Contacts of the strand formed by residues 119 - 124 (chain D) in PDB entry 3UA7
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 TRP 119 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D TYR* 3.3 27.6 - + - -
96D ARG* 5.2 2.5 - - - -
100D ASP* 4.2 6.3 - - - -
116D GLU* 2.5 47.3 + - + +
118D ASP* 1.3 88.1 - - + +
120D TRP* 1.3 63.7 + - - +
121D GLU 4.3 0.2 + - - -
132D TYR* 4.1 10.0 - - + -
133D ILE* 3.4 25.1 - - - -
134D PRO* 3.5 20.2 - - + -
4F ILE* 3.4 30.5 - - + -
5F PRO* 3.5 19.1 + - + +
6F PRO 2.6 26.3 + - - -
7F PRO* 4.3 5.9 - - + +
8F ARG* 3.4 44.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 120 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D PHE* 3.5 44.2 - + - -
111D ILE* 3.8 24.7 - - + -
113D ASN 3.4 5.4 - - - +
114D SER* 3.5 39.0 + - - -
117D GLY* 3.2 20.3 + - - -
119D TRP* 1.3 81.7 - - - +
121D GLU* 1.3 61.3 + - - +
122D ALA 3.5 1.0 + - - -
132D TYR* 3.2 5.6 - - - -
133D ILE* 2.8 42.5 + - + +
135D SER* 3.5 27.1 - - - -
138D VAL* 4.1 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 121 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D ILE* 3.4 5.4 - - - +
112D LEU* 2.7 57.8 + - + +
113D ASN* 2.8 34.0 + - + +
120D TRP* 1.3 69.7 - - - +
122D ALA* 1.3 55.3 - - - +
130D THR* 5.0 6.1 + - - -
131D GLY* 3.6 18.4 + - - +
132D TYR* 3.8 23.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 122 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D LEU* 3.8 2.3 - - - +
109D PHE* 4.2 8.7 - - + -
110D GLN 3.4 11.9 - - - +
111D ILE* 3.8 7.2 - - + -
112D LEU* 4.1 4.7 - - - +
120D TRP 3.5 0.2 + - - -
121D GLU* 1.3 76.0 - - - +
123D ARG* 1.3 61.1 + - - +
124D SER 4.2 0.2 - - - -
130D THR* 3.2 7.1 - - - -
131D GLY 2.9 32.5 + - - +
133D ILE* 3.5 38.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 123 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ASP* 3.4 47.7 + - - +
143A SER* 4.2 1.2 + - - -
84B VAL* 3.7 22.8 - - - +
85B THR* 4.3 9.7 + - - +
110B GLN* 5.3 0.4 - - - +
111B ILE* 2.9 25.5 + - - +
109D PHE* 3.2 8.3 - - - -
110D GLN* 2.8 73.0 + - + +
112D LEU* 4.1 9.6 - - + +
122D ALA* 1.3 74.4 - - - +
124D SER* 1.3 71.6 + - - +
125D LEU* 3.5 18.6 + - - +
128D GLY* 4.6 6.6 - - - +
129D GLU 3.5 5.6 - - - +
130D THR* 3.8 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 124 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B VAL* 4.1 1.2 - - - +
101D LEU* 4.0 9.1 - - - +
102D SER 5.7 2.5 - - - -
107D GLU* 4.5 6.9 + - - +
108D LYS 4.4 0.9 + - - -
109D PHE* 3.8 23.5 - - - -
123D ARG* 1.3 73.6 - - - +
125D LEU* 1.3 58.3 + - - +
126D THR* 3.1 10.3 + - - -
127D THR* 3.1 38.5 + - - +
128D GLY* 2.9 29.3 + - - -
129D GLU 3.0 13.5 + - - -
----------------------------------------------------------
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