Contacts of the strand formed by residues 101 - 109 (chain N) in PDB entry 5U07
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 ILE 101 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C GLN* 3.4 39.0 - - + -
163C TRP* 3.5 16.4 - - + -
164C LEU* 5.2 5.6 - - + -
43M G 4.6 3.8 - - + -
22N GLY* 6.2 0.7 - - - -
75N THR* 3.1 7.8 - - - -
76N ILE* 2.9 65.2 + - + +
86N VAL* 3.9 10.8 - - + -
99N ALA 4.2 6.3 - - - +
100N THR* 1.3 73.9 - - - +
102N VAL* 1.3 62.6 + - - +
103N THR* 3.9 17.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 102 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9K C 5.4 0.4 - - - +
43M G 3.4 56.1 - - + +
22N GLY* 4.9 5.7 - - - +
23N GLU* 4.9 6.1 - - - +
73N PHE* 3.4 38.4 - - + -
75N THR* 3.9 13.5 - - + -
100N THR* 3.8 1.1 + - - +
101N ILE* 1.3 81.2 - - - +
103N THR* 1.3 63.1 + - - +
104N SER* 4.1 2.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 103 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C TRP* 5.4 2.7 - - + -
164C LEU* 3.9 23.6 - - + -
22N GLY* 3.4 19.5 - - - +
24N ARG* 5.7 0.4 - - + -
73N PHE* 4.2 0.5 - - - -
74N HIS* 2.2 73.7 + - + +
76N ILE* 4.6 6.2 - - + +
101N ILE* 4.1 14.6 - - + -
102N VAL* 1.3 79.9 - - - +
104N SER* 1.3 61.4 + - - +
105N ARG* 3.7 19.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 104 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22N GLY 3.4 7.5 + - - -
23N GLU* 3.9 22.5 - - - +
24N ARG 3.5 18.2 + - - +
71N VAL* 3.1 27.8 - - - +
72N ASP 3.5 5.2 + - - -
73N PHE* 4.7 11.7 - - - +
74N HIS 4.6 0.4 - - - +
102N VAL* 4.1 2.6 + - - -
103N THR* 1.3 75.5 - - - +
105N ARG* 1.3 62.6 + - - +
106N SER* 3.5 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 105 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C TRP* 4.4 10.9 - - - +
164C LEU* 6.1 2.0 - - - +
4K G 3.5 22.2 + - - -
5K A 4.1 12.1 + - - -
6K C 5.1 4.0 - - - +
7K C 3.2 36.0 + - - -
24N ARG* 4.0 24.6 - - + +
72N ASP* 2.8 52.0 + - + +
74N HIS* 3.0 38.4 + - + -
103N THR* 3.7 15.3 + - - +
104N SER* 1.3 72.4 - - - +
106N SER* 1.3 55.2 + - - +
140N ARG* 3.4 32.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 106 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14N SER* 3.6 2.8 - - - -
24N ARG 3.1 21.4 + - - -
25N ASP* 3.9 7.1 - - - +
26N THR* 4.2 6.9 - - - +
69N ARG* 3.2 34.7 + - - -
70N LEU 3.5 10.1 - - - -
71N VAL* 3.9 14.4 - - - +
104N SER 4.2 2.3 + - - -
105N ARG* 1.3 73.0 - - - +
107N TYR* 1.3 57.9 + - - +
140N ARG* 2.7 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 107 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D THR 3.3 12.8 + - - -
28D VAL* 3.8 9.7 - - + +
37D ARG* 3.6 26.0 + - - -
12N MET* 3.6 29.8 - - + -
13N GLN 3.6 9.0 - - - +
14N SER* 3.7 5.2 - - - -
26N THR* 4.2 5.8 - - - +
69N ARG* 4.3 0.7 - - - -
70N LEU* 2.8 74.5 + - + +
71N VAL 4.4 0.4 - - - -
72N ASP* 3.6 21.8 - - + -
106N SER* 1.3 77.4 - - - +
108N LEU* 1.3 62.9 + - - +
109N ALA* 3.6 22.0 - - + -
140N ARG* 4.0 0.9 - - - +
143N PHE* 3.8 22.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 108 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12N MET* 3.3 3.1 - - - -
13N GLN* 2.5 56.6 + - + +
15N TRP* 4.9 6.1 - - + -
26N THR* 3.9 17.4 - - + +
27N LEU 3.6 17.3 - - - +
28N PRO* 4.3 15.7 - - + -
29N TYR 4.8 0.2 - - - +
66N PRO 4.7 9.9 - - - +
67N GLY 5.1 1.6 - - - +
68N VAL 4.9 0.7 - - - -
69N ARG* 3.5 28.9 - - + +
107N TYR* 1.3 72.6 - - - +
109N ALA* 1.3 60.7 + - - +
111N ALA* 4.3 7.6 + - + -
113N PHE* 4.1 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 109 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D VAL* 3.9 8.5 - - + -
29D VAL* 3.8 21.5 - - + +
11N PRO 3.5 8.5 - - - +
67N GLY* 3.5 0.7 - - - -
68N VAL* 3.0 30.0 + - - +
70N LEU* 4.2 1.8 - - + -
107N TYR* 3.6 23.3 + - + -
108N LEU* 1.3 74.9 - - - +
110N ASP* 1.3 79.7 + - - +
111N ALA 3.2 3.2 + - - -
----------------------------------------------------------
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