Contacts of the helix formed by residues 109 - 120 (chain A) in PDB entry 1UZF
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 ASN 109 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLU* 3.8 8.4 + - - +
107A LEU* 4.8 1.0 - - - +
108A GLN* 1.3 75.6 + - - +
110A THR* 1.3 58.6 + - - +
111A THR* 2.9 28.8 + - - -
112A ILE* 3.3 24.3 + - + +
113A LYS* 2.8 29.3 + - - +
693A NAG 1.5 73.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A GLN 2.9 13.6 + - - +
109A ASN* 1.3 71.1 + - - +
111A THR* 1.3 66.7 + - - +
113A LYS* 3.5 15.1 - - + +
114A ARG* 2.9 30.9 + - - +
572A ARG* 3.8 22.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ASN* 2.9 10.9 + - - -
110A THR* 1.3 83.9 + - - +
112A ILE* 1.3 60.5 + - - +
114A ARG* 3.7 8.1 - - - +
115A ILE* 3.4 28.3 + - + +
398A PRO* 5.6 2.9 - - + -
401A LEU* 4.2 20.8 - - + +
571A SER* 5.2 9.5 + - - -
572A ARG* 5.9 2.1 + - - -
693A NAG 4.2 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLU* 4.6 6.5 - - + +
44A ALA* 3.7 26.2 - - + -
45A SER* 3.1 32.8 - - - +
48A VAL* 4.1 14.1 - - + -
107A LEU* 3.9 9.0 - - + -
109A ASN* 3.3 25.0 + - + +
110A THR 3.2 0.2 - - - -
111A THR* 1.3 75.8 - - - +
113A LYS* 1.3 65.4 + - - +
114A ARG 3.1 1.9 + - - -
115A ILE* 3.2 6.2 + - - +
116A ILE* 3.1 30.1 + - + +
693A NAG 3.3 35.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A VAL* 2.7 53.6 + - + +
105A ASN* 3.5 18.0 + - - +
107A LEU* 4.0 27.3 + - + +
108A GLN 4.9 1.6 - - - +
109A ASN 2.8 18.6 + - - +
110A THR* 3.5 16.2 - - + +
112A ILE* 1.3 77.2 - - - +
114A ARG* 1.3 61.0 + - - +
116A ILE* 4.1 0.9 - - - +
117A LYS* 3.2 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A THR 2.9 17.2 + - - +
111A THR* 3.7 7.9 - - - +
112A ILE 3.1 0.2 - - - -
113A LYS* 1.3 75.1 - - - +
115A ILE* 1.3 63.8 + - - +
117A LYS* 3.5 6.4 + - - +
118A LYS* 3.2 20.8 + - - +
225A GLU* 2.8 42.7 + - - -
401A LEU* 4.5 9.4 - - + +
570A PHE* 2.8 49.5 + - + -
571A SER* 3.4 20.9 + - - +
572A ARG* 3.5 21.4 + - - +
573A PRO* 4.3 12.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PHE* 6.2 0.4 - - + -
48A VAL* 3.6 38.8 - - + -
51A TYR* 4.7 5.2 - - + -
111A THR* 3.4 19.0 + - + +
112A ILE* 3.2 7.5 + - - +
114A ARG* 1.3 76.2 - - - +
116A ILE* 1.3 64.3 + - - +
118A LYS* 3.0 9.2 + - - +
119A VAL* 2.9 30.4 + - + +
398A PRO* 3.8 29.8 - - + -
400A ALA* 3.7 19.7 - - + -
401A LEU* 3.9 25.4 - - + -
693A NAG 5.9 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ALA* 3.9 16.2 - - + +
47A PHE* 4.2 11.2 - - + -
48A VAL* 3.8 17.0 - - + -
99A ALA* 3.7 29.4 - - + +
102A PHE* 4.0 19.5 - - + -
104A VAL* 4.0 11.4 - - + -
107A LEU* 3.4 28.3 - - + -
112A ILE* 3.1 21.8 + - + +
113A LYS 4.1 2.9 - - - +
115A ILE* 1.3 76.2 - - - +
117A LYS* 1.3 59.4 + - - +
119A VAL* 3.2 8.4 + - - +
120A GLN* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A VAL* 4.3 14.1 - - + +
113A LYS 3.2 18.4 + - - +
114A ARG* 3.7 7.9 - - - +
115A ILE 3.2 0.2 - - - -
116A ILE* 1.3 76.2 - - - +
118A LYS* 1.3 65.0 + - - +
120A GLN* 3.4 34.6 + - - +
121A ASP* 4.0 4.9 + - - +
213A TYR* 5.4 7.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A TRP* 5.4 7.9 - - - -
114A ARG 3.2 9.5 + - - +
115A ILE* 3.0 12.0 + - - +
117A LYS* 1.3 85.1 - - - +
119A VAL* 1.3 61.1 + - + +
121A ASP* 3.2 25.1 + - + +
399A VAL 5.6 0.2 + - - -
400A ALA* 3.5 34.4 + - + +
401A LEU* 5.3 2.9 - - + -
403A GLU* 4.6 18.3 + - - +
570A PHE* 4.1 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PHE* 4.2 6.7 - - + -
51A TYR* 3.6 57.0 - - + +
92A THR* 5.5 1.1 - - - +
95A TYR 3.8 15.0 - - - +
96A GLY* 3.3 14.8 - - - +
99A ALA* 3.7 18.2 - - + -
115A ILE* 2.9 22.9 + - + +
116A ILE* 3.2 6.9 + - - +
118A LYS* 1.3 74.1 - - + +
120A GLN* 1.3 60.7 + - - +
121A ASP 3.0 12.7 + - - +
122A LEU* 4.0 0.7 - - - +
400A ALA* 5.1 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A GLY 4.3 2.0 - - - -
99A ALA 2.9 31.3 + - - +
100A ARG* 2.9 55.0 + - + +
102A PHE 3.3 18.4 + - - -
104A VAL* 3.5 19.7 - - - +
116A ILE* 2.9 22.4 - - - +
117A LYS* 3.5 22.4 + - - +
118A LYS 3.2 0.6 - - - -
119A VAL* 1.3 77.0 - - - +
121A ASP* 1.3 57.9 + - - +
122A LEU* 3.5 1.9 + - - +
211A ASN* 5.5 0.9 - - - +
----------------------------------------------------------
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