Contacts of the strand formed by residues 146 - 152 (chain A) in PDB entry 1H9D
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 PHE 146 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ALA* 4.0 13.9 - - + -
108A GLY* 3.7 24.7 - - - -
109A ASN* 4.1 4.7 - - - -
112A ASN* 3.9 13.2 - - + -
115A ALA* 3.3 28.5 - - + -
136A PHE* 4.3 13.2 - + - -
138A GLY 3.2 17.5 - - - -
139A ARG 3.1 30.1 - - - -
140A SER* 3.4 21.5 - - - -
145A SER* 1.3 75.0 - - - +
147A THR* 1.3 62.0 + - - +
148A LEU* 4.0 1.6 - - + -
164A ARG 3.4 2.1 + - - -
165A ALA* 2.9 27.4 + - - +
166A ILE* 2.7 21.0 + - + +
168A ILE* 3.9 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ALA* 3.4 2.9 - - - -
108A GLY 2.8 34.2 + - - -
109A ASN* 5.1 4.1 - - - +
145A SER 3.9 2.5 + - - -
146A PHE* 1.3 75.2 - - - +
148A LEU* 1.3 73.3 + - - +
149A THR* 4.0 3.6 + - - +
161A THR* 4.6 5.2 - - + -
162A TYR 3.4 7.9 - - - +
163A HIS* 3.4 41.8 - - + +
164A ARG 3.9 6.3 + - - +
60B THR 5.5 2.8 + - - -
61B GLY 5.1 2.3 - - - +
62B THR* 5.1 13.5 - - - +
63B ASN 6.0 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 3.8 26.5 - - + -
89A PHE* 4.2 15.9 - - + -
105A VAL* 4.3 12.8 - - + -
106A MET 3.4 3.8 - - - +
107A ALA* 3.6 24.2 - - + -
134A LEU* 5.9 0.4 - - + -
136A PHE* 3.7 21.5 - - + -
146A PHE* 4.5 5.8 - - + -
147A THR* 1.3 78.4 - - - +
149A THR* 1.3 64.9 + - - +
150A ILE* 4.1 5.8 - - + -
161A THR* 3.1 11.5 - - - -
162A TYR* 2.8 50.9 + - + +
165A ALA* 3.8 13.5 - - + -
166A ILE* 4.7 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A THR 3.6 1.6 - - - +
105A VAL* 3.4 4.0 - - - -
106A MET* 2.7 47.7 + - + +
147A THR* 5.0 3.3 + - - +
148A LEU* 1.3 77.0 + - - +
150A ILE* 1.3 62.3 + - - +
151A THR* 3.8 12.5 + - - +
159A VAL* 3.6 26.7 - - + -
160A ALA 3.8 2.2 - - - -
161A THR* 4.1 10.3 - - + +
62B THR* 4.3 3.1 - - - +
63B ASN* 2.6 43.1 + - - +
64B LEU* 4.2 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A THR* 4.3 13.5 - - + -
70A PHE* 5.6 1.1 - - + -
72A CYS* 4.0 31.2 - - + -
89A PHE* 4.2 7.6 - - + -
91A VAL* 3.7 34.3 - - + -
103A VAL* 4.0 11.0 - - + -
104A THR 3.4 3.8 - - - +
105A VAL* 4.4 15.0 - - + -
148A LEU* 4.9 7.9 - - + -
149A THR* 1.3 74.7 - - - +
151A THR* 1.3 60.9 + - - +
152A VAL* 4.3 6.4 + - + +
158A GLN 4.0 0.3 - - - +
159A VAL* 3.4 3.5 - - - +
160A ALA* 2.7 48.6 + - + +
162A TYR* 5.1 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A VAL* 3.2 5.5 - - - +
104A THR* 3.0 41.6 + - - -
106A MET* 4.1 12.3 - - - +
149A THR* 3.8 17.3 + - - +
150A ILE* 1.3 73.8 + - - +
152A VAL* 1.3 64.0 + - - +
153A PHE* 3.6 29.1 - - + -
157A PRO* 4.1 11.9 - - + -
158A GLN 3.5 2.9 - - - +
159A VAL* 4.0 20.1 - - + +
65B SER* 4.4 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A PHE* 3.5 42.8 - - + -
91A VAL* 4.5 2.7 - - + -
97A VAL* 4.4 10.5 - - + -
101A THR* 3.7 19.7 - - + -
102A LEU 3.6 3.1 - - - +
103A VAL* 3.9 24.2 - - + -
124A MET* 4.6 2.0 - - + -
150A ILE* 4.5 7.9 - - + -
151A THR* 1.3 75.9 - - - +
153A PHE* 1.3 60.5 + - - +
154A THR* 3.0 17.8 + - + +
157A PRO* 3.3 1.6 - - - +
158A GLN* 2.7 39.9 + - + +
----------------------------------------------------------
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