Contacts of the strand formed by residues 87 - 94 (chain A) in PDB entry 2YUZ
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 LEU 87 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 5.9 0.4 - - + -
10A ILE* 3.7 46.4 - - + -
13A PRO* 3.7 22.0 - - + -
14A LEU* 3.4 25.0 - - + +
29A CYS* 4.8 8.5 - - + -
31A ILE* 5.3 7.6 - - + -
77A VAL* 3.4 6.1 - - - +
78A PHE* 2.9 49.2 + - + +
85A VAL* 4.1 16.6 - - + -
86A THR* 1.3 76.7 - - - +
88A PRO* 1.3 69.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 4.4 10.7 + - - +
76A TYR 3.8 4.5 - - - +
77A VAL* 4.1 11.4 - - + -
86A THR* 3.3 13.2 - - - +
87A LEU* 1.3 88.1 - - + +
89A ALA* 1.3 65.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 4.1 28.0 - - + -
15A THR 5.4 4.5 - - - +
16A ASP 5.7 1.1 - - - +
27A LEU* 5.5 6.5 - - + -
75A ASP* 3.7 12.5 - - - +
76A TYR* 2.9 43.7 + - + +
77A VAL* 4.8 0.2 - - - +
88A PRO* 1.3 78.9 - - - +
90A LYS* 1.3 62.5 + - - +
91A VAL* 6.1 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ASP* 3.2 39.0 - - + +
17A GLN 3.2 4.0 + - - -
74A GLY 4.5 7.6 - - - +
75A ASP* 4.6 14.4 - - - +
89A ALA* 1.3 76.2 - - - +
91A VAL* 1.3 69.7 + - - +
92A HIS* 3.9 27.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A GLN* 3.0 34.8 - - + +
18A THR* 5.1 0.2 - - - -
25A ILE* 5.6 7.9 - - + -
27A LEU* 4.8 11.2 - - + -
72A ASP* 3.8 17.0 - - - +
73A GLU* 4.2 1.0 - - - +
74A GLY 3.8 25.2 + - - +
76A TYR* 3.2 42.6 - - + +
89A ALA* 6.1 1.1 - - + -
90A LYS* 1.3 83.6 - - - +
92A HIS* 1.3 81.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A GLN 3.4 5.5 + - - +
18A THR* 3.6 25.8 - - + +
19A VAL* 3.2 25.5 + - - +
72A ASP* 4.5 5.6 - - - +
73A GLU* 4.4 21.0 - - - +
74A GLY 5.8 0.4 - - - -
90A LYS* 3.9 26.1 - - + +
91A VAL* 1.3 92.9 + - - +
93A VAL* 1.3 62.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A VAL* 3.3 5.6 - - + +
20A ASN 4.0 1.6 - - - +
21A LEU* 3.6 42.6 - - + +
68A ALA* 4.1 7.9 - - + +
70A THR* 4.0 15.3 - - + -
72A ASP* 3.2 31.4 + - - +
73A GLU* 3.8 20.2 - - + +
92A HIS* 1.3 75.1 - - - +
94A ILE* 1.3 67.4 + - - +
95A SER 3.8 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A THR* 5.0 13.0 - - + -
19A VAL* 3.2 12.9 + - - +
20A ASN* 3.2 39.2 - - - +
21A LEU* 3.0 27.6 + - - +
92A HIS* 6.4 0.2 - - + -
93A VAL* 1.3 75.6 - - - +
95A SER* 1.3 79.5 + - - +
----------------------------------------------------------
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