Contacts of the strand formed by residues 99 - 104 (chain A) in PDB entry 1EX0
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 99 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU* 4.6 4.3 - - + -
86A ILE* 4.8 5.4 - - + -
88A PHE* 3.9 30.5 - + + -
92A TYR* 3.6 43.5 - + - -
98A LEU* 1.3 83.2 - - - +
100A ARG* 1.3 74.0 + - - +
101A VAL* 5.0 1.1 - - + -
121A ILE* 3.4 46.2 - - + +
134A ILE* 4.7 2.0 - - + -
142A VAL* 4.7 7.9 - - + -
144A LEU* 4.4 24.5 - - + -
161A VAL* 4.0 13.5 - - + -
162A ALA 3.1 13.5 - - - +
163A VAL* 4.0 14.8 - - + -
164A TRP* 4.7 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 4.0 24.7 - - - +
99A PHE* 1.3 85.6 + - - +
101A VAL* 1.3 67.7 + - - +
102A GLU* 4.8 3.6 - - + -
118A PRO* 3.9 24.2 - - + +
119A VAL 3.2 19.7 - - - +
120A PRO* 3.7 26.2 - - + +
121A ILE* 4.5 5.0 - - - +
161A VAL* 3.6 2.8 - - - +
162A ALA* 2.8 33.9 + - - +
164A TRP* 3.2 41.3 - - + -
447B ASP* 2.8 26.5 + - - +
448B GLY* 4.5 8.7 + - - -
449B THR* 4.7 10.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A VAL* 5.2 0.2 - - + -
86A ILE* 4.9 2.9 - - + -
99A PHE* 4.7 5.1 - - + -
100A ARG* 1.3 76.8 - - - +
102A GLU* 1.3 64.6 + - - +
103A TYR* 3.7 28.3 - - + +
118A PRO 3.8 0.2 - - - -
119A VAL* 2.9 39.3 + - + -
121A ILE* 5.5 1.2 - - + +
132A ALA* 5.4 1.8 - - + -
144A LEU* 3.8 29.2 - - + -
146A ILE* 4.3 10.8 - - + -
159A MET* 3.8 23.3 - - + -
160A TYR 3.4 10.8 - - - +
161A VAL* 4.5 13.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 4.3 1.6 - - - +
100A ARG* 4.8 3.8 - - + -
101A VAL* 1.3 78.1 - - - +
103A TYR* 1.3 66.2 + - - +
104A VAL* 4.5 4.9 - - + -
116A TYR* 2.4 45.4 + - + +
117A ILE 3.4 5.6 - - - +
118A PRO* 4.4 4.9 - - + -
158A ARG 3.5 1.0 - - - +
159A MET* 3.3 6.2 - - - +
160A TYR* 2.8 50.0 + - + +
162A ALA* 3.7 19.4 - - + +
164A TRP* 3.9 4.7 - - - -
171A ARG* 2.7 44.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 5.6 0.2 - - - +
74A LEU* 5.6 0.2 - - - +
82A PHE* 3.4 29.5 - + - -
84A VAL* 4.7 0.2 - - - +
101A VAL* 3.7 18.6 - - + -
102A GLU* 1.3 75.6 - - - +
104A VAL* 1.3 63.1 + - - +
115A THR 3.9 0.9 - - - +
116A TYR* 3.7 0.2 - - - -
117A ILE* 2.8 48.8 + - + +
119A VAL* 3.8 11.7 - - + -
130A TRP* 3.6 35.0 - + + -
146A ILE* 3.7 12.0 - - + +
157A PHE* 4.0 29.2 - + + -
158A ARG 3.3 8.5 - - - -
159A MET* 3.7 29.8 - - + +
180A THR* 4.2 19.7 + - + -
182A ILE* 5.2 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ASP* 3.9 4.9 - - - +
26A LEU* 4.2 11.0 - - + -
102A GLU* 4.5 0.4 - - + -
103A TYR* 1.3 83.4 - - - +
105A ILE* 1.3 67.5 + - - +
109A PRO* 3.3 34.3 - - + -
115A THR 3.4 3.4 - - - +
116A TYR* 3.9 20.6 - - + -
156A LYS 4.8 0.2 - - - +
157A PHE* 3.6 3.0 - - - -
158A ARG* 2.9 56.5 + - - +
160A TYR* 3.8 25.6 - - + -
----------------------------------------------------------
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