Contacts of the strand formed by residues 138 - 143 (chain A) in PDB entry 1UMZ
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 MET 138 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A LEU* 3.7 10.8 - - + +
134A TRP* 3.7 1.2 - - - -
135A ASN* 2.9 41.0 + - - +
137A TYR* 1.3 83.0 - - + +
139A ILE* 1.3 64.0 + - - +
140A VAL* 3.7 28.0 - - + -
150A VAL* 3.9 13.7 - - + -
151A PHE 3.4 12.1 - - - +
152A LYS* 3.8 15.7 - - + -
161A PHE* 3.7 5.4 - - - -
229A PHE* 3.5 23.6 - - + +
230A GLN 4.2 2.7 - - - +
231A ASP* 3.8 33.9 - - - +
232A LEU* 4.0 9.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ILE* 3.6 20.9 - - + -
105A VAL* 4.9 3.1 - - + -
132A VAL* 4.1 18.2 - - + -
133A LEU 3.2 6.7 - - - +
134A TRP* 3.6 23.1 - - + -
138A MET* 1.3 73.8 - - - +
140A VAL* 1.3 64.5 + - - +
141A PHE* 3.8 24.9 - - + -
149A ARG 4.0 0.5 - - - +
150A VAL* 3.3 5.0 - - - +
151A PHE* 2.8 50.2 + - + +
161A PHE* 4.0 7.2 - - + -
162A PRO* 3.0 41.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A SER 3.8 0.5 - - - +
132A VAL* 3.3 7.4 - - - +
133A LEU* 2.8 47.2 + - + +
138A MET* 3.7 37.0 - - + -
139A ILE* 1.3 77.7 - - - +
141A PHE* 1.3 67.8 + - - +
142A LEU* 3.8 28.0 - - + +
147A PRO* 4.1 8.3 - - + -
149A ARG 3.6 9.9 - - - +
150A VAL* 4.3 4.9 - - + -
232A LEU* 4.0 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ILE* 3.6 28.3 - - + -
87A ASP 3.4 22.9 - - - -
88A PHE* 4.0 19.3 - + + -
103A THR* 3.6 17.7 - - + -
104A ASN 3.8 4.0 - - - -
105A VAL* 3.7 22.2 - - + -
131A SER 3.6 5.4 - - - -
132A VAL* 4.9 1.1 - - + +
139A ILE* 3.8 19.1 - - + -
140A VAL* 1.3 75.1 - - - +
142A LEU* 1.3 60.6 + - - +
147A PRO* 3.4 4.9 - - - +
148A ILE* 2.8 44.2 + - + -
149A ARG* 3.0 44.7 + - + +
151A PHE* 5.0 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A HIS* 5.6 3.8 - - + +
88A PHE* 3.8 5.6 - - - -
130A TYR* 3.4 5.4 - - - -
131A SER* 2.9 51.6 + - - +
133A LEU* 4.5 10.3 - - + +
140A VAL* 3.8 31.4 - - + +
141A PHE* 1.3 78.5 - - - +
143A VAL* 1.3 61.5 + - - +
144A ASP 3.8 12.8 - - - +
145A ASP* 4.2 15.7 - - - +
146A VAL 3.2 4.7 - - - +
147A PRO* 4.1 22.4 - - + -
232A LEU* 6.2 0.4 - - + -
236A GLN* 5.3 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A PHE* 4.8 0.4 - - + -
101A LEU* 3.9 16.8 - - + -
119A LEU* 4.4 3.4 - - + -
120A TRP* 3.7 23.5 - - + -
121A PHE* 3.7 32.3 - - + -
129A TYR 3.4 4.3 - - - +
130A TYR* 3.8 15.3 - - + -
142A LEU* 1.3 73.0 - - - +
144A ASP* 1.3 62.4 + - - +
146A VAL* 2.8 40.7 + - - +
148A ILE* 3.7 34.3 - - + -
----------------------------------------------------------
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