Contacts of the strand formed by residues 149 - 154 (chain D) in PDB entry 4CQM
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 GLY 149 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D SER* 3.2 14.8 - - - -
142D LEU* 4.0 11.4 - - - -
148D ARG* 1.3 79.3 - - - +
150D SER* 1.3 61.8 + - - -
191D GLY 3.3 5.4 + - - +
192D ILE* 3.3 9.0 - - - +
193D ARG* 2.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 150 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D SER 2.7 11.1 + - - +
99D VAL* 3.5 4.1 - - - +
100D VAL* 3.1 22.9 + - - -
142D LEU* 5.0 1.2 - - - +
149D GLY* 1.3 73.9 - - - -
151D ILE* 1.3 63.3 + - - +
152D ILE* 3.8 11.4 + - - +
193D ARG* 3.4 26.4 + - - +
195D ASN* 5.1 1.6 + - - -
240D LEU* 2.7 30.8 + - - +
241D ALA* 4.2 13.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 151 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D VAL* 3.7 22.7 - - + +
102D SER* 5.7 0.2 - - - +
135D THR* 3.9 39.3 - - + +
138D ALA* 4.9 1.8 - - + -
139D ALA* 4.4 8.5 - - + +
142D LEU* 5.2 3.1 - - + -
150D SER* 1.3 74.0 + - - +
152D ILE* 1.3 64.2 + - - +
153D ASN* 3.7 22.2 - - - +
187D LEU* 3.8 17.3 - - + -
192D ILE* 3.8 13.9 - - + -
193D ARG 2.5 13.4 + - - +
194D CYS* 3.3 22.9 - - + -
195D ASN* 2.9 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 152 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D VAL* 4.5 2.2 - - + -
100D VAL 2.7 13.0 + - - +
101D VAL* 3.3 12.9 - - + +
102D SER 3.0 25.1 + - - -
150D SER* 3.9 13.2 - - - +
151D ILE* 1.3 76.9 - - - +
153D ASN* 1.3 63.8 + - - +
154D ILE* 4.4 4.0 - - + -
195D ASN* 3.5 3.4 - - + +
197D VAL* 3.8 28.5 - - + -
237D VAL* 3.3 47.8 - - + +
240D LEU* 3.7 16.6 - - + -
241D ALA* 3.6 22.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 153 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D VAL 5.1 0.2 - - - +
102D SER* 3.5 17.0 + - - -
131D THR* 3.5 15.7 - - + +
135D THR* 3.4 23.6 + - - +
151D ILE* 3.7 14.3 - - - +
152D ILE* 1.3 75.9 - - - +
154D ILE* 1.3 63.0 + - - +
155D SER 3.6 0.9 + - - -
176D VAL* 3.7 18.4 - - + -
179D LEU* 4.3 3.0 - - - +
180D THR* 2.7 36.0 + - - +
194D CYS* 5.6 0.4 - - - +
195D ASN 3.0 8.8 + - - +
196D SER* 3.2 5.0 - - - +
197D VAL* 2.8 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 154 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D ILE* 4.7 13.2 - - + -
101D VAL* 4.4 6.3 - - + -
102D SER 3.2 26.4 + - - +
103D CYS* 3.6 25.6 - - + -
131D THR* 5.7 0.7 + - - +
152D ILE* 4.4 1.6 - - + -
153D ASN* 1.3 73.1 - - - +
155D SER* 1.3 68.4 + - - +
173D LYS* 3.1 22.4 + - - +
176D VAL* 4.8 4.2 - - - +
197D VAL* 3.7 29.6 - - + -
199D PRO* 3.9 19.7 - - + -
233D VAL* 4.7 4.5 - - + -
237D VAL* 4.0 18.8 - - + -
----------------------------------------------------------
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