Contacts of the strand formed by residues 129 - 136 (chain G) in PDB entry 1ILN
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 HIS 129 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118G TRP* 5.1 0.9 - + - -
120G ASN* 3.2 34.1 + - - +
122G PHE* 3.7 35.4 - + + -
123G LEU* 3.3 34.3 - - + +
127G LEU* 3.8 10.8 + - + -
128G GLU* 1.3 107.2 + - - +
130G LEU* 1.3 60.0 + - - +
131G VAL* 4.1 4.3 - - + -
149G ARG* 3.5 6.8 + - - -
150G HIS* 3.0 51.6 + + + +
169G SER* 5.7 0.2 - - - +
170G ARG 4.0 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 130 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B LYS* 3.8 9.6 - - - +
128G GLU 3.6 1.2 + - - -
129G HIS* 1.3 75.7 - - - +
131G VAL* 1.3 74.2 + - - +
132G GLN* 4.3 0.9 - - + +
147G ASP* 3.3 27.1 - - - +
148G TYR 3.1 25.8 - - - +
149G ARG* 3.9 13.5 - - - +
170G ARG* 3.0 43.6 + - + +
172G ASN* 3.4 50.9 - - + +
174G LEU 4.8 6.1 - - - +
175G CYS* 6.0 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 131 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G PRO* 3.9 12.8 - - + -
118G TRP* 3.5 40.4 - - + -
122G PHE* 4.2 12.3 - - + -
129G HIS* 4.7 5.4 - - + -
130G LEU* 1.3 80.6 - - - +
132G GLN* 1.3 65.7 + - - +
133G TYR* 5.3 2.0 - - + -
148G TYR* 2.9 10.8 - - - +
149G ARG 2.8 39.3 + - - +
150G HIS* 5.0 0.2 - - + -
152G PHE* 5.2 0.9 - - + -
167G VAL* 3.4 25.1 - - + -
168G ARG 3.4 13.0 - - - +
169G SER* 4.3 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 132 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130G LEU* 4.3 1.3 + - + -
131G VAL* 1.3 78.5 - - - +
133G TYR* 1.3 64.8 + - - +
145G SER* 5.5 5.2 - - - -
146G VAL 3.2 20.0 - - - +
147G ASP* 3.0 36.2 + - - +
148G TYR 3.7 6.1 - - - +
167G VAL* 4.0 1.0 - - - +
168G ARG* 2.7 76.6 + - + +
170G ARG* 5.0 4.6 - - - +
184G TRP* 3.9 7.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 133 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105G THR 5.6 0.2 - - - -
106G LEU* 3.5 18.9 - - - +
116G LEU* 3.1 26.3 - - + +
118G TRP* 4.0 12.1 - + - -
131G VAL* 5.3 0.2 - - + -
132G GLN* 1.3 77.3 - - - +
134G ARG* 1.3 77.5 + - - +
135G THR* 4.4 3.4 - - + -
145G SER* 3.6 14.6 - - - -
146G VAL 3.3 13.3 - - - +
148G TYR* 3.3 27.6 - - + -
152G PHE* 4.1 13.5 - + + -
154G LEU* 3.4 17.0 - - + -
163G TYR* 3.3 22.2 - - - -
165G PHE* 3.2 54.1 - + + -
166G ARG 4.4 1.1 - - - -
167G VAL* 4.3 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 134 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133G TYR* 1.3 76.6 - - - +
135G THR* 1.4 78.5 + - - +
136G ASP* 5.5 0.2 - - - +
143G GLU* 2.7 49.8 + - - +
144G GLN 3.6 1.6 - - - -
145G SER* 2.9 25.1 + - - +
165G PHE* 3.1 8.0 - - - +
166G ARG* 3.0 53.8 + - - +
184G TRP* 3.5 47.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 135 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133G TYR* 4.3 6.1 - - + -
134G ARG* 1.4 93.1 + - - +
136G ASP* 1.4 70.8 + - - +
142G THR 3.4 1.4 - - - +
143G GLU* 3.8 1.0 - - - +
144G GLN* 3.1 62.4 + - + +
145G SER* 5.8 0.2 - - - -
148G TYR* 5.9 1.3 - - - +
154G LEU* 5.3 2.2 - - + -
156G SER* 4.5 4.3 - - - +
163G TYR* 2.9 43.7 + - - +
164G THR* 3.0 9.3 + - - -
165G PHE* 4.2 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 136 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134G ARG* 5.5 0.4 - - - +
135G THR* 1.4 80.7 + - - +
137G TRP* 1.4 74.3 + - - +
138G ASP 3.7 4.2 + - - +
140G SER 3.5 6.3 - - - +
141G TRP* 4.9 13.0 - - + -
142G THR* 3.0 39.0 + - - +
143G GLU* 4.4 10.1 - - - +
163G TYR* 3.6 1.4 - - - -
164G THR* 3.2 47.5 + - + +
----------------------------------------------------------
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