Contacts of the strand formed by residues 116 - 124 (chain I) in PDB entry 1UW9
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 116 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ILE* 6.6 0.2 - - + -
156A GLN* 4.1 26.7 - - + +
159A ARG* 4.5 10.1 - - + -
160A ASP* 3.8 20.6 - - - +
165A TYR* 4.0 8.3 - - + -
110I PHE* 4.3 6.4 - - - +
111I ASP* 3.0 27.9 + - - +
114I LYS* 3.9 35.7 - - + +
115I GLN* 1.3 77.3 - - - +
117I GLN* 1.3 77.5 + - - +
118I ILE* 3.4 6.4 + - + -
184K ASN* 6.0 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 117 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ARG* 4.8 2.9 - - - -
160A ASP* 5.0 1.0 + - - -
163A ASN* 5.3 0.2 + - - -
165A TYR* 3.1 65.8 - - + +
166A GLY 5.3 0.2 + - - -
43I GLU* 4.7 2.9 - - - +
106I ARG* 5.7 1.7 + - - +
108I VAL* 3.4 32.3 - - + +
109I ALA 3.4 11.4 - - - +
110I PHE* 3.8 23.7 - - + -
116I VAL* 1.3 83.7 - - - +
118I ILE* 1.3 58.7 + - - +
119I MET 3.0 27.9 + - - +
120I GLY* 3.9 4.2 - - - -
183K LYS* 5.0 0.9 + - - -
187K ARG* 4.3 9.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 118 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A GLY* 3.4 18.3 + - - -
396A ASP* 4.4 9.2 - - + +
38I TRP* 3.4 63.4 - - + -
109I ALA* 2.8 19.5 + - + +
111I ASP* 3.9 26.9 - - + +
114I LYS* 4.0 30.7 - - + +
116I VAL* 3.4 3.8 + - + -
117I GLN* 1.3 74.3 - - - +
119I MET* 1.3 64.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 119 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A TYR* 4.5 2.2 - - - -
166A GLY* 3.8 12.5 - - - +
432A ASN* 5.3 5.4 - - - +
15I PHE* 5.6 0.7 - - + -
29I GLN* 4.0 21.3 - - - +
32I TYR* 5.4 5.2 - - + -
33I ILE* 3.5 37.7 - - + -
38I TRP* 4.7 8.1 - - + -
107I LEU 4.4 1.3 - - - +
108I VAL* 4.1 4.5 - - - -
109I ALA* 3.2 40.4 + - + -
117I GLN* 3.0 19.7 + - - +
118I ILE* 1.3 86.5 - - + +
120I GLY* 1.3 62.1 + - - +
121I PHE* 3.5 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 120 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A TYR 4.3 5.9 + - - +
166A GLY* 4.6 0.8 - - - -
14I THR* 3.3 26.4 + - - +
15I PHE* 5.2 0.2 - - - -
106I ARG* 6.3 0.4 - - - -
107I LEU 3.1 13.9 - - - -
108I VAL* 4.4 1.8 - - - -
117I GLN* 3.9 10.8 - - - -
119I MET* 1.3 82.5 - - - +
121I PHE* 1.3 67.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 121 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I PHE 5.3 2.7 - - - -
14I THR* 3.4 20.2 - - - +
15I PHE* 3.8 20.9 - + + -
21I LEU* 3.8 21.8 - - + -
26I ILE* 4.2 13.7 - - + -
29I GLN* 3.6 26.9 - - + -
106I ARG* 3.4 8.0 - - - +
107I LEU* 3.0 49.6 + - + -
119I MET* 3.5 30.1 - - + -
120I GLY* 1.3 78.3 - - - +
122I LEU* 1.3 72.6 + - - +
123I VAL* 3.6 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 122 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I PHE* 3.8 60.7 + - + -
14I THR 4.8 1.2 + - - -
21I LEU* 5.4 2.3 - - - +
26I ILE* 5.8 0.7 - - - +
73I TRP* 4.1 6.3 - - + -
104I TYR* 3.9 7.2 - - + -
105I VAL 3.4 20.0 - - - +
106I ARG* 4.1 4.0 - - + +
121I PHE* 1.3 84.8 - - - +
123I VAL* 1.3 58.4 + - - +
124I GLN 3.5 22.7 - - - +
125I ARG* 4.1 34.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 123 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I ILE* 4.7 24.0 - - + +
42I LEU* 4.4 4.3 - - + -
93I ILE* 4.3 25.4 - - + +
97I THR* 5.2 1.6 - - + +
105I VAL* 2.8 37.8 + - + +
106I ARG 4.3 0.2 - - - -
107I LEU* 4.0 20.9 - - + +
121I PHE* 3.6 30.7 + - + +
122I LEU* 1.3 73.2 - - - +
124I GLN* 1.3 62.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 124 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97I THR* 3.2 39.5 - - + +
100I PHE 2.9 27.7 + - - -
101I PRO* 3.5 16.4 + - - +
103I ALA 3.0 17.4 + - - +
104I TYR* 3.3 3.5 - - - -
105I VAL* 3.0 38.3 + - + +
122I LEU* 3.5 12.9 - - - +
123I VAL* 1.3 81.4 - - - +
125I ARG* 1.3 71.7 + - - +
----------------------------------------------------------
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