Contacts of the strand formed by residues 110 - 115 (chain A) in PDB entry 1U3H
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 THR 110 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A GLN* 3.4 21.3 + - - +
7A PRO* 2.7 50.3 + - + +
8A GLN 4.6 0.7 - - - -
9A SER* 4.3 0.2 - - - -
10A LEU* 4.2 9.0 - - + +
20A LEU* 4.0 26.6 - - + +
21A ASN 4.9 0.7 + - - -
87A THR* 3.3 2.4 - - - -
88A TYR* 2.7 38.9 + - - +
109A GLY* 1.3 72.6 - - - -
111A LYS* 1.3 72.7 + - - +
112A LEU* 3.8 1.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A GLN 4.5 6.8 + - - +
9A SER* 3.9 13.4 + - - +
10A LEU* 3.0 27.4 + - - +
86A ALA 3.8 4.7 - - - +
87A THR* 3.2 30.7 - - + +
109A GLY 4.0 3.7 + - - +
110A THR* 1.3 75.7 - - - +
112A LEU* 1.3 59.0 + - - +
113A GLN* 5.6 0.2 - - - +
39B THR* 5.4 10.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 3.3 43.1 - - + +
11A THR 4.7 0.4 - - - +
12A VAL* 4.8 4.9 - - + -
18A ALA* 4.0 23.8 - - + -
20A LEU* 4.8 7.6 - - + -
77A ILE* 4.2 8.3 - - + -
80A SER* 6.3 0.4 - - - -
84A ASP* 4.1 10.3 - - + +
85A SER* 2.7 34.4 - - - +
86A ALA 2.8 14.6 + - - +
88A TYR* 3.9 30.7 - - + -
110A THR* 3.8 1.0 + - + +
111A LYS* 1.3 74.8 - - - +
113A GLN* 1.3 63.2 + - - +
114A VAL* 4.2 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU 3.1 6.8 + - - +
11A THR* 3.4 33.8 + - + +
12A VAL 3.0 26.9 + - - +
85A SER* 3.2 5.2 - - - +
111A LYS 5.8 0.2 - - - -
112A LEU* 1.3 75.0 - - - +
114A VAL* 1.3 67.7 + - - +
115A VAL* 4.6 6.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A VAL* 3.2 6.5 - - + +
14A GLU* 3.6 21.1 - - - +
80A SER* 4.1 7.2 - - - -
81A GLN* 3.2 29.2 - - - +
82A PRO* 3.2 35.1 - - + +
84A ASP* 4.4 2.7 - - + -
85A SER* 2.4 35.6 + - - +
112A LEU* 4.2 21.8 - - + -
113A GLN* 1.3 74.1 - - - +
115A VAL* 1.3 60.4 + - - +
116A PRO* 3.3 12.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A THR* 4.0 22.2 - - + -
12A VAL 3.0 6.4 + - - +
13A TRP* 3.3 37.5 - - + +
14A GLU* 2.7 26.8 + - - -
113A GLN* 4.6 8.1 - - + +
114A VAL* 1.3 70.9 - - - +
116A PRO* 1.3 83.2 - - + +
----------------------------------------------------------
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