Contacts of the strand formed by residues 118 - 124 (chain P) in PDB entry 4UJ3
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 118 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85P VAL 3.1 8.9 + - - +
86P GLY* 3.1 1.7 - - - -
87P ALA 2.8 26.7 + - - +
116P ASN 3.5 2.4 + - - +
117P ILE* 1.3 71.4 - - - +
119P ILE* 1.3 63.3 + - - +
149P SER* 4.7 0.9 - - - +
168P ILE* 3.8 21.6 - - + +
171P GLU* 3.8 25.4 - - + +
172P ILE* 3.3 37.2 - - + +
175P ILE* 3.9 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 119 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87P ALA* 3.6 7.6 - - + +
89P LEU* 4.6 7.9 - - + -
106P LEU* 3.7 18.6 - - + -
109P LEU* 3.1 43.1 - - + -
117P ILE* 3.3 25.9 + - + +
118P VAL* 1.3 78.2 - - - +
120P MET* 1.3 68.0 + - - +
121P LEU* 5.7 0.2 - - - -
147P GLY 4.7 2.3 - - - +
148P LEU* 3.6 28.5 - - + -
149P SER* 3.2 24.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 120 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87P ALA 3.0 8.1 + - - -
88P LEU* 3.3 37.2 - - + -
89P LEU 2.8 27.4 + - - -
119P ILE* 1.3 77.3 - - - +
121P LEU* 1.3 68.7 + - - +
122P VAL* 3.6 10.1 - - + +
149P SER* 3.4 31.0 - - - +
150P PHE* 4.1 2.2 - - - +
151P ILE* 3.8 11.2 - - + -
164P ALA* 2.9 48.0 - - + +
167P THR* 4.1 13.5 - - - -
168P ILE* 3.7 15.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 121 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89P LEU* 3.2 28.7 - - + +
91P TYR* 4.4 14.6 - - + -
99P TYR* 4.8 7.4 - - + -
102P VAL* 3.7 29.4 - - + -
119P ILE* 4.2 1.1 - - + -
120P MET* 1.3 73.5 - - - +
122P VAL* 1.3 61.5 + - - +
139P ALA 4.4 3.8 - - - +
142P PHE* 3.9 29.2 - - + -
143P ALA* 4.1 14.6 - - + -
148P LEU* 4.5 9.5 - - + +
149P SER 2.8 16.8 + - - +
150P PHE* 3.2 19.6 - - + -
151P ILE 3.1 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 122 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27P LEU* 4.7 11.0 - - + -
88P LEU* 4.0 17.9 - - + -
89P LEU 2.8 11.0 + - - +
90P VAL* 3.3 12.6 - - + +
91P TYR* 3.0 31.1 + - - -
120P MET* 3.6 35.2 - - + +
121P LEU* 1.3 77.8 - - - +
123P GLY* 1.3 62.0 + - - +
151P ILE* 3.3 5.6 - - + +
153P THR* 3.3 42.2 - - + +
164P ALA* 4.9 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 123 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91P TYR* 3.2 18.1 - - - -
93P ILE* 3.0 25.2 - - - +
121P LEU 4.3 0.2 - - - -
122P VAL* 1.3 71.8 - - - +
124P ASN* 1.3 53.4 + - - -
150P PHE* 4.6 0.6 - - - -
151P ILE 2.9 13.6 + - - -
152P GLU* 3.2 4.7 - - - +
153P THR* 2.4 37.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 124 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22P VAL 3.1 26.2 + - - +
23P GLY* 3.7 7.9 + - - -
27P LEU* 3.4 10.8 - - + +
90P VAL* 3.9 10.3 - - + -
91P TYR 3.0 11.6 + - - +
93P ILE* 3.0 22.0 + - - +
122P VAL 3.7 0.4 + - - -
123P GLY* 1.3 74.9 - - - -
125P LYS* 1.3 81.3 + - - +
126P SER 3.4 0.4 - - - -
153P THR* 3.0 23.3 + - - +
155P ALA* 3.2 16.3 + - - +
200P GNP 3.0 33.1 + - - -
----------------------------------------------------------
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