Contacts of the strand formed by residues 26 - 33 (chain G) 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 G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G VAL 4.6 6.1 - - - +
23G LEU* 2.9 10.2 + - - +
24G PRO* 4.2 2.6 - - - +
25G ALA* 1.3 78.2 - - + +
27G VAL* 1.3 66.8 + - - +
67G GLY 3.4 15.3 - - - +
68G VAL* 4.9 4.0 - - + -
95G ASN* 4.9 5.7 + - - +
127G ILE* 5.2 3.4 - - + -
144G VAL* 3.5 52.0 - - + +
145G GLY* 4.4 4.3 - - - +
152G GLN* 2.8 24.7 - - + +
189G GLY* 4.6 1.6 - - - -
190G ALA* 3.7 27.8 - - + +
192G LEU* 5.2 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 27 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G PRO 4.4 2.5 - - - +
26G VAL* 1.3 78.9 - - - +
28G SER* 1.3 63.0 + - - +
29G VAL* 4.7 0.2 - - + -
66G SER* 3.5 7.1 - - - -
67G GLY* 3.0 43.4 + - - +
68G VAL 4.4 0.7 - - - +
69G ILE* 3.6 22.0 - - + -
77G VAL* 4.0 17.0 - - + -
92G ILE* 4.0 20.6 - - + -
93G GLN 3.5 10.8 - - - +
94G LEU* 3.4 33.9 - - + +
145G GLY* 5.7 0.5 - - - -
146G ASN* 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 28 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G VAL* 1.3 75.7 - - - +
29G VAL* 1.3 62.4 + - - +
30G ARG* 4.0 3.5 + - - +
64G LEU* 4.1 10.7 - - - +
65G GLY 3.6 10.3 - - - -
66G SER* 4.9 0.2 - - - -
91G SER 3.9 0.3 - - - +
92G ILE* 3.4 6.1 - - - +
93G GLN* 2.9 51.7 + - - +
146G ASN* 3.2 28.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 29 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G VAL* 4.7 1.1 - - + -
28G SER* 1.3 73.7 - - - +
30G ARG* 1.4 60.4 + - - +
31G VAL* 4.2 4.2 + - + -
63G GLY 4.0 0.5 - - - +
64G LEU* 3.5 5.8 - - - +
65G GLY 2.8 38.5 + - - +
66G SER 3.3 29.2 - - - +
67G GLY* 3.8 8.1 - - - +
77G VAL* 4.8 0.9 - - + -
79G THR* 4.1 8.1 - - - +
83G VAL* 3.9 10.1 - - + +
84G ILE* 3.6 30.5 - - + -
90G ILE* 4.0 15.5 - - + -
91G SER 3.6 2.7 - - - +
92G ILE* 4.2 15.0 - - + -
116G LEU* 4.3 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 30 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G SER* 4.0 3.9 + - - +
29G VAL* 1.4 72.2 - - - +
31G VAL* 1.3 67.8 + - - +
32G GLU* 5.3 8.0 + - + +
62G GLU* 3.1 37.1 + - + +
63G GLY 3.6 7.6 - - - +
64G LEU* 4.4 19.3 - - + +
89G LYS 4.0 0.2 - - - +
90G ILE* 3.5 4.7 - - - +
91G SER* 2.8 55.0 + - - +
93G GLN* 6.3 1.8 - - + +
99G GLU* 5.9 3.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 31 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G VAL* 4.2 5.6 - - + +
30G ARG* 1.3 80.1 - - - +
32G GLU* 1.3 66.1 + - - +
61G PHE* 3.7 24.9 - - + -
62G GLU* 3.3 6.4 - - - +
63G GLY* 2.8 38.7 + - - +
83G VAL* 3.7 25.8 - - + +
84G ILE* 3.9 18.6 - - + -
86G GLN 5.8 0.2 - - - +
87G ALA* 3.7 32.5 - - + +
89G LYS 3.4 2.9 - - - -
90G ILE* 4.0 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 32 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G ARG* 5.3 10.2 + - + +
31G VAL* 1.3 81.3 - - - +
33G GLY* 1.3 52.5 + - - +
61G PHE 3.4 5.6 - - - +
62G GLU* 3.1 35.3 - - + +
87G ALA 3.7 0.3 - - - -
88G GLN* 2.8 32.1 + - - +
89G LYS* 2.9 43.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 33 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32G GLU* 1.3 75.6 - - - +
34G THR* 1.3 58.9 + - - -
60G PRO* 3.3 23.7 - - - +
61G PHE* 3.2 26.0 + - - +
86G GLN 3.7 9.9 - - - -
88G 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