Contacts of the strand formed by residues 103 - 112 (chain G) in PDB entry 1I3R
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 ASN 103 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93G SER* 4.8 1.6 - - - -
94G ARG* 3.8 2.8 + - - +
95G SER* 3.1 45.2 + - - -
96G PRO 3.2 16.0 + - - -
97G VAL* 3.9 9.5 - - - +
98G ASN 4.8 0.4 - - - +
101G GLU* 3.9 11.8 + - - +
102G PRO* 1.3 76.8 + - - +
104G ILE* 1.3 92.0 + - - +
152G THR* 3.6 3.5 - - - -
153G PHE* 3.0 50.6 + - + +
155G PRO* 4.1 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 104 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93G SER* 3.6 2.4 - - - -
94G ARG* 2.8 64.7 + - + +
103G ASN* 1.3 90.8 + - - +
105G LEU* 1.3 72.5 + - - +
106G ILE* 4.4 0.2 - - + -
150G TYR* 4.0 27.4 - - + -
151G LEU 3.3 9.6 - - - +
152G THR* 4.5 16.8 - - + -
153G PHE* 3.6 4.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 105 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G VAL* 4.4 2.9 - - + -
92G LEU 3.6 20.9 - - - +
93G SER* 4.0 5.2 - - - -
104G ILE* 1.3 75.0 - - - +
106G ILE* 1.3 61.6 + - - +
121G TRP* 3.6 22.6 - - + -
150G TYR* 3.4 6.9 - - - -
151G LEU* 2.7 40.7 + - + +
153G PHE* 3.6 19.7 - - + -
161G TYR* 3.5 49.1 - - + -
178G TRP* 3.8 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 106 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G VAL* 3.1 7.4 - - - +
92G LEU* 2.6 60.0 + - + +
93G SER 4.3 2.7 - - - +
94G ARG* 3.5 31.9 - - + +
104G ILE* 4.4 0.2 - - + -
105G LEU* 1.3 78.1 - - - +
107G CYS* 1.3 63.9 + - - +
108G PHE* 4.2 1.6 - - + +
121G TRP* 3.9 2.5 - - - -
148G PHE* 3.9 28.9 - - + -
149G HIS 3.7 2.7 - - - +
150G TYR* 3.9 18.6 - - + -
175H ARG 5.9 0.2 - - - +
176H ASN* 3.5 38.4 - - + +
182H GLN* 4.6 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 107 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89G VAL* 3.8 20.4 - - - -
90G THR 3.6 2.5 - - - -
91G VAL* 4.6 2.2 - - - +
106G ILE* 1.3 72.7 - - - +
108G PHE* 1.3 59.2 + - - +
109G ILE* 3.7 9.4 + - - +
119G VAL* 4.7 0.2 - - - -
121G TRP* 3.6 18.5 - - + -
147G LYS 3.6 1.7 - - - +
148G PHE* 3.6 3.3 - - - -
149G HIS* 2.9 36.5 + - + +
163G CYS* 2.0 49.1 - - + -
165G VAL* 4.2 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 108 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88G GLU 3.5 1.6 - - - +
89G VAL* 3.4 5.6 - - - +
90G THR* 2.8 46.6 + - - +
92G LEU* 4.7 7.4 - - + -
106G ILE* 3.8 5.8 - - + -
107G CYS* 1.3 70.8 - - - +
109G ILE* 1.3 64.5 + - - +
110G ASP* 3.8 27.9 + - + +
146G ARG* 3.8 33.9 - - + -
147G LYS 3.7 6.1 - - - -
148G PHE* 3.4 47.8 - + + -
175H ARG* 5.9 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 109 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87G PRO* 3.4 32.1 - - + -
88G GLU 3.5 4.5 - - - +
89G VAL* 4.6 1.3 - - + -
107G CYS* 4.0 10.5 - - - +
108G PHE* 1.3 75.3 - - - +
110G ASP* 1.3 59.5 + - - +
112G PHE* 3.4 17.9 - - + -
117G VAL* 4.7 9.6 - - + -
119G VAL* 3.5 35.0 - - + -
146G ARG* 3.1 5.5 - - - +
147G LYS* 2.7 47.0 + - + +
149G HIS* 4.1 13.0 - - + +
165G VAL* 4.0 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 110 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87G PRO* 3.3 3.3 - - - +
88G GLU* 2.9 43.6 + - + +
108G PHE* 3.8 32.3 - - + -
109G ILE* 1.3 75.6 - - - +
111G LYS* 1.3 91.8 + - + +
112G PHE* 3.5 2.9 - - - -
140G ARG* 3.1 33.7 + - - +
145G PHE 3.7 2.2 - - - -
146G ARG* 3.4 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 111 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F GLY 5.8 1.2 + - - -
24F SER* 5.9 1.8 - - - -
61F GLU* 4.5 21.0 + - - +
85G VAL* 3.9 9.2 - - - +
86G ALA 3.2 16.3 - - - +
88G GLU* 2.8 37.1 + - + +
110G ASP* 1.3 94.9 + - - +
112G PHE* 1.3 57.7 + - - +
140G ARG* 3.4 32.5 - - - +
144G LEU* 3.9 23.7 - - + +
145G PHE 3.1 7.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 112 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85G VAL 3.3 15.0 - - - +
87G PRO* 3.4 33.4 - - + -
109G ILE* 3.4 31.0 - - + -
110G ASP 3.7 4.9 - - - -
111G LYS* 1.3 76.6 - - - +
113G SER* 1.3 62.9 + - - +
114G PRO 3.7 17.0 - - - -
115G PRO* 4.2 1.8 - - + -
117G VAL* 3.8 12.6 - - + -
137G PHE* 3.7 39.5 - + - -
144G LEU* 3.7 5.3 - - - +
145G PHE* 2.9 49.9 + - + -
146G ARG* 3.8 0.9 - - - -
147G LYS* 4.2 8.1 - - + -
167G HIS* 3.8 7.9 - + + -
----------------------------------------------------------
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