Contacts of the strand formed by residues 41 - 47 (chain H) in PDB entry 3SDI
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 ILE 41 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H ILE* 2.7 48.1 + - + +
38H SER* 3.1 29.9 + - - +
39H PRO 3.6 0.2 - - - -
40H LYS* 1.3 84.3 - - + +
42H TRP* 1.3 57.4 + - - +
63H ILE* 5.2 0.7 - - + -
74H PRO* 3.8 19.7 - - + +
75H ARG 3.8 30.5 - - - +
76H VAL* 3.9 15.9 - - + +
79H ALA* 4.4 8.7 - - + -
101H VAL* 4.1 20.9 - - + -
102H ALA 3.6 9.9 - - - +
104H VAL 4.7 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 42 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A TYR* 4.0 38.1 - - + -
14H ILE* 3.5 20.4 - - + +
34H LEU* 4.2 13.5 - - + -
35H HIS* 3.2 26.0 - - - -
36H ARG* 4.0 26.0 - - + -
37H ILE* 4.7 1.8 - - - -
38H SER 4.0 0.4 + - - -
39H PRO 3.0 20.2 + - - -
40H LYS* 4.0 0.7 - - - -
41H ILE* 1.3 89.4 - - - +
43H CYS* 1.3 64.0 + - - +
101H VAL* 3.6 2.9 - - - +
102H ALA* 2.9 31.7 + - - +
176H CYS* 3.7 17.0 - - + -
178H MET* 3.8 17.0 - - + -
184H ALA* 3.9 6.1 - - - +
186H TYR* 3.5 45.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 43 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H ILE* 3.8 6.7 - - - +
33H LYS 3.5 1.2 - - - +
34H LEU* 3.6 1.4 - - - -
35H HIS* 2.8 43.0 + - - +
37H ILE* 3.9 21.5 - - + -
42H TRP* 1.3 76.8 - - - +
44H ALA* 1.3 61.6 + - - +
56H THR* 3.2 30.3 - - - -
83H LEU* 6.1 0.2 - - + -
99H LEU* 4.4 17.3 - - + -
100H ILE 3.1 15.5 - - - +
101H VAL* 3.9 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 44 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3H ILE* 3.4 34.5 - - + +
4H VAL 5.8 0.7 - - - +
14H ILE* 4.6 4.4 - - + +
15H ALA 4.8 1.3 - - - +
33H LYS 3.4 12.1 - - - +
34H LEU* 3.8 17.9 - - + -
43H CYS* 1.3 75.6 - - - +
45H GLY* 1.3 60.1 + - - +
99H LEU* 3.2 8.0 - - - +
100H ILE* 2.9 35.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 45 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1H THR* 4.0 13.2 + - - +
3H ILE* 4.1 5.7 - - - +
33H LYS* 3.8 15.0 + - - +
35H HIS* 5.2 4.4 - - - -
44H ALA* 1.3 76.1 - - - +
46H ALA* 1.3 60.2 + - - +
52H THR* 4.0 15.0 + - - -
98H TYR 3.2 9.0 - - - -
99H LEU* 3.7 12.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 46 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1H THR* 4.3 16.4 - - + -
3H ILE* 4.3 6.7 - - + +
45H GLY* 1.3 73.9 - - - +
47H GLY* 1.3 61.2 + - - +
52H THR* 3.7 5.0 - - - +
98H TYR* 2.8 43.8 + - + +
127H LEU* 4.7 0.4 - - + -
128H GLY* 4.0 30.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 47 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1H THR* 5.8 0.4 + - - -
46H ALA* 1.3 76.9 - - - +
48H THR* 1.3 66.4 + - - -
49H ALA* 3.0 6.8 + - - +
96H GLY 3.7 4.9 - - - -
98H TYR* 4.2 9.6 - - - -
----------------------------------------------------------
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