Contacts of the strand formed by residues 131 - 139 (chain D) in PDB entry 3UNF
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 VAL 131 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D ILE* 3.7 6.8 - - - +
71D SER 3.4 10.1 - - - +
73D LEU 3.2 28.9 - - - +
76D ASP* 3.5 10.3 - - + -
77D ALA* 3.4 35.4 - - + +
80D LEU* 4.7 4.2 - - + +
129D PHE* 2.8 17.9 + - + +
130D GLY* 1.3 76.9 - - - +
132D ALA* 1.3 76.4 + - - +
133D LEU* 3.8 16.2 - - + -
148D MET* 4.3 5.2 - - - +
149D ASP* 4.2 2.3 - - - -
150D PRO* 3.4 22.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 132 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D ILE* 3.8 28.8 - - + +
69D ALA 4.0 0.2 - - - +
70D MET* 3.7 0.3 - - - -
71D SER 3.1 30.4 + - - +
131D VAL* 1.3 79.0 - - - +
133D LEU* 1.3 63.6 + - - +
147D HIS* 4.8 3.4 - - - +
148D MET 3.3 11.7 - - - +
149D ASP* 4.9 2.7 - - + -
162D ILE* 4.3 29.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 133 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D CYS* 3.7 15.0 - - - -
69D ALA 3.4 1.3 - - - +
70D MET* 3.7 28.3 - - + -
77D ALA* 4.5 4.0 - - + -
80D LEU* 4.3 13.0 - - + -
81D ILE* 4.2 13.5 - - + -
108D VAL* 4.2 9.2 - - + -
131D VAL* 3.8 12.1 - - + -
132D ALA* 1.3 77.4 - - - +
134D LEU* 1.3 62.4 + - - +
135D PHE* 3.6 36.0 + - + -
146D PHE 3.6 0.9 - - - +
147D HIS* 3.5 6.5 - - - +
148D MET* 3.0 55.7 + - + +
162D ILE* 5.2 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 134 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D ALA 3.9 13.7 - - - +
30D ILE 3.9 5.4 - - - -
31D GLY* 3.5 30.5 - - - +
40D LEU* 3.9 3.5 - - + +
67D GLY 3.5 1.0 - - - +
68D CYS* 3.3 5.3 - - - -
69D ALA* 2.8 48.4 + - + -
133D LEU* 1.3 72.9 - - - +
135D PHE* 1.3 62.6 + - - +
136D GLY 3.5 1.2 + - - -
145D LEU* 4.0 16.6 - - + -
146D PHE 3.3 12.1 - - - +
147D HIS* 3.9 22.7 - - + -
160D ARG* 3.8 24.5 - - + +
162D ILE* 4.1 16.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 135 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D ILE* 3.5 32.5 - - + -
66D ILE* 4.6 4.5 - - + -
67D GLY 3.5 3.1 - - - -
68D CYS* 3.8 8.1 - - + -
81D ILE* 5.0 2.2 - - + -
84D ALA* 4.6 0.7 - - + -
101D VAL* 4.0 12.5 - - + +
104D VAL* 4.2 14.8 - - + -
105D THR* 3.5 42.0 - - + +
108D VAL* 3.7 31.4 - - + -
133D LEU* 3.6 40.6 - - + -
134D LEU* 1.3 71.2 - - - +
136D GLY* 1.3 58.4 + - - +
144D GLN 4.0 0.7 - - - +
145D LEU* 3.3 2.9 - - - -
146D PHE* 2.7 40.5 + - + +
148D MET* 4.7 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 136 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D VAL* 3.9 20.6 - - - -
40D LEU* 4.4 5.6 - - - +
66D ILE* 4.7 0.4 - - - +
67D GLY* 2.7 44.6 + - - +
101D VAL* 4.5 2.5 - - - -
134D LEU 3.5 2.4 + - - -
135D PHE* 1.3 74.1 - - - +
137D GLY* 1.3 54.7 + - - -
144D GLN 3.4 8.5 - - - -
145D LEU* 4.2 5.2 - - - -
212D VAL* 3.8 6.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 137 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D VAL* 4.2 4.2 - - - +
65D HIS 3.1 14.8 - - - -
66D ILE* 4.3 1.1 - - - -
101D VAL* 4.0 16.6 - - - +
136D GLY* 1.3 74.3 - - - -
138D VAL* 1.3 61.6 + - - -
143D PRO* 3.5 1.6 - - - +
144D GLN* 2.8 38.7 + - - +
212D VAL* 3.8 9.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 138 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D HIS* 3.1 35.9 + - + +
101D VAL* 4.3 0.4 - - - +
137D GLY* 1.3 75.2 - - - +
139D ASP* 1.3 71.5 + - - +
142D GLY* 3.6 9.9 - - - +
143D PRO* 3.8 17.0 - - + -
212D VAL* 3.3 33.6 - - + +
213D GLN 4.6 0.7 - - - -
214D PRO* 3.9 39.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 139 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D HIS* 4.4 7.4 - - + -
99D MET 4.7 0.9 - - - +
100D THR* 3.4 26.6 - - - -
101D VAL* 3.0 21.6 + - + -
137D GLY 4.2 0.8 + - - -
138D VAL* 1.3 81.8 - - - +
140D GLU* 1.3 64.7 + - + +
141D LYS* 2.8 36.6 + - - +
142D GLY* 3.1 18.5 + - - +
144D GLN* 2.8 32.1 + - - -
----------------------------------------------------------
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