Contacts of the strand formed by residues 124 - 130 (chain F) in PDB entry 1XWD
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 124 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D THR* 5.4 0.4 - - + -
87D CYS 5.5 1.1 + - - -
88D TYR* 3.6 45.5 + + + +
91D LYS* 4.5 3.5 + - - -
98F HIS 2.9 7.2 + - - +
99F GLU* 3.3 19.8 - - + -
100F ILE 2.8 26.7 + - - +
101F ARG* 3.9 16.9 + - - -
122F LEU* 3.8 4.4 - - - +
123F GLN* 1.3 80.1 - - + +
125F LEU* 1.3 58.7 + - - +
126F LEU* 3.2 42.1 - - + +
148F LEU* 3.4 43.7 - - + -
150F ASP* 3.2 30.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 125 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100F ILE* 3.5 25.4 - - + +
102F ILE* 5.2 0.2 - - + -
116F PHE* 4.1 19.1 - - + -
122F LEU* 4.1 16.4 - - + -
123F GLN 4.3 0.2 - - - -
124F TYR* 1.3 76.1 - - - +
126F LEU* 1.3 60.7 + - - +
127F ILE* 3.9 26.9 - - + -
136F PRO* 5.2 0.9 - - + -
138F VAL* 4.2 18.4 - - + -
141F ILE* 4.2 14.1 - - + -
147F VAL* 5.1 3.3 - - + +
148F LEU 3.1 9.3 + - - +
149F LEU* 3.5 28.8 - - + +
150F ASP 2.9 25.2 + - - +
151F ILE* 4.9 0.2 - - - +
168F LEU* 4.9 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 126 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D LYS* 4.2 7.4 - - - +
94E CYS 6.0 0.9 - - - +
100F ILE 2.8 10.7 + - - +
101F ARG* 3.1 41.5 - - + +
102F ILE* 2.8 24.8 + - - +
103F GLU* 3.9 17.3 - - + +
124F TYR* 3.2 34.3 - - + +
125F LEU* 1.3 73.6 - - - +
127F ILE* 1.3 68.5 + - - +
128F SER* 2.8 26.0 - - - +
150F ASP* 3.2 37.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 127 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102F ILE* 3.2 24.2 - - + +
111F ILE* 4.4 16.4 - - + -
116F PHE* 4.7 2.7 - - + -
125F LEU* 3.9 19.3 - - + -
126F LEU* 1.3 80.1 - - - +
128F SER* 1.3 60.0 + - - +
130F THR* 4.1 15.0 - - + +
132F ILE* 3.9 22.4 - - + -
136F PRO* 3.3 36.3 - - + -
150F ASP 2.8 9.8 + - - -
151F ILE* 3.4 13.3 - - + -
152F GLN 3.2 11.1 + - - -
154F ASN* 2.8 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 128 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D LYS* 5.0 1.7 + - - -
102F ILE 2.8 8.7 + - - -
103F GLU* 3.4 14.0 - - - +
104F LYS* 3.0 22.3 + - - -
126F LEU* 2.8 31.4 - - - +
127F ILE* 1.3 72.6 + - - +
129F ASN* 1.3 69.4 + - - +
130F THR* 3.2 7.8 + - - -
152F GLN* 3.2 19.4 - - - +
153F ASP* 5.0 3.8 - - - -
154F ASN* 4.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 129 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D THR 4.2 1.0 - - - +
47D MET* 3.5 24.6 - - + +
48D LEU* 3.2 11.4 + - - +
49D VAL* 3.0 38.6 + - - +
51D LYS* 4.7 6.3 - - - +
93E ASP* 5.1 5.3 + - - -
104F LYS* 3.4 21.4 - - + +
105F ALA 3.1 23.7 + - - -
106F ASN* 3.8 2.9 + - - -
128F SER* 1.3 76.3 - - - +
130F THR* 1.3 57.6 + - - +
152F GLN 3.2 11.3 + - - -
153F ASP* 3.3 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 130 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D LEU* 3.5 14.5 - - - +
102F ILE* 4.4 2.8 - - - +
105F ALA* 3.3 14.0 - - - +
108F LEU* 3.2 42.3 - - + +
127F ILE* 4.1 10.9 - - + +
128F SER 3.2 14.4 + - - -
129F ASN* 1.3 73.9 + - - +
131F GLY* 1.3 72.9 + - - +
132F ILE* 3.3 17.6 + - + +
153F ASP 3.8 1.4 + - - -
154F ASN* 2.8 38.4 + - - +
155F ILE 4.5 0.3 + - - -
156F ASN* 4.9 0.9 + - - -
----------------------------------------------------------
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