Contacts of the strand formed by residues 151 - 156 (chain H) in PDB entry 3IT8
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 151 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94G LEU* 3.4 20.1 - - + +
120G LEU* 4.1 1.2 - - - -
121G GLY 3.0 39.3 + - - -
15H HIS* 3.4 33.7 - + + +
16H VAL 3.3 11.0 - - - +
17H VAL* 4.7 3.6 - - + -
28H TRP* 3.6 5.6 - - - -
59H TYR* 3.7 13.9 - + - -
60H SER* 2.9 6.4 + - - -
61H GLN* 2.8 78.6 + - + +
119H TYR* 3.6 5.1 - + - -
148H GLY* 3.5 23.3 - - - -
150H VAL* 1.3 78.3 - - - +
152H PHE* 1.3 62.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 152 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H HIS* 4.5 1.6 - - - -
16H VAL* 2.8 45.0 + - + +
28H TRP* 3.6 34.3 - + + -
47H GLN* 5.2 1.1 - - - -
48H LEU* 3.4 36.2 - - + +
58H ILE* 4.1 20.9 - - + -
59H TYR* 3.3 16.4 - - - -
60H SER* 3.9 2.9 - - - -
80H ILE* 4.3 5.8 - - + -
132H LEU* 3.9 33.0 - - + -
133H SER* 4.1 0.9 - - - -
134H ALA* 3.5 34.1 - - + -
151H TYR* 1.3 78.7 - - - +
153H GLY* 1.3 64.3 + - - +
154H ILE* 4.6 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 153 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H ALA 2.8 14.4 - - - -
15H HIS* 4.0 0.4 - - - -
48H LEU* 4.4 3.1 - - - -
58H ILE* 4.0 0.3 - - - +
59H TYR* 2.9 51.6 + - - +
152H PHE* 1.3 77.6 - - - +
154H ILE* 1.3 73.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 154 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H VAL* 3.3 6.6 - - - +
14H ALA* 2.8 39.2 + - + +
41H VAL* 4.8 12.8 - - + -
48H LEU* 4.1 26.7 - - + -
50H VAL* 4.1 19.5 - - + +
56H TYR* 4.0 23.8 - - + -
57H LEU 3.0 10.8 - - - +
58H ILE* 3.9 17.3 - - + -
59H TYR* 4.0 4.1 - - - -
132H LEU* 3.9 24.0 - - + -
152H PHE* 4.6 1.3 - - + -
153H GLY* 1.3 85.0 - - - +
155H ILE* 1.3 61.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 155 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55G LEU* 4.1 15.7 - - + -
123G VAL* 4.0 22.7 - - + -
157G LEU* 3.9 23.8 - - + -
11H LYS* 4.1 16.6 - - + -
12H PRO 3.8 4.5 - - - +
13H VAL* 3.5 28.9 - - + -
56H TYR* 3.5 4.9 - - - -
57H LEU* 2.9 59.3 + - + +
59H TYR* 5.3 0.4 - - + -
154H ILE* 1.3 75.3 - - - +
156H ALA* 1.3 72.0 + - - +
157H LEU* 3.4 5.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 156 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H LYS* 3.2 29.4 + - + +
12H PRO* 3.0 47.6 + - + +
54H GLY* 6.5 0.2 - - - -
55H LEU 3.7 7.2 - - - +
56H TYR* 3.7 17.0 - - + -
155H ILE* 1.3 73.8 - - - +
157H LEU* 1.3 60.7 + - - +
----------------------------------------------------------
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