Contacts of the strand formed by residues 145 - 152 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ILE* 3.5 29.6 - - + -
30B ILE* 4.4 7.2 - - + -
76B GLY* 4.3 6.1 - - - -
77B VAL 3.7 22.7 - - - -
78B ILE* 3.6 20.4 - - + -
104B VAL* 3.6 21.5 - - + -
105B VAL 3.2 20.6 - - - -
106B GLY* 2.9 42.4 - - - -
107B ILE* 3.2 9.0 + - - +
143B ALA 3.7 0.2 - - - -
144B ASP* 1.3 82.2 - - - +
146B ALA* 1.3 61.5 + - - +
183B ILE* 3.7 5.5 - - - +
184B VAL* 2.9 22.9 - - + +
186B ILE* 3.6 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ILE* 3.2 18.6 - - + +
109B VAL* 3.9 17.9 - - + -
135B CYS* 5.7 0.7 - - - -
145B PHE* 1.3 79.6 - - - +
147B LYS* 1.3 61.6 + - - +
174B TYR* 3.2 10.3 - - + +
178B CYS* 4.1 10.8 - - - -
183B ILE* 3.7 14.6 - - + +
184B VAL 2.8 7.7 + - - +
186B ILE* 2.8 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ALA* 5.1 0.8 - - - +
34B ASP* 3.2 32.1 + - - +
78B ILE* 4.0 28.9 - - + -
107B ILE 3.0 4.9 + - - -
108B LYS* 3.4 11.4 - - + +
109B VAL* 3.0 27.5 + - - +
110B ASP* 3.9 2.3 + - - +
146B ALA* 1.3 76.9 - - - +
148B TRP* 1.3 64.8 + - - +
149B ARG* 4.2 16.7 - - - +
174B TYR* 3.3 4.3 - - - -
186B ILE* 4.0 9.0 - - + +
188B GLU* 2.8 29.0 + - + +
230B LYS* 3.0 31.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B VAL* 4.0 3.6 - - + -
110B ASP* 3.6 22.0 - - + -
125B THR* 3.3 35.8 - - + -
126B GLN 3.5 0.7 - - - -
127B GLY* 3.4 28.0 - - - -
128B LEU* 3.4 38.4 - - + -
131B LEU* 4.4 5.4 - - + -
147B LYS* 1.3 76.1 - - - +
149B ARG* 1.3 65.3 + - - +
150B CYS* 3.6 12.4 - - - -
170B VAL* 3.3 26.2 - - + +
171B LEU* 3.6 19.3 - - + +
174B TYR* 3.3 49.7 + + + -
186B ILE 3.7 1.8 + - - -
188B GLU* 3.3 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B LYS* 5.7 2.9 - - - +
110B ASP* 3.2 17.8 + - - +
113B VAL* 5.6 2.3 + - - +
125B THR* 2.8 20.7 + - - +
147B LYS* 4.2 11.9 - - - +
148B TRP* 1.3 76.2 - - - +
150B CYS* 1.3 69.8 + - - +
151B VAL* 3.4 31.7 + - + +
188B GLU* 3.3 32.5 - - + +
190B GLU* 2.4 44.7 + - - +
192B LEU* 4.3 7.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B THR* 3.3 10.1 - - - -
148B TRP* 3.6 24.1 + - - -
149B ARG* 1.3 79.3 - - - +
151B VAL* 1.3 66.5 + - - +
152B LEU* 5.6 2.2 - - + -
167B ASN* 3.3 35.7 - - + +
170B VAL* 4.6 2.9 - - - -
171B LEU* 3.6 25.8 - - + -
188B GLU 3.0 12.6 + - - +
189B PRO* 4.5 6.5 - - + -
190B GLU* 3.2 21.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B VAL* 4.7 13.1 - - + +
123B THR* 3.5 30.7 + - - +
124B THR 5.9 0.2 - - - -
125B THR* 4.5 1.6 + - - -
149B ARG* 3.4 40.4 - - + +
150B CYS* 1.3 83.5 - - - +
152B LEU* 1.3 72.7 + - - +
153B LYS* 5.9 0.2 - - + -
167B ASN* 4.2 3.1 + - - +
190B GLU 3.4 2.9 - - - +
192B LEU* 3.5 41.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B GLU* 5.5 0.4 - - - +
150B CYS* 5.6 1.6 - - + -
151B VAL* 1.3 81.5 - - - +
153B LYS* 1.3 61.6 + - - +
159B PRO* 5.0 9.2 - - + -
163B ALA* 3.8 20.0 - - + +
164B ILE* 4.6 12.3 - - + -
167B ASN* 3.5 34.1 - - + +
189B PRO* 5.6 6.1 - - + -
190B GLU 2.8 12.8 + - - +
191B ILE* 4.2 13.2 - - + -
192B LEU* 2.9 31.5 + - - +
209B VAL* 3.3 46.0 - - + -
----------------------------------------------------------
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