Contacts of the strand formed by residues 93 - 97 (chain G) in PDB entry 1XBT
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 VAL 93 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G VAL* 4.4 20.4 - - + -
43G PHE* 3.8 47.3 - - + -
48G TYR* 4.1 16.2 - - + -
49G LYS 3.1 2.6 + - - -
50G CYS* 3.3 18.5 - - - +
51G LEU 2.9 26.0 + - - +
91G VAL* 3.2 3.8 - - - +
92G ALA* 1.3 83.0 - - - +
94G ILE* 1.3 65.8 + - - +
118G THR* 3.4 17.0 - - - +
120G ILE* 4.6 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 94 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G LEU* 3.3 8.3 - - + +
53G ILE* 3.7 29.6 - - + -
88G ALA* 3.7 34.8 - - + +
91G VAL* 3.5 18.2 - - + -
93G VAL* 1.3 74.8 - - - +
95G GLY* 1.3 59.7 + - - +
96G ILE* 4.2 8.3 - - + -
108G PHE* 4.2 8.3 - - + -
112G MET* 4.0 23.6 - - + -
117G LYS* 4.1 18.2 - - + -
118G THR 2.8 11.6 + - - +
119G VAL* 3.3 8.6 - - + +
120G ILE* 2.8 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 95 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36G LEU* 3.7 15.7 - - - -
40G VAL* 4.2 12.4 - - - +
51G LEU 2.8 13.0 + - - +
52G VAL* 3.3 8.0 - - - -
53G ILE* 2.7 32.2 + - - +
93G VAL 4.2 0.4 - - - -
94G ILE* 1.3 73.7 - - - +
96G ILE* 1.3 60.3 + - - +
97G ASP 4.1 0.4 - - - -
120G ILE 3.3 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 96 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36G LEU* 3.7 4.6 - - - +
53G ILE* 3.5 11.4 - - + +
81G LEU* 4.0 13.9 - - + -
94G ILE* 4.2 1.8 - - + -
95G GLY* 1.3 76.0 - - - +
97G ASP* 1.3 60.7 + - - +
99G GLY* 4.0 8.7 - - - -
102G PHE* 3.8 27.6 - - + -
105G ILE* 4.0 20.0 - - + -
108G PHE* 3.8 27.8 - - + -
109G CYS* 3.9 13.5 - - - -
119G VAL* 3.8 23.1 - - + -
120G ILE 2.8 11.7 + - - +
121G VAL* 3.5 5.5 - - + -
122G ALA 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 97 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32G LYS* 5.6 0.2 - - - +
33G SER* 3.0 34.4 + - - -
36G LEU* 3.8 11.0 - - + +
37G MET* 5.6 0.7 - - + -
52G VAL* 5.3 1.6 - - + -
53G ILE 2.8 15.8 + - - +
54G LYS* 3.8 32.7 - - + +
55G TYR 3.9 8.3 + - - -
63G SER* 4.9 4.0 - - - +
96G ILE* 1.3 71.8 - - - +
98G GLU* 1.3 90.9 + - - +
102G PHE* 3.7 13.7 - - - -
122G ALA* 3.7 12.5 - - - +
7194G MG 4.0 4.7 - - - -
7195G TTP 4.7 0.3 + - - -
----------------------------------------------------------
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