Contacts of the strand formed by residues 54 - 66 (chain F) in PDB entry 3ALQ
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 GLY 54 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E SER* 5.2 9.2 - - - -
53F GLU* 1.3 85.4 - - - +
55F LEU* 1.3 66.4 + - - -
56F TYR* 3.7 6.4 - - - -
125F GLN* 3.4 8.4 - - - +
126F LEU 3.0 26.9 + - - +
156F ALA* 6.3 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E SER* 3.4 30.7 + - - +
11E MET 5.1 1.3 - - - +
13E VAL* 3.6 38.6 - - + -
36E LEU* 3.7 24.9 - - + -
39E ASN* 5.6 0.9 - - - +
155E ILE* 4.1 13.9 - - + -
54F GLY* 1.3 72.7 - - - -
56F TYR* 1.3 60.7 + - - +
123F VAL* 4.4 7.2 - - + -
124F PHE 3.4 1.6 - - - +
125F GLN* 3.8 29.6 - - + +
156F ALA* 3.4 5.0 - - - +
157F LEU* 2.8 42.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 56 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F PRO* 3.7 15.1 - - + +
50F VAL* 3.6 13.9 - - + -
51F PRO* 3.3 18.7 - - + +
52F SER* 3.1 35.9 + - - -
53F GLU 4.6 1.8 - - - -
54F GLY 3.7 10.3 - - - -
55F LEU* 1.3 79.6 - - - +
57F LEU* 1.3 61.2 + - - +
58F ILE* 3.7 8.3 + - + +
122F GLY 3.7 0.3 - - - +
123F VAL* 3.2 8.7 - - - +
124F PHE 2.8 35.3 + - - +
126F LEU* 3.6 33.2 - - + -
154F ILE* 4.1 26.9 - - + -
155F ILE 3.2 17.7 - - - -
156F ALA* 3.8 20.6 - - + +
157F LEU* 4.9 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 57 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D LEU* 4.0 32.8 - - + -
123D VAL* 4.9 1.6 - - + -
157D LEU* 5.5 1.3 - - + -
57E LEU* 3.8 22.2 - - + -
59E TYR* 5.0 2.5 - - + -
119E TYR* 5.9 0.9 - - - +
56F TYR* 1.3 72.3 - - - +
58F ILE* 1.3 60.2 + - - +
59F TYR* 4.2 22.3 - - + -
121F GLY* 5.2 1.3 - - - -
122F GLY* 3.5 23.6 - - - +
123F VAL* 3.9 11.2 - - + +
153F GLY 3.9 0.2 - - - +
154F ILE* 3.0 28.8 - - - +
155F ILE* 2.8 30.7 + - + +
157F LEU* 4.5 12.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 58 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56F TYR* 4.0 9.9 - - + +
57F LEU* 1.3 80.2 - - - +
59F TYR* 1.3 61.8 + - - +
80F ILE* 4.1 28.5 - - + -
93F LEU* 4.1 14.4 - - + -
94F LEU* 3.7 4.3 - - + +
121F GLY* 3.1 2.8 - - - -
122F GLY 2.8 40.4 + - - +
124F PHE* 3.3 40.4 - - + -
126F LEU* 4.1 20.0 - - + -
132F LEU* 4.2 9.2 - - + -
152F PHE* 4.5 3.8 - - + -
153F GLY 3.7 2.7 - - - +
154F ILE* 3.7 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 59 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D LEU* 5.9 0.2 - - + -
121D GLY 3.5 13.7 - - - -
122D GLY* 3.3 14.6 - - - -
123D VAL* 2.7 48.6 + - + +
14F ALA 4.0 0.7 + - - -
15F HIS* 2.8 30.7 + - - +
57F LEU* 4.3 21.1 - - + -
58F ILE* 1.3 78.6 - - - +
60F SER* 1.3 65.9 + - - +
80F ILE* 3.9 4.0 - - - -
119F TYR* 3.6 13.5 - - - +
120F LEU 3.3 11.9 - - - +
121F GLY* 4.0 3.8 - - - -
151F TYR* 3.9 13.2 - + - -
152F PHE* 3.3 3.8 - - - -
153F GLY* 2.9 56.5 + - - +
