Contacts of the strand formed by residues 151 - 157 (chain G) in PDB entry 3PHW
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 151 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B GLN* 3.7 14.0 + - - -
37B PRO* 3.5 24.2 - - + +
38B PRO* 4.2 8.7 - - + +
39B ASP* 2.8 26.7 + - - +
34G GLN 3.9 6.0 + - - -
35G PRO 3.8 21.1 - - - -
40G CYS* 3.9 10.1 - - + -
145G LEU 3.3 0.7 - - - +
146G HIS* 3.2 7.3 + - - -
147G SER* 2.8 36.0 + - - +
150G THR* 1.3 81.6 - - - +
152G PHE* 1.3 83.4 + - - +
153G ASP* 3.0 34.9 + - - -
75H GLY* 3.7 2.4 - - - -
76H NEH 4.1 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 152 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G GLN* 4.1 1.4 - - - +
40G CYS* 3.3 17.9 - - - +
41G PHE* 3.7 42.4 - + + -
44G SER* 3.5 8.7 + - - +
100G GLY 3.6 10.8 - - - -
101G SER* 4.4 3.1 - - - -
118G ILE* 3.7 35.7 - - + -
144G LEU* 4.3 14.6 - - + -
145G LEU 3.2 6.7 - - - -
146G HIS* 3.7 23.8 - - + -
151G HIS* 1.3 89.0 + - - +
153G ASP* 1.3 64.1 - - - +
73H LEU* 3.9 16.6 - - + -
75H GLY* 3.5 38.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 153 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B GLN* 3.3 8.8 + - - +
31G ILE* 4.2 10.1 - - + -
32G VAL 3.8 6.5 - - - +
33G ARG* 2.8 36.9 + - - -
34G GLN* 2.9 26.9 + - - -
44G SER* 3.1 11.3 + - - -
144G LEU* 3.5 6.9 - - - +
145G LEU* 2.9 38.4 + - + +
147G SER* 4.5 3.1 + - - -
151G HIS* 3.0 22.2 + - - -
152G PHE* 1.3 70.6 - - - +
154G ALA* 1.3 64.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 154 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31G ILE* 3.8 1.6 - - - +
32G VAL* 2.9 36.9 + - + +
34G GLN* 4.0 3.3 - - - +
44G SER* 3.4 26.9 + - - +
47G GLU* 3.9 24.0 - - + -
48G LEU* 4.0 11.7 - - + -
143G ASN 4.0 3.8 - - - -
153G ASP* 1.3 75.7 - - - +
155G LEU* 1.3 68.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 155 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G ILE* 3.9 24.0 - - + -
29G PHE* 3.7 18.2 - - + -
30G GLU 3.4 11.0 - - - +
31G ILE* 4.0 19.7 - - + -
32G VAL 4.8 0.2 - - - +
48G LEU* 3.4 22.3 - - - +
119G TRP* 3.6 30.1 - - + -
143G ASN* 2.9 24.6 + - + +
144G LEU 3.7 14.1 - - - +
145G LEU* 3.8 24.0 - - + +
154G ALA* 1.3 81.5 - - - +
156G ARG* 1.3 63.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 156 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G PHE* 3.4 4.2 - - - -
30G GLU* 2.7 61.6 + - - +
32G VAL* 3.9 20.4 - - + +
47G GLU* 3.1 42.6 + - - +
48G LEU* 3.7 22.6 + - + +
155G LEU* 1.3 78.5 - - - +
157G ILE* 1.3 66.0 + - - +
162G GLU* 5.6 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 157 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G LEU* 5.5 5.8 - - + -
28G TYR 3.7 8.7 - - - +
29G PHE* 3.6 23.2 - - + -
30G GLU* 5.4 0.7 - - - +
138G VAL* 3.6 31.2 - - + +
139G PHE* 3.6 32.8 - - + +
143G ASN* 4.5 4.0 - - - +
156G ARG* 1.3 76.5 - - - +
158G LEU* 1.3 77.3 + - - +
159G PRO* 3.7 1.6 - - - +
161G PHE* 3.7 27.4 - - + +
162G GLU* 3.5 27.0 + - + +
----------------------------------------------------------
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