Contacts of the strand formed by residues 104 - 109 (chain A) in PDB entry 2E7Y
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 PHE 104 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LEU* 4.5 6.1 - - + -
61A VAL* 3.4 35.4 - - + -
75A LEU* 3.1 23.1 - - + +
77A VAL* 4.0 15.7 - - + -
90A THR* 3.9 19.3 - - + -
93A ILE* 3.9 24.7 - - + -
94A LYS* 3.1 50.7 + - + -
100A LEU 3.6 15.3 - - - -
101A ARG 4.0 2.4 - - - +
102A PHE 3.3 1.3 - - - -
103A SER* 1.3 78.7 - - - +
105A ASN* 1.3 67.7 + - - +
106A VAL* 3.5 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A PRO* 3.4 30.2 - - - +
75A LEU 2.8 6.7 + - - +
76A ASP* 3.6 14.8 + - - +
77A VAL* 2.8 28.1 + - - +
94A LYS* 4.6 4.0 + - - +
102A PHE* 4.9 5.2 - - - +
104A PHE* 1.3 78.7 - - - +
106A VAL* 1.3 62.9 + - - +
107A HIS* 3.6 24.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A VAL* 3.3 8.7 - - + +
79A TYR* 3.1 35.7 - - + +
86A VAL* 4.6 1.3 - - + -
87A GLU* 5.8 0.9 - - + -
90A THR* 3.8 29.6 - - + +
94A LYS* 4.7 9.8 - - - +
104A PHE* 3.5 34.1 - - + -
105A ASN* 1.3 75.2 - - - +
107A HIS* 1.3 64.6 + - - +
108A PRO* 3.8 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ASP* 2.8 30.3 + - + -
77A VAL 2.7 12.1 + - - -
78A PHE* 3.3 42.4 - + + -
79A TYR* 3.2 24.6 + - - -
105A ASN* 3.6 27.5 - - + +
106A VAL* 1.3 76.2 + - - +
108A PRO* 1.3 70.2 - - + +
109A LEU* 3.6 1.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A TYR* 3.3 36.3 - - + +
81A GLU* 3.9 34.7 - - + +
87A GLU* 4.7 1.8 - - - +
106A VAL 3.8 6.7 - - - +
107A HIS* 1.3 88.1 - - + +
109A LEU* 1.3 63.4 + - - +
110A LYS* 5.9 0.2 - - - +
113A GLU* 4.3 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PHE* 4.0 17.0 - - + -
78A PHE* 3.8 41.3 - - + -
79A TYR 2.8 13.3 + - - +
81A GLU* 2.8 26.0 + - - +
107A HIS* 4.3 0.9 - - + +
108A PRO* 1.3 77.1 - - - +
110A LYS* 1.3 65.7 + - - +
113A GLU* 3.4 29.6 - - + +
115A VAL* 3.7 22.4 - - + -
129A PRO* 4.4 10.8 - - + -
141A PHE* 3.3 15.9 - - + -
143A TYR* 4.3 14.8 - - + +
----------------------------------------------------------
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