Contacts of the strand formed by residues 45 - 52 (chain I) in PDB entry 3H3P
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 LEU 45 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I VAL* 3.8 18.4 - - + -
38I ARG 3.5 2.2 - - - -
39I GLN* 3.8 30.1 - - + +
44I GLY* 1.3 74.0 - - - -
46I GLU* 1.3 63.9 + - - +
95I TYR* 4.4 4.7 - - + -
117I TRP* 4.7 1.6 - - + -
37M TYR* 5.3 1.6 - - + -
45M PRO* 3.9 32.1 - - + -
88M TYR* 3.6 41.7 - - + -
99M PHE* 3.4 52.9 - - + +
100M GLY 4.5 3.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 46 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I VAL* 3.3 3.4 - - - +
38I ARG* 2.8 77.3 + - + +
40I ALA* 4.8 8.7 + - - +
43I ARG* 6.0 0.5 - - - +
44I GLY 4.2 8.5 - - - +
45I LEU* 1.3 79.9 - - - +
47I TRP* 1.3 65.2 + - - +
48I MET* 3.4 2.1 + - - +
63I ARG* 3.3 26.6 + - - +
64I PHE* 4.2 8.8 - - + -
99M PHE* 4.2 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 47 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35I SER* 3.1 28.6 + - - -
36I TRP 4.0 4.5 - - - -
37I VAL* 4.2 5.4 - - + -
46I GLU* 1.3 72.5 - - - +
48I MET* 1.3 61.1 + - - +
49I GLY* 3.4 19.7 + - - -
50I GLY* 3.9 1.8 - - - -
59I ASN* 3.2 50.5 - - - -
60I TYR 4.0 0.7 - - - -
61I ALA* 3.5 37.6 - - + +
64I PHE* 3.8 6.8 - - - -
114I PHE* 4.0 20.6 - + - -
95M SER 3.5 11.7 - - - -
96M LEU* 4.3 4.2 - - + +
97M SER* 3.5 42.1 - - - +
98M THR* 5.5 0.6 - - - +
99M PHE* 3.7 18.8 - - + +
47T TRP* 4.8 0.4 - + - -
48T PHE* 3.9 14.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 48 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36I TRP* 2.8 26.6 + - + +
37I VAL 4.7 0.9 - - - -
38I ARG* 3.6 13.5 - - + +
46I GLU 3.8 11.4 - - - +
47I TRP* 1.3 74.3 - - - +
49I GLY* 1.3 57.8 + - - +
60I TYR* 3.9 0.9 - - - -
61I ALA* 2.8 30.4 + - - +
64I PHE* 3.5 49.1 - - + -
68I ILE* 3.9 35.2 - - + +
81I LEU* 4.5 12.3 - - + -
83I LEU* 5.5 1.6 - - + -
94I TYR* 3.6 37.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 49 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35I SER* 3.4 3.8 + - - -
36I TRP 2.8 24.6 + - - +
47I TRP* 3.4 15.4 + - - -
48I MET* 1.3 81.9 - - - +
50I GLY* 1.3 57.8 + - - -
59I ASN 3.0 16.2 - - - -
60I TYR* 4.2 2.0 - - - -
70I ILE* 3.5 15.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 50 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34I LEU 3.0 13.9 - - - -
35I SER* 3.9 2.9 - - - -
36I TRP* 5.2 0.2 - - - -
47I TRP* 3.9 1.8 - - - -
49I GLY* 1.3 75.8 - - - -
51I VAL* 1.3 61.6 + - - +
58I THR* 3.4 5.2 - - - +
59I ASN 2.9 31.5 + - - -
70I ILE* 3.5 12.2 - - - +
47T TRP* 3.5 16.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 51 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34I LEU* 2.7 48.8 + - + +
50I GLY* 1.3 74.4 - - - +
52I ILE* 1.3 75.9 + - - +
53I PRO* 3.5 6.7 - - + +
56I THR* 4.2 10.5 - - + -
57I ILE 3.5 3.8 - - - +
58I THR* 4.0 19.3 - - + -
70I ILE* 3.6 24.2 - - + -
71I THR 4.6 2.7 - - - +
72I ALA* 4.1 28.5 - - + +
79I ALA* 4.7 2.2 - - + -
47T TRP* 3.5 2.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 52 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I SER 4.0 13.5 - - - +
31I THR* 4.9 0.9 - - - -
32I TYR 4.5 2.0 - - - +
33I ALA* 4.3 8.1 - - + -
51I VAL* 1.3 73.9 - - - +
53I PRO* 1.3 68.6 - - + +
54I LEU 3.2 8.5 - - - +
56I THR* 3.4 0.9 + - - -
57I ILE* 3.0 37.9 + - + +
47T TRP* 3.7 37.0 - - + +
50T ILE* 3.6 35.7 - - + -
51T THR* 4.0 28.0 - - + -
54T LEU* 4.2 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