Contacts of the strand formed by residues 204 - 208 (chain B) in PDB entry 1XL4
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 ARG 204 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A HIS* 5.2 11.2 - - + -
173B GLU* 3.4 48.7 + - - +
174B ALA 3.0 16.8 - - - -
175B ASP* 2.8 37.4 + - - +
202B ARG* 3.2 29.3 + - - +
203B SER* 1.3 84.2 + - - +
205B SER* 1.3 68.1 + - - +
206B PRO* 4.0 8.6 - - + +
212B TRP* 4.2 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A PHE* 5.0 6.4 - - - -
173B GLU* 3.6 0.2 - - - -
174B ALA* 2.8 41.7 + - - +
202B ARG* 4.6 5.2 - - - +
204B ARG* 1.3 77.0 - - - +
206B PRO* 1.3 64.8 - - - +
207B ILE* 3.3 23.2 + - - -
208B PHE* 3.9 5.0 + - - +
212B TRP* 3.6 33.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A HIS* 3.5 31.0 - - + +
179A VAL* 3.8 19.3 - - + -
195A PHE* 5.1 6.7 - - + -
197A ASP* 4.7 1.8 - - - +
240A LEU* 5.4 4.7 - - + -
242A LEU* 3.4 32.1 - - + +
172B ILE* 3.5 3.3 - - - -
173B GLU* 3.0 24.1 + - + +
202B ARG* 4.3 11.7 - - - +
204B ARG* 4.0 11.0 - - + +
205B SER* 1.3 84.5 - - - +
207B ILE* 1.3 68.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 6.2 1.3 - - + -
19A GLY 4.7 4.5 - - - +
195A PHE* 4.6 13.4 - - - -
240A LEU* 3.7 39.1 - - + +
241A VAL 4.7 0.4 - - - +
242A LEU* 4.6 9.4 - - + -
257A ARG* 3.6 35.9 - - + -
170B GLN* 3.6 23.1 - - + +
171B ILE 3.6 2.7 - - - -
172B ILE* 3.9 10.5 - - + -
205B SER* 3.4 10.0 + - - -
206B PRO* 1.3 90.7 - - + +
208B PHE* 1.3 60.0 + - - +
209B SER* 3.5 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B VAL* 4.4 6.5 - - + -
163B LEU* 3.8 22.2 - - + -
164B ALA 3.9 3.4 - - - -
165B ASN* 3.5 41.0 + - + -
170B GLN* 3.6 2.3 - - - -
171B ILE* 2.8 51.5 + - + +
174B ALA* 3.9 16.4 - - + -
205B SER* 3.9 5.3 + - - +
206B PRO 4.3 0.2 - - - -
207B ILE* 1.3 69.6 - - - +
209B SER* 1.3 62.8 + - - +
210B LEU 3.9 3.8 - - - -
211B SER 3.9 12.1 - - - -
212B TRP* 3.4 40.4 - + + -
243B PHE* 3.8 27.1 - + - -
----------------------------------------------------------
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