Contacts of the helix formed by residues 99 - 116 (chain O) in PDB entry 4R2G
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 99 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97O LYS 3.5 4.8 + - - +
98O ASN* 1.3 75.1 + - - +
100O MET* 1.3 59.9 + - - +
101O VAL 2.9 6.1 - - - -
102O GLU* 3.0 32.3 + - - +
103O GLN* 3.5 14.8 + - - +
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Residues in contact with MET 100 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98O ASN* 2.6 29.2 + - - +
99O ASN* 1.3 71.5 - - - +
101O VAL* 1.3 56.3 + - - +
103O GLN* 3.3 7.8 + - - +
104O MET* 2.9 31.2 + - - +
217O TYR* 3.5 28.9 - - + +
225O ILE* 4.1 3.8 - - + -
248O THR* 3.5 31.6 - - + -
483O LEU* 3.7 26.2 - - + +
486O TYR* 3.6 27.1 - - + -
487O LYS 4.3 0.2 - - - -
488O VAL* 3.5 32.3 - - + -
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Residues in contact with VAL 101 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98O ASN* 3.1 26.5 + - + +
100O MET* 1.3 81.2 - - - +
102O GLU* 1.3 75.5 + - + +
104O MET* 3.5 5.8 + - - +
105O GLN* 2.9 27.7 + - - +
476O ARG* 3.2 37.5 - - + +
479O TRP* 3.8 12.8 - - + -
480O ARG* 3.7 36.1 - - + +
483O LEU* 4.1 6.8 - - + +
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Residues in contact with GLU 102 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98O ASN 5.1 0.2 - - - +
99O ASN* 3.0 28.6 + - - +
101O VAL* 1.3 84.6 - - + +
103O GLN* 1.3 61.8 + - - +
105O GLN* 3.2 9.8 + - - +
106O GLU* 2.8 30.4 + - - +
476O ARG* 3.4 38.4 + - - -
480O ARG* 4.8 2.6 + - - -
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Residues in contact with GLN 103 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157I LYS* 6.2 0.4 - - - +
99O ASN* 3.5 12.6 + - - +
100O MET* 3.3 8.4 + - - +
102O GLU* 1.3 78.3 - - - +
104O MET* 1.3 52.9 + - - +
106O GLU* 3.3 12.3 + - - +
107O ASP* 2.8 46.2 + - - +
217O TYR* 3.8 32.8 + - + -
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Residues in contact with MET 104 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100O MET 2.9 17.8 + - - +
101O VAL 3.5 4.9 - - - +
103O GLN* 1.3 75.5 - - - +
105O GLN* 1.3 65.2 + - - +
107O ASP* 3.1 8.9 + - - +
108O VAL* 3.0 28.2 + - + +
215O ILE* 4.3 21.8 - - + -
217O TYR* 5.6 8.9 - - + -
251O ILE* 3.5 48.9 - - + -
253O PRO* 5.0 5.4 - - + -
479O TRP* 3.4 46.9 - - + -
483O LEU* 4.2 10.3 - - + -
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Residues in contact with GLN 105 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101O VAL 2.9 19.2 + - - +
102O GLU* 3.4 15.0 - - - +
104O MET* 1.3 75.3 - - - +
106O GLU* 1.3 66.6 + - - +
108O VAL* 4.2 1.4 - - - +
109O ILE* 3.1 46.4 + - + +
427O TRP* 3.7 27.0 + - - -
428O GLN 4.5 6.7 + - - -
474O ASP* 5.7 0.6 + - - -
475O MET* 3.9 8.9 - - - +
476O ARG* 4.2 22.2 - - + +
479O TRP* 3.2 27.9 + - + +
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Residues in contact with GLU 106 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157I LYS* 5.4 6.5 + - - +
102O GLU 2.8 16.1 + - - +
103O GLN* 3.5 14.6 - - - +
105O GLN* 1.3 79.9 - - - +
107O ASP* 1.3 55.7 + - - +
109O ILE* 3.4 22.6 + - - +
110O ASN* 3.0 50.7 + - - +
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Residues in contact with ASP 107 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154I SER* 3.4 21.4 + - - -
155I PRO* 3.3 37.6 - - + +
103O GLN* 2.8 31.7 + - - +
104O MET* 3.1 13.1 + - - +
106O GLU* 1.3 73.8 - - - +
108O VAL* 1.3 59.7 + - + +
110O ASN* 3.3 9.4 + - - +
111O LEU* 2.8 26.1 + - - +
215O ILE* 4.7 15.1 - - + +
216O HIS 5.4 3.1 - - - +
217O TYR* 5.1 6.8 - - - -
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Residues in contact with VAL 108 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104O MET* 3.0 20.4 + - - +
105O GLN 4.3 0.7 - - - +
107O ASP* 1.3 72.6 - - - +
109O ILE* 1.3 61.0 - - - +
111O LEU* 3.9 9.6 - - + -
112O TRP* 2.8 51.1 + - + +
215O ILE* 4.7 7.9 - - + -
253O PRO* 3.5 31.6 - - + +
255O VAL* 4.0 11.4 - - + -
427O TRP* 3.8 14.4 - - + -
479O TRP* 3.8 20.0 - - + -
