Contacts of the strand formed by residues 138 - 149 (chain F) in PDB entry 1N13
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 138 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96F ALA* 3.5 28.9 - - + -
97F ILE 3.5 16.4 - - - +
99F LYS* 3.6 15.1 + - - -
128F LYS* 4.5 20.9 - - + -
131F PHE* 3.8 20.6 - - + -
136F TRP 3.4 3.2 + - - +
137F GLU* 1.3 74.5 + - - +
139F ASP* 1.3 62.2 + - - +
140F ARG* 3.5 14.8 - - - +
141F ILE* 3.8 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 139 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F ILE* 2.8 21.1 + - - +
98F PRO 3.6 15.7 - - - +
99F LYS* 3.7 19.1 - - + +
101F LYS* 3.3 14.8 + - - -
137F GLU 3.8 2.0 + - - -
138F LEU* 1.3 75.5 - - - +
140F ARG* 1.3 97.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 140 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61F ILE* 4.7 8.9 - - - +
97F ILE* 2.9 55.9 + - + +
101F LYS* 4.5 3.8 - - - +
138F LEU* 3.5 7.0 - - - +
139F ASP* 1.3 117.0 + - - +
141F ILE* 1.3 69.6 + - - +
142F GLU* 2.8 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 141 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94F SER* 3.8 19.7 - - - -
95F VAL 3.4 11.4 - - - +
96F ALA* 4.2 4.5 - - - -
124F ARG* 2.8 75.0 + - + +
127F ALA* 4.3 2.9 - - + -
128F LYS* 4.0 15.0 - - + +
138F LEU* 3.8 28.5 - - + -
140F ARG* 1.3 83.3 - - - +
142F GLU* 1.3 71.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 142 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E LEU* 3.7 15.6 - - + +
61F ILE* 4.3 24.7 - - + +
94F SER* 3.3 2.6 - - - -
95F VAL* 2.8 34.5 + - + +
97F ILE* 3.6 23.3 - - + -
140F ARG* 2.8 31.9 + - - +
141F ILE* 1.3 74.1 - - - +
143F SER* 1.3 63.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 143 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E LEU* 3.8 6.9 - - - +
93F ILE 3.2 14.8 - - - -
94F SER* 4.1 3.6 - - - -
120F GLU* 2.7 29.8 + - - +
123F VAL* 4.7 0.7 - - - -
124F ARG* 2.9 40.7 + - - +
141F ILE 4.1 0.2 + - - -
142F GLU* 1.3 77.2 + - - +
144F ILE* 1.3 63.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 144 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E LEU* 3.9 26.2 - - + +
21E VAL* 3.8 42.0 - - - +
22E ALA* 3.8 13.5 - - + +
92F ALA* 3.2 4.2 - - - +
93F ILE* 2.9 47.4 + - + +
120F GLU* 4.1 4.5 - - - -
143F SER* 1.3 77.3 - - - +
145F ALA* 1.3 69.6 + - - +
158F ALA* 4.5 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 145 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E ALA* 4.4 4.4 - - - +
91F ALA 3.3 7.2 - - - +
92F ALA* 3.6 16.6 - - + +
116F LYS* 3.2 50.1 - - + +
119F ALA* 4.8 0.4 - - + -
120F GLU* 3.8 14.4 + - + +
144F ILE* 1.3 85.4 - - - +
146F VAL* 1.3 64.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 146 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E ALA* 3.9 9.9 - - + -
23E GLY* 3.7 26.5 - - - +
24E SER* 4.2 8.1 - - - +
40E ASN* 5.6 0.4 - - - +
90F SER* 3.1 6.9 - - - -
91F ALA* 2.9 39.4 + - + +
116F LYS* 4.2 7.2 - - - +
145F ALA* 1.3 76.8 - - - +
147F GLU* 1.3 71.5 + - - +
156F ALA* 4.3 2.9 - - + -
157F PHE 3.3 34.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 147 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E SER* 4.2 3.3 + - - -
88F THR* 4.0 12.8 - - + +
89F ILE 3.2 6.1 - - - +
90F SER* 3.1 15.5 - - - +
115F SER* 3.6 12.5 - - - -
116F LYS* 3.0 37.0 + - + +
146F VAL* 1.3 84.8 - - - +
148F HIS* 1.3 62.3 + - - +
149F THR* 6.1 0.9 - - - +
156F ALA* 5.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 148 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E SER* 3.1 30.5 + - - -
25E SER* 3.9 21.5 - - - -
26E GLU* 2.8 35.3 + - + -
87F GLU 3.5 2.3 - - - +
88F THR* 3.3 3.5 - - - -
89F ILE* 2.7 46.0 + - + +
147F GLU* 1.3 75.8 - - - +
149F THR* 1.3 77.6 + - - +
150F VAL* 3.8 6.1 - - + -
151F GLU* 5.4 2.5 - - - -
154F GLY* 3.8 17.8 - - - -
155F CYS 4.3 4.3 - - - +
156F ALA* 4.4 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 149 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E GLU* 4.1 0.2 - - - +
86F GLY* 3.9 26.7 - - - +
87F GLU 3.5 3.6 - - - +
88F THR* 3.9 15.5 + - - +
147F GLU* 6.1 0.9 - - - +
148F HIS* 1.3 84.7 + - - +
150F VAL* 1.3 68.9 + - - +
151F GLU* 3.5 9.5 + - - +
----------------------------------------------------------
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