Contacts of the strand formed by residues 103 - 107 (chain Y) in PDB entry 1XDM
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 103 (chain Y).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18Y ILE* 4.6 8.1 - - + -
21Y SER* 4.1 22.2 - - - +
22Y ILE* 4.7 5.8 - - + -
74Y GLY 3.3 17.2 + - - +
75Y GLY* 3.2 4.1 - - - -
76Y VAL 2.9 24.9 + - - -
101Y GLY 4.4 5.2 - - - +
102Y ILE* 1.3 79.6 - - - +
104Y VAL* 1.3 67.3 + - - +
105Y GLY 3.9 0.3 + - - -
143Y ASP* 3.9 31.4 - - + +
144Y PHE* 4.1 12.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 104 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76Y VAL 3.7 2.9 - - - +
78Y LEU* 3.3 33.0 - - + -
83Y LEU* 4.5 14.4 - - + -
94Y ARG* 3.4 29.4 - - + +
97Y LEU* 4.1 15.3 - - + -
98Y LYS* 4.3 10.1 - - + +
102Y ILE* 5.4 0.2 - - - -
103Y VAL* 1.3 78.6 - - - +
105Y GLY* 1.3 65.6 + - - +
141Y GLY 3.6 19.3 + - - +
142Y VAL* 3.4 5.1 - - + -
143Y ASP* 2.9 27.4 + - - -
144Y PHE* 3.9 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 105 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76Y VAL 2.8 13.0 + - - +
77Y ILE* 3.0 4.7 - - - -
78Y LEU* 2.5 36.9 + - - +
104Y VAL* 1.3 78.6 - - - +
106Y ILE* 1.3 53.8 + - - -
142Y VAL* 3.5 2.7 - - - -
144Y PHE* 3.0 29.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 106 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77Y ILE* 3.9 4.6 - - - +
78Y LEU* 3.4 17.9 - - + +
79Y PHE 4.2 0.9 - - - -
80Y HIS* 3.9 21.5 - - - +
83Y LEU* 4.1 13.7 - - + -
105Y GLY* 1.3 72.8 - - - -
107Y LYS* 1.3 69.9 + - - +
108Y LEU* 3.4 20.6 + - + -
137Y TYR* 3.3 43.3 - - + -
142Y VAL* 2.9 30.2 - - + +
144Y PHE 3.0 3.9 + - - +
145Y GLY* 3.0 23.7 - - - -
146Y LYS 3.2 2.3 + - - -
182Y LEU* 4.7 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 107 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33Y ASP* 3.2 49.0 + - + +
34Y GLU* 4.7 1.0 - - - +
35Y SER* 4.2 15.0 - - - +
77Y ILE* 4.1 3.3 - - - +
78Y LEU 3.0 15.2 + - - +
79Y PHE* 4.3 17.1 - - + -
80Y HIS* 5.0 3.8 + - - +
106Y ILE* 1.3 83.1 - - - +
108Y LEU* 1.3 62.6 + - - +
109Y ASP* 3.3 38.6 + - - +
133Y ARG* 5.4 0.3 + - - -
137Y TYR* 4.5 4.5 + - - -
146Y LYS* 4.2 25.7 - - + +
----------------------------------------------------------
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