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Residues in contact with ILE 109 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105O GLN* 3.1 32.9 + - + +
106O GLU* 3.4 25.8 - - - +
107O ASP 3.3 0.2 - - - -
108O VAL* 1.3 76.8 - - - +
110O ASN* 1.3 64.1 + - - +
112O TRP* 3.5 1.9 - - - +
113O ASP* 2.9 32.8 + - + +
427O TRP* 3.7 23.3 - - + -
428O GLN* 3.6 40.5 + - + +
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Residues in contact with ASN 110 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155I PRO 4.1 7.8 + - - +
156I VAL 3.8 14.4 - - - +
157I LYS* 3.9 44.7 - - - +
106O GLU* 3.0 39.4 + - - +
107O ASP* 3.6 10.5 + - - +
108O VAL 3.2 0.2 - - - -
109O ILE* 1.3 78.4 - - - +
111O LEU* 1.3 66.9 + - - +
112O TRP 3.4 0.3 + - - -
113O ASP* 3.5 6.7 + - - +
114O GLN* 3.4 27.2 + - - +
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Residues in contact with LEU 111 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148I ALA* 4.5 11.7 - - + -
149I TRP 6.1 0.4 - - - +
155I PRO* 4.1 17.9 - - + +
156I VAL 5.2 0.2 - - - -
107O ASP 2.8 17.0 + - - +
108O VAL* 3.2 13.9 + - + +
110O ASN* 1.3 76.4 - - - +
112O TRP* 1.3 63.2 + - + +
114O GLN* 3.4 4.5 + - + +
115O SER* 2.9 40.3 + - - +
210O PHE* 4.8 14.4 - - + -
212O PRO* 5.3 0.7 - - + -
213O ILE* 4.1 27.4 - - + +
215O ILE* 4.1 20.6 - - + -
253O PRO* 4.3 16.6 - - + -
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Residues in contact with TRP 112 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108O VAL* 2.8 30.4 + - + +
111O LEU* 1.3 75.8 - - + +
113O ASP* 1.3 58.2 + - - +
114O GLN 2.8 11.6 + - - -
115O SER* 4.4 1.8 - - - +
116O LEU* 2.9 58.1 + - + +
210O PHE* 3.7 27.0 - + - -
253O PRO 5.2 0.6 + - - -
255O VAL* 3.4 29.4 - - + +
377O ASN* 4.4 9.6 - - + -
382O PHE* 3.5 31.6 - + - -
424O ILE* 5.6 0.9 - - + -
427O TRP* 3.3 37.0 - + - -
428O GLN* 3.1 26.2 - - - +
435O TYR* 3.7 24.0 - + - -
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Residues in contact with ASP 113 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157I LYS 5.3 3.4 - - - +
109O ILE* 2.9 22.5 + - + +
110O ASN* 3.5 9.6 + - - +
111O LEU 3.4 0.4 - - - -
112O TRP* 1.3 75.7 - - - +
114O GLN* 1.3 72.1 + - - +
116O LEU 5.0 2.2 - - - -
117O LYS* 3.9 14.7 - - - +
118O PRO* 4.8 8.5 - - - +
121O LYS* 3.7 28.6 + - - +
203O GLN* 4.3 13.0 + - - -
428O GLN* 4.2 7.2 - - - +
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Residues in contact with GLN 114 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156I VAL* 3.9 17.0 - - + +
157I LYS 3.5 5.0 - - - +
158I ALA* 3.1 27.7 - - - +
159I GLY 4.0 1.5 + - - +
160I VAL* 3.4 49.8 - - + +
110O ASN 3.4 16.4 - - - +
111O LEU* 3.8 3.8 - - + +
112O TRP 2.8 2.0 + - - -
113O ASP* 1.3 94.2 - - - +
115O SER* 1.3 62.7 + - - +
116O LEU 3.6 0.2 - - - -
117O LYS* 3.7 32.2 - - - +
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Residues in contact with SER 115 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146I THR* 4.7 6.9 - - - +
147I VAL 3.7 20.1 + - - -
148I ALA* 4.9 1.7 - - - +
111O LEU* 2.9 30.0 + - - +
112O TRP 4.5 0.2 - - - -
114O GLN* 1.3 78.9 - - - +
116O LEU* 1.3 63.1 + - - +
117O LYS* 3.6 3.0 + - - +
208O VAL* 4.7 16.8 - - - +
209O SER 5.3 2.0 - - - +
210O PHE* 3.5 30.9 - - - -
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Residues in contact with LEU 116 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112O TRP* 2.9 46.8 + - + +
115O SER* 1.3 77.7 - - - +
117O LYS* 1.3 65.4 + - - +
118O PRO* 3.0 10.9 - - - +
208O VAL 4.7 8.5 - - - +
210O PHE* 3.5 55.0 - - + -
377O ASN* 4.1 9.0 - - - +
380O GLY* 4.0 19.7 - - - +
382O PHE* 4.4 5.2 - - + -
435O TYR* 3.3 20.4 - - + -
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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
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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) + - + + + + + -
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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