Contacts of the strand formed by residues 125 - 130 (chain A) in PDB entry 3RCY
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 ILE 125 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ASN* 4.2 18.4 - - + +
124A ARG* 1.3 76.0 - - - +
126A ARG* 1.3 76.3 + - - +
127A ALA 3.4 0.2 + - - -
322A VAL* 3.4 42.6 - - + +
325A ALA* 4.0 10.5 - - + -
326A ALA* 3.7 17.0 - - + +
331A ILE* 4.4 11.9 - - + -
334A CYS* 3.8 25.6 - - + -
356A TYR* 3.3 5.5 - - - -
357A ILE* 2.8 48.3 + - + +
359A PRO* 4.1 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ARG 4.0 1.6 + - - -
125A ILE* 1.3 77.0 - - - +
127A ALA* 1.3 56.2 - - - +
162A THR* 2.7 45.0 + - - +
163A ALA* 4.0 1.0 - - - +
204A ASP* 2.8 29.5 + - - -
231A LEU* 4.4 3.2 - - - +
331A ILE* 5.9 1.2 - - - +
332A LEU* 3.7 30.0 + - - +
333A MET* 3.1 32.3 - - + +
334A CYS 2.8 30.1 + - - -
355A GLY 4.9 0.2 - - - +
356A TYR* 3.6 22.8 - - + -
179B MET* 5.1 1.0 - - - +
395B TYR* 3.4 51.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ILE 3.4 0.4 + - - -
126A ARG* 1.3 81.3 - - - +
128A TYR* 1.3 64.5 + - - +
161A TYR* 3.8 10.0 - - + -
162A THR* 4.3 9.5 + - - -
163A ALA* 4.6 1.2 + - - +
333A MET* 4.7 1.8 - - - -
334A CYS 3.4 5.2 - - - +
336A SER* 3.8 18.2 - - - +
352A VAL* 4.0 19.1 - - + -
355A GLY 3.0 24.9 + - - +
357A ILE* 3.9 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ALA* 1.3 77.1 - - - +
129A THR* 1.3 74.6 - - - +
161A TYR* 3.8 7.0 - - - -
163A ALA* 3.4 17.9 - - + +
165A LYS* 2.8 45.6 + - + -
206A LEU* 3.4 15.3 - - + -
232A TRP* 3.5 25.8 - + - -
281A GLN* 4.4 2.8 + - - -
308A ALA* 5.1 3.5 + - + -
309A PRO 5.2 0.8 + - - -
333A MET* 3.4 35.2 - - + -
334A CYS 3.1 6.7 + - - -
335A GLU* 3.1 48.4 + - + +
336A SER* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A TYR* 1.3 85.2 - - - +
130A TYR* 1.3 82.6 + - - +
132A TYR* 3.4 16.8 - - - -
156A CYS* 3.7 25.6 - - + -
159A ARG* 4.4 4.6 + - - +
161A TYR* 3.9 30.1 - - + -
163A ALA 3.9 2.5 + - - +
164A VAL* 3.5 5.2 - - + -
165A LYS 3.0 21.1 + - - -
335A GLU* 5.6 0.2 - - - -
336A SER 3.4 14.8 + - - +
337A ILE* 4.9 1.4 - - - -
338A GLU 5.2 2.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A TYR* 4.5 1.6 - - - -
129A THR* 1.3 95.1 + - - +
131A LEU* 1.3 65.9 + - - +
132A TYR* 3.4 42.4 + + + -
143A TRP* 6.1 4.5 - + + -
156A CYS* 4.6 1.2 - - - -
165A LYS* 3.3 47.8 + - + +
166A PHE* 4.2 9.6 - - - -
167A ASP* 4.8 1.6 - - + -
208A GLY 4.2 3.5 + - - -
210A HIS* 3.1 35.8 + + - -
234A GLU* 5.4 1.4 + - - -
312A TYR* 4.3 21.8 - + + -
335A GLU* 3.8 22.5 + - + +
336A SER 4.7 1.4 + - - -
337A ILE* 6.2 0.4 - - + -
----------------------------------------------------------
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