Contacts of the strand formed by residues 145 - 152 (chain L) in PDB entry 1XFB
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 PHE 145 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23L ILE* 3.6 29.2 - - + -
30L ILE* 4.4 7.0 - - + -
76L GLY* 4.3 5.4 - - - -
77L VAL 3.7 22.9 - - - -
78L ILE* 3.6 20.6 - - + -
104L VAL* 3.6 21.8 - - + -
105L VAL 3.2 20.2 - - - -
106L GLY* 2.9 43.0 - - - -
107L ILE* 3.2 8.7 + - - +
143L ALA 3.7 0.2 - - - -
144L ASP* 1.3 81.6 - - - +
146L ALA* 1.3 60.9 + - - +
183L ILE* 3.7 5.8 - - - +
184L VAL* 2.9 22.0 - - + +
186L ILE* 3.6 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 146 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78L ILE* 5.8 0.2 - - - -
107L ILE* 3.2 17.5 - - + +
109L VAL* 3.9 17.9 - - + -
135L CYS* 5.7 0.7 - - - -
145L PHE* 1.3 78.6 - - - +
147L LYS* 1.3 60.9 + - - +
174L TYR* 3.2 9.9 - - + +
178L CYS* 4.1 11.0 - - - -
183L ILE* 3.9 15.0 - - + -
184L VAL 2.8 7.5 + - - +
186L ILE* 2.8 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 147 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32L ALA* 5.1 0.6 - - - +
34L ASP* 3.2 33.9 + - - +
78L ILE* 4.0 26.9 - - + -
107L ILE 3.0 4.8 + - - -
108L LYS* 3.4 12.4 - - - +
109L VAL* 3.0 27.2 + - - +
110L ASP* 3.9 2.0 + - - +
146L ALA* 1.3 77.2 - - - +
148L TRP* 1.3 65.3 + - - +
149L ARG* 4.2 15.4 - - - +
174L TYR* 3.3 4.0 - - - -
186L ILE* 4.0 9.9 - - + +
188L GLU* 2.8 31.0 + - + +
230L LYS* 3.0 31.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 148 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109L VAL* 4.0 2.5 - - + -
110L ASP* 3.6 22.9 - - + -
125L THR* 3.3 35.3 - - + -
126L GLN 3.5 0.9 - - - -
127L GLY* 3.4 28.3 - - - -
128L LEU* 3.4 39.0 - - + -
131L LEU* 4.4 5.2 - - + -
147L LYS* 1.3 75.2 - - - +
149L ARG* 1.3 64.5 + - - +
150L CYS* 3.6 12.4 - - - -
170L VAL* 3.3 26.7 - - + +
171L LEU* 3.6 17.9 - - + +
174L TYR* 3.3 49.9 + + + -
186L ILE 3.7 1.6 + - - -
188L GLU* 3.3 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 149 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108L LYS* 5.7 3.1 - - - +
110L ASP* 3.2 17.3 + - - +
112L GLY 5.7 0.2 - - - -
113L VAL* 5.6 2.3 + - - +
125L THR* 2.8 20.7 + - - +
147L LYS* 4.2 12.1 - - - +
148L TRP* 1.3 76.9 - - - +
150L CYS* 1.3 69.3 + - - +
151L VAL* 3.4 30.8 + - + +
188L GLU* 3.3 34.1 - - + +
190L GLU* 2.4 43.8 + - - +
192L LEU* 4.3 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 150 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125L THR* 3.3 10.5 - - - -
148L TRP* 3.6 24.2 + - - -
149L ARG* 1.3 77.6 - - - +
151L VAL* 1.3 66.2 + - - +
152L LEU* 5.8 2.0 - - + -
167L ASN* 3.3 35.4 - - + +
170L VAL* 4.6 2.7 - - - -
171L LEU* 3.6 26.5 - - + -
188L GLU 3.0 12.7 + - - +
189L PRO* 4.5 6.5 - - + -
190L GLU* 3.2 21.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 151 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113L VAL* 4.7 14.0 - - + +
123L THR* 3.5 30.7 + - - +
124L THR 5.9 0.4 - - - -
125L THR* 4.5 1.0 + - - -
149L ARG* 3.4 40.2 - - + +
150L CYS* 1.3 82.6 - - - +
152L LEU* 1.3 72.5 + - - +
153L LYS* 5.9 0.2 - - + -
167L ASN* 4.2 2.5 + - - +
190L GLU 3.4 4.0 - - - +
192L LEU* 3.5 39.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 152 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122L GLU* 5.5 0.9 - - - +
123L THR 5.2 0.2 - - - +
150L CYS* 5.6 1.6 - - + -
151L VAL* 1.3 80.8 - - - +
153L LYS* 1.3 60.4 + - - +
159L PRO* 5.0 9.9 - - + -
163L ALA* 3.8 19.3 - - + +
164L ILE* 4.6 13.2 - - + -
167L ASN* 3.5 34.3 - - + +
189L PRO* 5.6 5.2 - - + -
190L GLU 2.8 12.3 + - - +
191L ILE* 4.2 14.1 - - + -
192L LEU* 2.9 31.9 + - - +
209L VAL* 3.3 46.4 - - + -
----------------------------------------------------------
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