Contacts of the strand formed by residues 25 - 31 (chain B) in PDB entry 1PQ3
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 SER 25 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B HIS* 1.3 84.0 + - - +
26B VAL* 1.3 62.8 + - - +
64B HIS* 3.4 24.2 - - - -
109B ASP 5.4 0.5 + - - -
110B GLY 3.6 17.7 + - - -
111B TYR* 3.8 20.5 - - - -
112B SER* 3.1 26.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B HIS* 4.5 3.6 - - + +
25B SER* 1.3 79.4 - - - +
27B ALA* 1.3 66.6 + - - +
28B VAL* 4.4 2.4 - - + +
58B LEU* 4.3 16.4 - - + -
63B CYS* 4.1 19.7 - - + -
64B HIS 2.8 9.8 + - - +
65B LEU* 3.5 14.2 - - + +
66B LYS 3.1 21.5 + - - -
111B TYR* 3.8 5.4 - - - -
112B SER 3.5 4.9 - - - +
114B VAL* 3.5 30.1 - - + -
323B PHE* 3.6 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B VAL* 1.3 76.2 - - - +
28B VAL* 1.3 62.8 + - - +
66B LYS 3.2 5.2 - - - -
68B PHE* 3.6 25.8 - - + -
106B ALA* 4.0 9.2 - - + -
111B TYR* 3.6 24.6 - - + -
112B SER 2.9 8.7 + - - +
113B CYS* 4.5 6.1 - - - -
114B VAL* 2.8 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B VAL* 4.4 4.3 - - + +
27B ALA* 1.3 79.7 - - - +
29B ILE* 1.3 65.8 + - - +
50B ARG* 4.1 14.8 - - - +
54B LEU* 4.5 5.4 - - + -
55B MET* 3.3 42.0 - - + -
58B LEU* 4.1 20.0 - - + -
65B LEU* 5.3 2.5 - - + -
66B LYS 3.0 8.3 + - - +
67B ASP* 3.4 4.3 - - - +
68B PHE 2.9 25.8 + - - -
114B VAL* 3.4 12.6 - - + +
116B LEU* 4.2 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B VAL* 1.3 83.0 - - - +
30B GLY* 1.3 65.0 + - - +
31B ALA 3.8 1.0 + - - +
68B PHE* 4.0 16.4 - - + -
69B GLY 3.8 3.1 - - - +
71B LEU* 3.7 38.1 - - + -
99B LEU* 4.3 7.4 - - + -
102B VAL* 3.5 23.6 - - + +
103B VAL* 3.9 16.8 - - + -
106B ALA* 4.8 1.3 - - + -
113B CYS* 3.3 32.1 - - - -
114B VAL 2.8 10.9 + - - +
115B THR* 3.3 7.0 - - + +
116B LEU* 2.8 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ILE* 1.3 75.4 - - - +
31B ALA* 1.3 56.7 + - - -
32B PRO* 3.1 7.4 - - - +
46B PRO* 4.2 8.3 - - - -
50B ARG* 4.7 2.0 - - - +
69B GLY 3.0 11.5 + - - -
70B ASP* 3.8 19.2 + - - -
71B LEU* 2.7 34.7 + - - +
116B LEU* 3.8 9.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ILE 3.8 0.4 + - - -
30B GLY* 1.3 72.6 - - - -
32B PRO* 1.3 51.3 - - - +
33B PHE 2.7 18.2 + - - -
46B PRO* 3.9 2.4 - - - +
71B LEU* 5.4 0.4 - - + -
73B PHE* 3.8 21.8 - - + -
99B LEU* 4.4 6.7 - - + -
115B THR* 4.0 15.0 - - + -
116B LEU 2.6 17.4 + - - +
118B GLY 3.0 18.2 + - - -
122B LEU* 3.5 22.5 - - + +
----------------------------------------------------------
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