Contacts of the strand formed by residues 59 - 64 (chain G) in PDB entry 2YHT
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 ILE 59 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G ILE* 3.6 26.2 - - + -
25G TYR 3.6 8.3 - - - +
26G LEU* 4.1 0.9 - - + -
27G VAL* 4.3 1.6 - - - -
44G ILE* 3.7 31.6 - - + -
54G VAL* 3.5 22.9 - - + -
55G TYR 3.4 11.7 - - - +
56G LYS* 2.9 17.8 + - - +
58G ALA* 1.3 78.9 - - - +
60G SER* 1.3 62.8 + - - +
61G THR 3.7 10.1 - - - +
62G VAL* 3.9 8.1 - - + -
55H TYR* 3.5 27.3 - - + +
57H HIS* 3.0 24.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 60 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G TYR* 2.7 28.9 + - - +
26G LEU 3.7 11.4 + - - -
27G VAL* 4.5 5.2 - - - -
58G ALA 3.7 2.2 + - - -
59G ILE* 1.3 75.0 - - - +
61G THR* 1.3 65.8 + - - +
26H LEU* 4.0 23.6 - - - +
27H VAL* 5.9 0.2 - - - -
28H ASN* 4.2 4.9 + - - -
54H VAL* 3.5 5.3 - - - +
55H TYR* 2.8 28.9 + - - +
58H ALA* 3.4 23.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 61 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G SER 3.7 1.7 - - - +
24G ILE* 3.7 1.7 - - - -
25G TYR* 2.8 57.6 + - + +
59G ILE* 3.7 2.1 - - - +
60G SER* 1.3 88.4 + - - +
62G VAL* 1.3 62.3 + - - +
63G VAL* 4.1 6.5 - - + +
26H LEU* 5.1 2.9 - - + -
32H LEU* 4.4 15.0 - - + -
52H GLN* 3.6 27.9 - - - +
53H MET 3.0 16.9 + - - -
54H VAL* 3.7 9.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 62 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G PHE* 3.9 3.6 - - + -
12G LEU* 4.4 10.3 - - + -
15G LEU* 4.1 25.4 - - + -
22G VAL* 4.6 6.3 - - + -
23G SER 3.7 3.1 - - - +
24G ILE* 4.5 20.4 - - + +
36G ILE* 4.6 6.1 - - + -
44G ILE* 4.9 1.6 - - + -
59G ILE* 3.9 20.6 - - + -
61G THR* 1.3 74.1 + - - +
63G VAL* 1.3 61.8 + - - +
64G PRO* 3.4 7.4 - - - +
52H GLN* 3.5 0.7 - - - -
53H MET* 2.8 59.8 + - + +
55H TYR* 4.0 4.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 63 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G VAL* 4.5 2.0 - - - -
23G SER* 2.8 40.1 + - - +
25G TYR* 3.9 29.8 - - + -
61G THR* 4.1 5.8 - - + -
62G VAL* 1.3 76.8 - - - +
64G PRO* 1.3 77.0 - - - +
65G SER* 4.5 0.5 - - - -
50H VAL* 3.8 18.4 - - + -
52H GLN* 3.6 29.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 64 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G PHE* 3.8 17.5 - - + -
15G LEU* 3.5 24.9 - - + -
20G VAL* 4.3 2.0 - - + -
21G PRO 4.1 0.2 - - - +
22G VAL* 4.0 11.8 - - + -
62G VAL 3.4 8.3 - - - +
63G VAL* 1.3 90.0 - - + +
65G SER* 1.3 60.1 + - - +
66G ARG 3.2 20.4 + - - +
67G PRO* 5.8 0.7 - - + -
68G VAL* 4.4 4.3 - - + +
50H VAL* 3.6 22.0 - - + +
51H SER* 3.2 27.1 - - - +
----------------------------------------------------------
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