Contacts of the strand formed by residues 257 - 263 (chain A) in PDB entry 1ULH
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 GLN 257 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ASP* 4.7 1.8 - - - +
98A GLN* 2.9 51.2 + - - +
99A VAL* 3.5 29.8 - - + -
102A ALA* 6.0 3.8 - - + -
108A PRO 4.4 4.1 + - - +
109A PHE* 3.4 10.5 - - + -
110A TYR* 2.9 26.5 + - - -
255A ASP 3.6 5.1 + - - -
256A ILE* 1.3 76.9 - - - +
258A CYS* 1.3 61.6 + - - +
283A PRO* 4.8 14.0 - - + +
284A LYS 2.6 27.3 + - - -
285A PRO 4.3 0.2 - - - -
286A ALA* 3.7 15.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A TYR* 3.3 31.6 - - + -
112A TYR* 3.7 22.2 - - - -
241A SER* 3.1 37.2 - - - +
256A ILE 3.7 0.4 + - - +
257A GLN* 1.3 80.8 - - - +
259A LEU* 1.3 54.4 + - - +
260A ILE* 3.9 9.9 - - - -
283A PRO* 5.9 0.2 - - - +
284A LYS 4.7 0.8 + - - -
285A PRO* 3.1 13.0 - - + +
286A ALA 2.7 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A MET* 3.6 39.0 - - + -
99A VAL* 4.4 2.7 - - + -
109A PHE* 3.6 30.2 - - + -
110A TYR 2.7 14.7 + - - +
111A LEU* 3.3 18.2 - - + -
112A TYR 3.1 21.7 + - - -
136A LEU* 4.1 8.1 - - + -
257A GLN 4.2 0.6 - - - -
258A CYS* 1.3 69.9 - - - +
260A ILE* 1.3 63.3 + - - +
261A PRO* 3.3 8.0 - - + +
286A ALA* 3.6 25.1 - - + -
287A LEU 4.3 1.3 - - - +
288A LEU* 3.9 27.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A TYR* 3.5 34.8 - - + +
113A THR* 5.4 0.9 - - - -
241A SER* 3.5 20.6 - - - +
258A CYS* 3.9 8.7 - - - +
259A LEU* 1.3 76.3 - - - +
261A PRO* 1.4 69.9 - - - +
262A CYS* 3.5 4.5 + - + -
270A PHE* 3.4 47.1 - - + -
285A PRO* 3.9 15.5 - - + -
286A ALA 2.8 11.9 + - - +
287A LEU* 3.5 19.2 - - + +
288A LEU 3.4 19.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A PHE* 4.1 16.4 - - + -
111A LEU* 4.1 8.1 - - + -
112A TYR 3.5 14.1 - - - +
113A THR* 4.1 15.0 + - - -
129A PRO* 4.6 7.3 - - + +
132A PHE* 4.5 6.7 - - + -
133A THR* 3.8 23.1 - - + +
136A LEU* 3.7 27.6 - - + -
259A LEU* 3.3 13.9 - - + +
260A ILE* 1.4 84.2 - - - +
262A CYS* 1.3 65.3 + - - +
288A LEU* 3.8 10.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A PHE* 3.7 7.8 - - - -
129A PRO* 5.3 6.3 - - - -
260A ILE* 4.3 13.2 - - + -
261A PRO* 1.3 77.1 - - - +
263A ALA* 1.3 77.7 + - - +
266A GLN* 3.9 22.0 - - + -
267A ASP 5.3 0.2 - - - -
270A PHE* 4.3 19.3 - - + -
287A LEU* 4.5 9.6 - - - -
288A LEU 2.8 21.7 + - - +
289A HIS* 4.7 5.4 - - - -
290A SER* 2.9 14.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A CYS* 1.3 88.2 - - - +
264A ILE* 1.3 61.4 + - + +
265A ASP* 3.8 9.2 - - + +
266A GLN* 3.7 27.2 + - - +
289A HIS* 3.0 17.5 - - - -
290A SER* 3.5 21.3 + - - +
291A THR 5.0 4.7 - - - +
292A PHE* 5.6 4.7 - - + -
----------------------------------------------------------
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