Contacts of the strand formed by residues 201 - 205 (chain C) in PDB entry 5HMG
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 201 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ASN* 4.6 18.0 - - - +
216A ASN* 5.6 1.1 - - - +
217A ILE* 3.2 41.4 + - - +
218A GLY* 5.1 0.8 - - - -
163C VAL* 4.6 12.5 - - - +
199C SER 5.1 0.2 - - - +
200C GLY* 1.3 76.0 - - - +
202C VAL* 1.3 64.1 + - - +
203C THR* 4.3 7.9 + - - +
212C THR* 4.0 20.4 - - + -
213C ILE 3.8 7.9 - - - -
214C ILE* 4.5 6.5 - - + -
215C PRO* 4.2 1.7 - - - +
246C ASN* 4.0 19.0 + - - +
247C SER* 2.9 28.6 + - - +
248C ASN* 3.2 39.7 + - - +
249C GLY 3.4 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 202 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C TRP* 3.8 26.9 - - + -
182C ILE* 3.7 23.8 - - + -
201C ARG* 1.3 79.7 - - - +
203C THR* 1.3 61.4 + - - +
204C VAL* 4.0 11.2 - - + -
211C GLN 3.7 0.7 - - - +
212C THR* 3.1 3.8 - - - +
213C ILE* 2.9 37.1 + - - +
245C ILE* 4.9 0.7 - - + -
246C ASN 3.7 5.2 - - - +
247C SER* 3.7 11.9 - - - +
249C GLY 3.8 6.3 - - - +
251C LEU* 3.8 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 203 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A ASN* 4.6 2.8 - - - +
217A ILE 4.7 3.6 + - - -
218A GLY* 5.3 4.5 - - - -
219A SER 5.1 3.4 - - - +
220A ARG* 4.0 22.2 + - - +
201C ARG* 4.3 9.2 + - - +
202C VAL* 1.3 70.2 - - - +
204C VAL* 1.3 65.6 + - - +
205C SER* 3.8 16.6 + - - +
210C GLN* 4.8 0.7 - - + -
211C GLN 3.1 9.6 - - - +
212C THR* 2.9 34.1 + - - +
244C VAL 3.8 1.6 - - - +
245C ILE* 3.7 0.5 - - - +
246C ASN* 2.9 45.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 204 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C TRP* 3.4 46.7 - - + +
202C VAL* 4.0 11.0 - - + -
203C THR* 1.3 77.1 - - - +
205C SER* 1.3 62.8 + - - +
209C SER* 5.6 0.2 + - - -
210C GLN* 3.4 2.1 - - - -
211C GLN* 2.9 31.7 + - - +
235C THR* 3.5 22.2 - - + +
243C LEU* 3.5 27.1 - - + -
244C VAL 3.5 4.3 - - - +
245C ILE* 4.1 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 205 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A SER 3.6 11.6 + - - -
220A ARG* 3.6 29.7 - - - +
221A PRO* 4.0 9.4 - - - -
203C THR* 3.8 8.8 + - - +
204C VAL* 1.3 77.3 - - - +
206C THR* 1.3 68.4 + - - +
209C SER* 3.3 13.9 - - - -
210C GLN* 4.0 4.5 - - - +
235C THR* 5.9 0.4 - - - -
243C LEU* 3.5 3.1 - - - +
244C VAL* 2.9 36.1 + - - +
----------------------------------------------------------
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