Contacts of the strand formed by residues 297 - 301 (chain C) in PDB entry 1SID
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 HIS 297 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B THR* 3.5 27.0 + - + +
152B GLY* 3.8 10.5 - - - -
153B ILE* 3.0 41.0 - - + +
79C ILE* 2.8 25.6 + - + +
247C THR 5.7 1.6 + - - -
288C TRP* 3.4 41.3 - + + -
289C ARG 3.2 6.1 - - - -
290C VAL* 4.0 29.2 - - + +
295C ASP* 3.3 9.8 + - - -
296C VAL* 1.3 76.6 - - - +
298C HIS* 1.3 64.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 298 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C TYR* 4.4 9.4 - + - -
75C TRP* 3.7 5.3 - + - -
76C SER* 2.8 23.6 + - - +
77C ARG 2.7 21.2 + - - +
78C GLY* 3.6 14.1 - - - -
79C ILE* 4.1 3.6 - - - -
289C ARG* 2.7 65.4 + - + +
291C THR* 3.8 7.0 - - + +
296C VAL* 4.0 8.7 - - + -
297C HIS* 1.3 79.9 - - - +
299C TRP* 1.3 65.8 + - - +
3I SIA 3.2 34.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 299 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LEU* 3.7 24.4 - - + +
138B VAL* 4.1 7.0 - - + -
139B HIS* 6.2 0.7 - + - -
57C MET* 3.9 3.9 - - - +
75C TRP* 3.0 4.5 - - - -
76C SER* 2.5 66.3 + - - -
79C ILE* 3.2 29.6 - - + -
94C THR* 3.2 26.7 - - + -
96C PRO* 3.4 25.1 - - + -
225C GLU* 5.1 2.9 - - - -
285C ILE* 3.3 39.3 - - + +
287C GLY 2.8 20.0 - - - +
288C TRP* 2.9 45.4 - + + +
298C HIS* 1.3 74.7 - - - +
300C ARG* 1.3 56.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 300 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C MET* 3.5 7.4 - - - +
73C TYR 4.2 0.4 + - - -
74C GLY* 2.6 35.4 + - - -
75C TRP* 3.0 44.2 - - - +
134C SER* 3.9 14.4 + - - -
135C LEU* 5.0 10.1 - - + -
157C VAL* 5.2 9.4 - - + -
285C ILE* 3.8 2.6 - - - +
286C MET* 2.8 40.0 + - + +
287C GLY 2.9 11.9 + - - +
288C TRP* 4.6 0.2 - - - +
289C ARG* 4.8 0.6 - - + +
299C TRP* 1.3 74.6 - - - +
301C GLY* 1.3 81.2 + - - +
302C LEU* 3.9 20.3 - - + +
177D LEU* 5.2 2.2 - - - +
178D VAL 3.3 12.2 + - - -
179D THR* 4.3 5.9 - - - +
206D GLN 2.4 30.8 + - - -
207D VAL* 4.3 5.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 301 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C PRO* 3.8 12.7 - - - +
57C MET* 3.0 21.8 - - - +
284C ASP 3.0 16.4 - - - -
286C MET* 4.1 2.5 - - - -
300C ARG* 1.3 102.0 + - - +
302C LEU* 1.3 64.5 + - - -
----------------------------------------------------------
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