58D THR* 1.3 82.7 + - - +
60D MET* 1.3 59.4 + - - +
76D MET* 4.0 27.0 - - + +
81D SER* 3.4 38.9 + - - +
82D VAL* 3.5 23.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 60 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C LEU* 5.3 3.1 - - - -
48C ASN* 3.5 32.3 - - - +
52C ASN* 2.9 24.5 + - - -
25D LEU* 3.4 39.9 - - + +
27D GLN* 3.1 44.0 - - + +
40D ASN* 5.7 2.2 - - + +
43D VAL* 6.2 0.2 - - + -
44D LEU* 4.0 30.5 - - + -
47D ILE* 6.0 0.2 - - + -
58D THR* 6.4 0.4 - - + -
59D ARG* 1.3 74.4 - - - +
61D THR* 1.3 65.5 + - - +
76D MET* 4.5 2.5 - - - -
88D LEU* 4.0 15.7 - - + -
----------------------------------------------------------
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