Contacts of the strand formed by residues 131 - 136 (chain I) 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 ARG 131 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44I ARG* 3.5 51.2 + - - +
45I ASP* 3.8 14.9 + - - +
47I GLN* 3.0 32.8 + - + +
48I LEU 3.5 4.7 - - - +
49I VAL* 4.2 14.4 - - + +
82I ARG* 3.5 3.8 - - - +
83I ILE* 2.9 63.2 + - + +
129I GLY 4.1 7.6 + - - +
130I ASP* 1.3 76.3 - - - +
132I LEU* 1.3 61.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 132 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47I GLN* 3.3 7.4 - - - +
48I LEU* 2.8 37.0 + - + +
50I VAL* 4.2 6.1 - - + -
58I ILE* 3.6 34.3 - - + -
80I ILE* 4.9 3.4 - - + -
81I SER 3.3 10.8 - - - +
82I ARG* 4.0 18.6 - - + -
93I LEU* 4.1 4.5 - - + -
126I LEU* 3.8 22.9 - - + -
130I ASP* 5.2 0.9 - - + -
131I ARG* 1.3 79.7 - - - +
133I SER* 1.3 61.7 + - - +
152I PHE* 3.9 18.3 - - + -
154I ILE* 3.9 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 133 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46I ASN 5.1 1.6 - - - -
47I GLN* 2.9 32.7 + - - +
79I THR 3.6 0.9 - - - +
80I ILE* 3.0 8.3 - - - +
81I SER* 2.8 37.4 + - - -
83I ILE* 4.4 6.6 - - - +
90I LYS* 4.0 10.4 + - - -
132I LEU* 1.3 74.6 - - - +
134I ALA* 1.3 60.2 + - - +
135I GLU* 3.6 27.3 + - - -
152I PHE* 4.1 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 134 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I LEU* 3.9 6.5 - - - +
28I TRP* 3.6 30.8 + - + +
46I ASN* 5.4 2.7 + - - -
60I SER* 4.0 12.8 - - - +
78I HIS* 4.6 4.3 - - - +
79I THR 3.6 5.2 - - - -
80I ILE* 4.4 4.5 - - + +
133I SER* 1.3 73.8 - - - +
135I GLU* 1.3 62.2 + - - +
152I PHE* 3.5 43.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 135 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I LEU* 4.8 2.0 - - - -
46I ASN* 5.9 4.3 - - - +
47I GLN* 4.7 2.1 + - - +
78I HIS* 3.4 6.6 - - - -
79I THR* 3.0 41.7 + - + +
81I SER* 5.0 3.0 + - - -
90I LYS* 3.1 39.7 + - - +
133I SER* 3.6 15.5 + - - -
134I ALA* 1.3 78.6 - - - +
136I ILE* 1.3 69.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 136 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I LEU* 4.0 13.9 - - + +
62I VAL* 3.7 28.5 - - + -
64I PHE* 3.8 22.9 - - + -
77I THR* 3.2 12.1 - - - +
78I HIS* 4.0 4.0 - - + -
79I THR* 5.7 0.7 - - - -
135I GLU* 1.3 83.8 - - - +
137I ASN* 1.3 61.5 + - - +
138I ARG 4.1 3.1 - - - -
139I PRO* 3.5 40.0 - - + +
142I LEU* 3.5 30.1 - - + -
----------------------------------------------------------
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