Contacts of the strand formed by residues 26 - 33 (chain J) in PDB entry 3STJ
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 VAL 26 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22J VAL* 4.8 6.1 - - + +
23J LEU* 3.0 10.5 + - - +
24J PRO 4.0 3.5 - - - +
25J ALA* 1.3 80.3 - - + +
27J VAL* 1.3 66.2 + - - +
67J GLY 3.3 17.3 - - - +
68J VAL* 4.8 4.0 - - + -
95J ASN 4.7 7.1 + - - -
127J ILE* 5.2 3.6 - - + -
144J VAL* 3.7 50.5 - - + +
145J GLY* 4.5 3.1 - - - +
152J GLN* 3.0 22.7 - - + +
189J GLY* 4.6 2.7 - - - -
190J ALA* 3.7 29.2 - - + +
192J LEU* 5.3 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 27 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24J PRO 4.6 0.4 - - - +
25J ALA 3.9 0.7 - - - +
26J VAL* 1.3 80.5 - - - +
28J SER* 1.3 61.5 + - - +
29J VAL* 4.1 7.6 - - + -
66J SER* 3.4 9.5 - - - -
67J GLY* 3.0 48.8 + - - +
68J VAL* 5.0 0.2 - - - -
69J ILE* 3.7 24.0 - - + -
77J VAL* 4.0 15.5 - - + -
92J ILE* 4.0 15.3 - - + -
93J GLN 3.6 9.2 - - - +
94J LEU* 3.6 30.3 - - + -
145J GLY* 5.6 0.3 - - - -
146J ASN* 4.4 3.0 - - - +
152J GLN* 5.8 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 28 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27J VAL* 1.3 76.0 - - - +
29J VAL* 1.3 63.8 + - - +
30J ARG* 4.0 3.3 + - - +
64J LEU* 3.7 19.8 - - - +
65J GLY 3.6 4.9 - - - -
91J SER 3.8 0.2 - - - +
92J ILE* 3.3 7.1 - - - +
93J GLN* 2.9 52.6 + - - +
146J ASN* 3.2 22.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 29 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27J VAL* 4.1 7.2 - - + -
28J SER* 1.3 77.9 + - - +
30J ARG* 1.3 60.3 + - - +
31J VAL* 4.1 3.7 + - + +
63J GLY 4.0 0.5 - - - +
64J LEU* 3.5 3.8 - - - +
65J GLY 2.8 38.5 + - - +
66J SER 3.5 30.3 - - - +
67J GLY* 3.7 9.6 - - - +
77J VAL* 4.7 1.1 - - + -
79J THR* 4.4 3.6 - - - +
83J VAL* 4.5 7.0 - - + +
84J ILE* 3.8 20.4 - - + -
90J ILE* 3.7 27.4 - - + -
91J SER 3.5 1.8 - - - -
92J ILE* 3.8 12.6 - - + -
116J LEU* 3.9 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 30 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28J SER* 4.0 4.6 + - - +
29J VAL* 1.3 73.2 - - - +
31J VAL* 1.3 67.0 + - - +
32J GLU* 5.3 8.4 + - + +
62J GLU* 3.1 35.7 + - + +
63J GLY 3.6 7.4 - - - +
64J LEU* 4.4 19.5 - - + +
89J LYS 3.9 0.2 - - - +
90J ILE* 3.4 4.5 - - - +
91J SER* 2.8 55.7 + - - +
92J ILE 6.3 0.2 - - - -
93J GLN* 6.5 1.1 - - + -
99J GLU* 6.2 2.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 31 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29J VAL* 4.5 4.0 - - + +
30J ARG* 1.3 79.4 - - - +
32J GLU* 1.3 64.7 + - - +
61J PHE* 3.7 26.7 - - + -
62J GLU* 3.3 6.4 - - - +
63J GLY* 2.9 39.4 + - - +
83J VAL* 3.7 27.8 - - + +
84J ILE* 3.9 19.1 - - + -
87J ALA* 3.7 29.6 - - + +
89J LYS 3.4 2.7 - - - -
90J ILE* 3.9 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 32 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30J ARG* 5.3 10.8 + - + +
31J VAL* 1.3 81.0 - - - +
33J GLY* 1.3 52.4 + - - +
61J PHE 3.4 6.1 - - - +
62J GLU* 3.1 34.2 - - + +
88J GLN* 2.7 31.2 + - - +
89J LYS* 2.9 43.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 33 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32J GLU* 1.3 74.5 - - - +
34J THR* 1.4 58.9 - - - -
60J PRO* 3.3 23.2 - - - +
61J PHE* 3.2 27.2 + - - +
86J GLN 3.7 9.9 - - - -
88J GLN* 3.7 18.8 - - - +
----------------------------------------------------------
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