Contacts of the strand formed by residues 104 - 108 (chain D) in PDB entry 1EV2
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 ASN 104 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D GLU* 3.5 18.7 + - - -
97D ARG 3.3 8.3 - - - +
98D LEU* 3.6 12.0 - - - +
103D TYR* 1.3 76.0 - - - +
105D THR* 1.3 63.7 + - - +
106D TYR* 3.1 34.8 + - + +
137D ILE 3.4 4.3 - - - +
138D LEU* 3.7 0.9 - - - -
139D PHE* 2.6 40.7 + - - +
141D PRO* 4.1 13.6 - - + +
251H ARG* 2.9 34.9 + - - +
284H ALA* 5.5 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 105 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D PHE 3.3 4.0 + - - +
96D GLU* 3.5 3.1 - - - +
97D ARG* 3.0 38.7 + - - +
99D GLU* 2.8 39.2 + - + +
104D ASN* 1.3 79.4 - - - +
106D TYR* 1.3 67.9 + - - +
107D ARG* 5.7 0.3 - - - +
115D TYR* 4.1 19.4 - - - -
137D ILE* 3.7 32.1 - - + +
138D LEU* 4.0 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 106 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D LEU* 4.0 30.2 - - + +
55D LEU* 4.2 9.7 - - + +
63D VAL* 4.0 16.4 - - + -
65D ILE* 4.1 18.6 - - + -
94D PHE* 4.2 9.6 - - + -
95D PHE 3.4 3.1 - - - -
96D GLU* 2.9 49.1 + - + -
104D ASN* 3.1 29.8 + - + +
105D THR* 1.3 77.4 - - - +
107D ARG* 1.3 60.4 + - - +
108D SER 4.2 0.2 + - - -
115D TYR* 3.4 7.1 - - - -
116D VAL* 3.0 48.6 + - + +
137D ILE 4.7 2.4 + - - -
139D PHE* 4.3 20.9 - + + -
141D PRO* 5.2 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 107 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D PHE* 3.2 3.2 - - - -
95D PHE* 2.6 84.6 + - + +
105D THR* 4.1 0.6 - - - +
106D TYR* 1.3 72.1 - - - +
108D SER* 1.3 67.9 + - - +
112D THR* 3.1 44.2 + - - +
113D SER* 4.9 1.1 - - - +
114D TRP 3.6 12.8 - - - +
115D TYR* 3.9 33.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 108 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D MET* 4.0 20.0 - - - +
91D GLU* 5.8 2.4 + - - -
93D PHE 3.9 1.7 + - - -
94D PHE* 3.7 19.5 - - - -
95D PHE* 4.1 1.4 - - - -
106D TYR 4.2 0.4 + - - -
107D ARG* 1.3 73.6 - - - +
109D ARG* 1.3 62.2 + - - +
110D LYS* 3.2 5.9 + - - +
111D TYR* 2.9 42.3 + - - -
112D THR* 3.2 22.2 - - - +
114D TRP 3.1 12.7 + - - -
----------------------------------------------------------
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