Contacts of the strand formed by residues 109 - 117 (chain F) in PDB entry 5EHD
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 109 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F CYS 4.0 0.3 - - - +
22F GLU* 3.3 3.3 - - - -
23F LEU* 2.7 40.3 + - + +
47F VAL* 3.6 30.3 - - + -
48F SER 3.6 6.5 - - - +
49F LEU* 3.7 10.5 - - + -
58F HIS* 3.7 23.8 - - + +
60F VAL* 3.6 12.1 - - + -
79F LEU* 4.5 4.3 - - + -
102F LEU* 3.6 27.4 - - + -
107F GLY* 4.0 2.5 - - - -
108F PRO* 1.3 79.2 - - - +
110F HIS* 1.3 65.5 + - - +
111F ILE* 4.5 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 110 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F CYS 3.6 5.4 - - - +
22F GLU* 3.0 45.2 + - + -
46F THR 3.8 0.6 - - - +
47F VAL* 3.3 7.4 - - - +
48F SER* 2.6 41.4 + - - +
49F LEU 4.4 0.6 - - - -
50F GLY* 3.7 30.4 + - - -
108F PRO* 4.4 5.2 - - + -
109F VAL* 1.3 73.8 - - - +
111F ILE* 1.3 64.2 + - - +
59J ILE* 5.7 0.9 - - + +
75J THR* 3.5 38.1 + - - +
103J LYS* 3.5 26.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 111 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F PHE* 4.1 9.2 - - + -
20F GLY* 3.2 4.7 - - - -
21F CYS* 3.0 44.8 + - - +
23F LEU* 3.4 40.6 - - + -
44F LEU* 3.7 34.5 - - + -
46F THR 3.3 6.7 - - - +
47F VAL* 4.3 17.5 - - + -
60F VAL* 4.5 7.4 - - + -
76F LEU* 5.7 1.8 - - + -
100F LEU* 4.5 9.2 - - + -
109F VAL* 4.2 7.9 - - + +
110F HIS* 1.3 81.6 - - - +
112F SER* 1.3 67.5 + - - +
74J VAL* 4.9 1.6 - - - +
75J THR 4.7 3.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 112 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F PHE* 3.5 7.2 - - - -
44F LEU* 3.8 1.0 - - - -
45F ARG 2.8 20.3 + - - -
46F THR* 2.6 34.8 + - - +
111F ILE* 1.3 81.6 - - - +
113F GLY* 1.3 58.6 + - - +
74J VAL* 3.3 19.1 - - - -
75J THR 3.2 21.9 + - - -
76J LEU* 4.5 0.6 - - - +
92J PHE* 3.4 19.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 113 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F LEU* 3.7 1.7 - - - +
19F PHE* 2.9 35.3 + - - +
43F SER 3.1 14.1 - - - -
44F LEU* 4.2 1.1 - - - -
45F ARG* 3.8 5.8 - - - -
112F SER* 1.3 78.4 + - - +
114F GLN* 1.3 64.9 + - - -
92J PHE* 3.4 20.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 114 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F ASN* 3.5 12.2 + - - +
17F TYR 3.3 7.9 - - - +
19F PHE* 4.1 4.5 - - - -
41F GLN 3.8 0.3 - - - +
42F LEU* 3.7 5.2 - - - +
43F SER* 2.7 57.2 + - - +
45F ARG* 3.9 20.1 + - + +
113F GLY* 1.3 77.8 - - - +
115F HIS* 1.3 59.8 + - - +
116F LEU* 3.8 21.6 + - + +
92J PHE* 3.7 17.0 - - + -
93J GLU* 2.9 40.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 115 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F GLN 3.7 1.7 - - - +
16F ASN* 3.4 2.3 - - - -
17F TYR* 2.7 45.7 + - + +
18F LEU 5.0 2.0 - - - +
19F PHE* 4.1 10.1 - - + +
31F PHE* 3.3 34.2 - + + -
33F VAL* 3.9 5.8 - - + -
40F HIS* 2.8 40.5 - + + +
41F GLN 3.7 7.4 - - - -
42F LEU* 4.9 1.6 - - - -
114F GLN* 1.3 72.3 - - - +
116F LEU* 1.3 72.9 + - - +
117F VAL* 4.1 3.9 - - + +
67J TYR* 3.4 37.6 - + + +
68J GLU* 4.8 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 116 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14F PRO* 4.0 27.1 - - + +
15F GLN 3.4 2.5 - - - -
16F ASN* 3.4 28.9 - - + -
40F HIS* 3.3 6.1 - - - -
41F GLN* 2.9 47.9 + - + +
43F SER* 3.9 24.7 - - - -
93F GLU* 4.0 22.0 - - - +
114F GLN* 4.0 17.3 - - + +
115F HIS* 1.3 74.7 - - - +
117F VAL* 1.3 62.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 117 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F ARG 4.2 0.5 - - - +
14F PRO* 3.1 5.6 - - - +
15F GLN* 2.9 48.3 + - + +
17F TYR* 3.8 26.7 - - + -
36F ASP* 4.1 0.2 - - - +
38F ASN* 3.6 35.7 - - + +
39F GLU 3.3 5.6 - - - +
40F HIS* 4.0 11.2 - - + +
115F HIS* 4.1 11.4 - - + +
116F LEU* 1.3 80.0 - - - +
118F ALA* 1.3 62.2 + - - +
67J TYR* 4.0 19.7 - - + -
----------------------------------------------------------
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