Contacts of the strand formed by residues 116 - 122 (chain F) in PDB entry 3U8M
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 SER 116 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F ILE* 4.5 1.0 - - - +
51F VAL* 3.8 12.5 - - - +
52F PHE 3.6 4.2 + - - -
53F TRP* 3.4 28.7 + - - -
97F VAL* 3.8 0.9 - - - -
98F LEU* 2.8 44.7 + - - +
99F THR* 2.9 27.8 + - - +
114F MET 3.9 0.8 + - - -
115F PRO* 1.3 73.7 - - - +
117F ILE* 1.3 61.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 117 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50F VAL 3.6 1.2 - - - +
51F VAL* 3.1 4.0 - - - -
52F PHE* 2.7 60.5 + - + +
54F GLN* 3.9 36.3 - - + +
95F PRO* 3.7 33.0 - - + -
96F GLU 3.4 4.5 - - - +
97F VAL* 4.3 17.7 - - + -
98F LEU* 4.3 3.4 - - - -
115F PRO* 4.2 17.0 - - + +
116F SER* 1.3 79.3 + - - +
118F ARG* 1.3 71.3 + - - +
119F GLN* 4.1 2.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 118 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F LEU* 3.1 32.4 - - - +
40F GLU* 4.7 8.1 + - - -
49F ASP* 2.9 39.5 + - - +
50F VAL 3.3 7.4 - - - +
51F VAL* 3.7 12.6 - - + -
93F SER* 5.0 0.3 + - - -
94F LYS 4.5 0.7 - - - +
96F GLU* 3.0 57.4 + - + +
98F LEU* 4.1 13.7 - - + +
117F ILE* 1.3 72.1 - - - +
119F GLN* 1.3 65.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 119 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49F ASP* 4.4 2.2 - - - -
50F VAL 3.0 28.8 + - - +
52F PHE* 3.9 11.8 - - + -
54F GLN* 5.5 0.9 - - - +
88F ALA* 4.2 9.8 - - - +
91F ALA* 3.2 26.2 - - + +
93F SER* 3.0 32.5 + - - +
95F PRO* 3.2 36.0 - - + +
117F ILE* 4.1 6.8 + - + +
118F ARG* 1.3 76.9 - - - +
120F ARG* 1.3 65.2 + - - +
121F PHE* 3.5 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 120 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40F GLU* 5.9 1.6 - - - -
47F GLU* 4.8 10.4 + - + -
48F VAL 3.2 15.5 - - - +
49F ASP* 3.5 31.6 + - + +
91F ALA* 3.5 4.5 - - - +
92F ILE* 2.6 63.4 + - + +
93F SER* 3.0 32.8 + - - +
119F GLN* 1.3 73.6 - - - +
121F PHE* 1.3 54.6 + - - +
39G LEU* 5.9 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 121 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F GLU* 3.2 8.1 - - - +
48F VAL* 2.9 49.2 + - + +
50F VAL* 4.4 7.4 - - + -
52F PHE* 3.8 23.8 - + - -
88F ALA* 3.5 26.5 - - + -
90F ASN* 3.5 19.5 - - - +
91F ALA* 3.6 21.3 - - + -
92F ILE* 4.2 4.9 - - - -
119F GLN* 3.5 38.6 - - + -
120F ARG* 1.3 73.0 - - - +
122F SER* 1.3 61.6 + - - +
123F CYS* 3.9 4.0 + - - -
138F ILE* 3.7 35.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 122 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F THR 5.9 0.2 - - - -
46F ASN* 3.4 10.8 + - - +
47F GLU* 4.7 3.4 - - - +
90F ASN* 2.9 38.7 + - - +
92F ILE* 3.9 14.9 - - - +
121F PHE* 1.3 70.1 - - - +
123F CYS* 1.3 62.0 + - - +
37G ASN* 3.0 31.9 + - - -
39G LEU* 5.3 0.4 - - - -
----------------------------------------------------------
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