154F ILE* 4.0 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 60 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F TRP* 4.3 1.4 - - - -
59F TYR* 1.3 81.9 - - - +
61F GLN* 1.3 60.5 + - - +
78F HIS* 2.8 34.1 + - - -
80F ILE* 3.5 18.8 - - - +
119F TYR* 3.6 4.9 - - - -
120F LEU* 3.0 33.1 + - - +
134F ALA* 4.1 1.4 - - - +
151F TYR* 2.8 23.0 + - - -
152F PHE* 3.7 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 61 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D SER 2.8 27.9 + - - -
96D ALA* 4.2 6.8 - - - +
119D TYR 3.3 19.6 - - - +
120D LEU* 3.5 7.2 - - - +
60F SER* 1.3 75.0 + - - +
62F VAL* 1.3 75.4 + - - +
63F LEU* 5.2 1.4 - - - +
78F HIS* 4.3 0.9 - - - -
117F PRO* 5.1 4.0 - - - +
118F ILE 3.4 14.4 - - - +
119F TYR* 3.8 7.9 - - + +
148F GLY 3.3 10.5 + - - -
149F GLN 3.1 15.7 + - - +
150F VAL* 3.2 4.5 - - - +
151F TYR* 2.9 65.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 62 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F LEU* 4.7 5.8 - - + -
28F TRP* 5.1 0.7 - - + -
60F SER* 4.8 0.9 - - - +
61F GLN* 1.3 82.8 - - - +
63F LEU* 1.3 61.0 + - - +
64F PHE* 3.6 25.4 - - + -
78F HIS* 3.5 46.0 - - + -
116F GLU 4.1 0.2 - - - +
117F PRO* 3.5 3.3 - - - +
118F ILE* 3.1 33.1 + - + +
136F ILE* 3.6 13.7 - - + -
142F LEU* 4.0 12.6 - - + -
149F GLN 3.7 4.7 - - - -
150F VAL* 4.0 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 63 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D ALA* 4.5 3.8 - - - -
97D ILE* 3.8 27.4 - - + +
61F GLN* 5.2 1.1 - - - +
62F VAL* 1.3 75.2 - - - +
64F PHE* 1.3 69.5 + - - +
115F TYR* 4.7 5.8 - - + -
116F GLU 3.7 5.6 - - - +
117F PRO* 3.5 40.2 - - + -
142F LEU* 3.6 5.4 - - - +
143F ASP* 2.8 35.9 + - + +
149F GLN* 3.6 53.1 + - + +
150F VAL* 3.7 4.4 - - - +
113W ARG* 4.2 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 64 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62F VAL* 3.6 22.2 - - + -
63F LEU* 1.3 78.9 - - - +
65F SER* 1.3 64.2 + - - +
76F LEU* 3.4 55.9 - - + -
77F THR 4.0 10.3 - - - -
114F TRP* 3.7 6.1 - - + -
115F TYR* 3.3 3.8 - - - +
116F GLU* 2.9 42.2 + - + +
118F ILE* 4.2 12.1 - - + -
136F ILE* 3.9 33.9 - - + -
138F ARG* 3.5 19.5 - - + -
141F TYR* 3.1 22.2 - - + +
142F LEU* 4.1 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 65 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64F PHE* 1.3 78.1 - - - +
66F GLY* 1.3 59.3 + - - +
114F TRP* 3.0 20.6 - - - -
115F TYR* 3.5 26.8 - - - -
141F TYR* 3.0 26.0 + - - +
142F LEU 5.0 0.9 + - - -
143F ASP* 3.1 23.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 66 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F SER* 1.3 75.3 - - - +
67F GLN* 1.3 65.4 + - - -
68F GLY 3.3 2.9 - - - -
113F PRO* 3.6 2.8 - - - +
114F TRP* 3.1 52.0 + - - -
141F TYR* 4.0 10.8 - - - -
----------------------------------------------------------
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