Contacts of the strand formed by residues 69 - 75 (chain A) in PDB entry 2HRC
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 THR 69 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LYS* 1.3 80.1 + - - +
70A GLY* 1.3 62.6 + - - +
71A ILE* 3.8 6.9 - - + +
154A THR* 2.6 35.1 + - - -
156A PRO 3.1 4.1 + - - +
157A HIS* 3.2 21.3 - - + +
158A LYS* 2.9 26.2 + - - +
182A LEU* 4.0 3.3 - - - +
184A ARG* 3.6 34.6 + - + +
186A ILE* 4.2 15.3 - - + -
389A ILE* 4.8 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A THR* 1.3 74.7 - - - +
71A ILE* 1.3 63.3 + - - +
72A LEU 3.9 0.4 - - - -
158A LYS 3.2 7.2 - - - -
160A TYR* 3.8 4.5 - - - -
177A MET* 3.8 4.6 - - - +
182A LEU* 3.5 24.1 - - - +
184A ARG 2.9 10.9 + - - +
185A ALA* 3.4 2.9 - - - -
186A ILE* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A THR* 3.8 12.8 - - + +
70A GLY* 1.3 76.5 - - - +
72A LEU* 1.3 61.1 + - - +
73A MET* 3.4 4.4 + - + +
143A MET* 3.6 25.8 - - + -
144A VAL* 5.0 0.7 - - + -
147A LEU* 3.8 29.8 - - + -
157A HIS* 4.0 15.7 - - + +
158A LYS 2.8 21.4 + - - +
159A TYR* 3.3 3.5 - - - +
160A TYR* 2.9 26.8 + - - +
186A ILE* 3.7 10.1 - - + +
188A PHE* 3.8 33.2 - - + -
385A VAL* 4.2 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A GLY 3.9 2.0 + - - -
71A ILE* 1.3 69.2 - - - +
73A MET* 1.3 59.8 + - - +
74A LEU* 3.4 24.6 + - + +
160A TYR* 3.4 19.5 - - + +
162A GLY* 3.7 13.9 - - - +
170A THR* 4.5 2.9 - - + -
173A ALA* 3.5 29.4 - - + -
174A ILE* 4.3 11.9 - - + -
177A MET* 4.0 16.1 - - + +
186A ILE 2.8 16.3 + - - +
187A ALA* 3.8 2.6 - - - -
188A PHE* 2.8 30.7 + - - +
206A ILE* 4.1 11.0 - - + -
221A TRP* 3.7 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ILE* 4.1 15.7 - - + +
72A LEU* 1.3 70.8 - - - +
74A LEU* 1.3 62.4 + - - +
75A ASN* 4.0 1.3 + - - +
136A THR* 3.8 36.0 - - + +
139A GLN* 4.4 4.3 - - + +
140A GLY* 3.7 28.5 - - - +
143A MET* 4.2 9.6 - - + -
159A TYR* 4.0 13.9 - - - -
160A TYR 2.7 14.8 + - - +
161A ILE* 3.8 4.0 - - - +
162A GLY 2.9 26.4 + - - +
163A PHE* 5.3 0.3 - - - -
188A PHE 3.5 5.6 - - - -
190A GLN* 3.7 35.7 - - + +
381A LEU* 4.2 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LEU* 3.7 34.5 - - + +
73A MET* 1.3 71.8 - - - +
75A ASN* 1.3 62.4 + - - +
162A GLY 3.5 12.8 - - - +
170A THR* 4.0 16.8 - - + -
187A ALA* 3.9 32.8 - - + -
188A PHE 3.1 7.0 + - - +
189A THR* 3.9 16.8 + - - +
190A GLN* 2.9 33.2 + - - +
191A TYR* 4.5 1.7 - - - -
199A THR 5.6 0.2 - - - +
202A SER* 3.8 28.9 - - - +
203A LEU* 4.1 13.5 - - + -
206A ILE* 4.2 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A MET 4.0 0.8 + - - +
74A LEU* 1.3 77.2 - - - +
76A MET* 1.3 66.0 + - - +
77A GLY 3.2 4.7 + - - +
132A ILE* 4.2 12.3 - - - +
136A THR* 4.7 5.1 + - + +
162A GLY 3.4 4.3 + - - +
163A PHE* 3.2 25.0 - - + -
164A ARG* 3.0 18.2 + - - +
190A GLN* 3.8 19.3 - - + +
191A TYR* 2.8 35.7 + - - -
202A SER* 4.2 6.6 + - - -
337A PHE* 3.2 31.5 - - - -
338A THR* 5.8 1.2 + - - -
339A SER* 6.0 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