Contacts of the strand formed by residues 112 - 118 (chain C) in PDB entry 4J1R
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 LEU 112 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C GLY* 3.7 27.8 - - - -
46C GLN* 4.2 7.2 + - - +
98C LEU* 4.0 22.7 - - + -
101C MET* 3.7 47.2 + - + +
102C ARG* 4.4 2.5 - - + -
110C VAL 3.8 2.4 + - - -
111C ARG* 1.3 80.1 - - - +
113C ARG* 1.3 62.9 + - - +
114C TYR 3.2 23.6 - - - +
115C PHE* 4.4 3.6 - - + -
130C LEU* 4.1 13.0 - - + -
131C VAL 3.5 16.2 - - - +
132C LEU* 3.7 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 113 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C PRO* 3.5 2.8 - - - +
45C GLY 2.9 17.1 + - - -
46C GLN 4.7 0.3 + - - -
75C LEU* 3.8 18.5 - - - +
78C SER* 4.4 1.6 + - - -
80C GLU* 2.7 36.2 + - - +
81C LEU 4.2 6.3 + - - -
82C VAL* 3.8 18.3 - - + +
111C ARG* 3.3 38.2 - - - +
112C LEU* 1.3 73.1 - - - +
114C TYR* 1.3 90.6 + - + +
131C VAL* 2.7 29.4 + - + +
132C LEU 4.1 9.0 - - - -
133C ASP* 2.9 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 114 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C ALA* 3.7 13.7 - - + -
43C THR 3.2 11.2 - - - +
44C PRO* 3.7 21.8 - - + -
45C GLY 3.9 1.3 - - - +
52C GLN* 4.1 22.6 + - - -
54C VAL* 4.2 37.0 - - + -
75C LEU* 4.4 16.3 - - + +
77C ASP* 4.6 10.4 + - - -
112C LEU* 3.2 12.7 - - - +
113C ARG* 1.3 103.4 + - + +
115C PHE* 1.3 65.5 + - - +
131C VAL* 3.1 38.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 115 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C ALA* 3.4 2.7 - - - +
43C THR* 3.0 61.9 + - + -
44C PRO 4.1 3.6 - - - -
45C GLY* 4.3 8.3 - - - -
49C ASP* 5.5 0.9 - - - -
98C LEU* 3.8 33.2 - - + -
102C ARG* 3.7 43.1 - - - -
112C LEU* 4.4 1.6 - - + -
114C TYR* 1.3 80.7 - - - +
116C PHE* 1.3 64.2 + - - +
117C TYR* 4.5 15.0 - + - -
128C LEU* 4.1 7.0 - - + -
129C ASN 3.1 15.0 - - - +
130C LEU* 4.0 15.5 - - + -
503C K 4.2 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 116 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C VAL* 3.8 39.3 - - + -
41C VAL 3.4 22.9 - - - +
42C ALA* 3.7 8.7 - - + -
56C TYR* 3.9 23.8 - + - -
84C ILE* 4.4 6.3 - - + -
115C PHE* 1.3 79.3 - - - +
117C TYR* 1.3 82.1 + - - +
118C SER* 4.4 8.5 - - - -
127C TYR 3.7 0.2 - - - +
128C LEU* 3.8 1.6 - - - +
129C ASN* 2.8 70.3 + - + +
131C VAL* 3.9 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 117 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C VAL 5.0 1.2 + - - -
89C GLN* 5.3 8.2 - - + +
98C LEU* 4.0 13.5 - - - +
115C PHE* 4.5 15.2 - + - -
116C PHE* 1.3 86.5 - - - +
118C SER* 1.3 62.3 + - - +
126C VAL* 4.7 19.7 - - + -
127C TYR 3.3 15.7 - - - +
128C LEU* 3.8 35.0 - - + +
503C K 4.6 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 118 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C LYS* 3.6 23.4 - - - -
116C PHE* 4.6 8.3 - - - -
117C TYR* 1.3 76.0 - - - +
119C SER* 1.3 63.4 + - - +
120C GLY 3.6 0.3 + - - -
126C VAL* 3.7 5.6 - - - +
127C TYR* 3.0 30.5 + - - +
129C ASN* 2.7 27.7 + - - -
----------------------------------------------------------
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