Contacts of the helix formed by residues 115 - 129 (chain O) in PDB entry 3H1I
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 115 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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359N ASN* 5.1 9.8 + - - -
92O VAL* 4.1 40.0 - - + +
111O CYS* 3.5 8.5 - - - -
112O LEU* 2.9 35.7 + - + +
113O ARG 2.8 3.0 + - - -
114O ASP* 1.3 97.9 + - + +
116O VAL* 1.3 68.5 + - - +
117O ASP* 3.1 4.0 - - - +
118O THR* 3.0 16.4 + - - +
119O VAL* 3.0 21.1 + - - +
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Residues in contact with VAL 116 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45O SER* 3.4 29.2 - - - +
47O ILE* 3.6 16.6 - - + -
111O CYS* 3.5 4.6 - - - -
113O ARG* 3.1 19.7 + - - +
114O ASP 3.8 0.4 - - - -
115O HIS* 1.3 76.7 - - - +
117O ASP* 1.3 67.8 + - - +
119O VAL* 3.2 10.8 - - + +
120O MET* 2.8 50.8 + - + +
211O VAL* 4.4 14.4 - - + -
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Residues in contact with ASP 117 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113O ARG 5.3 0.5 - - - +
114O ASP* 4.5 13.2 - - - +
115O HIS* 4.8 0.4 - - - -
116O VAL* 1.3 82.6 + - - +
118O THR* 1.3 66.4 + - - +
120O MET* 3.4 13.8 - - - +
121O GLU* 3.6 5.9 + - - +
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Residues in contact with THR 118 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88O GLY* 5.1 8.3 - - - +
92O VAL* 5.1 9.9 - - + -
115O HIS* 3.0 21.4 + - - +
117O ASP* 1.3 75.4 - - - +
119O VAL* 1.3 56.6 + - + +
120O MET 2.6 16.3 + - - -
121O GLU* 2.9 25.5 + - - +
122O TYR* 3.7 25.2 - - + +
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Residues in contact with VAL 119 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47O ILE* 5.7 0.9 - - + -
89O ILE* 4.8 13.6 - - + +
92O VAL* 4.0 20.0 - - + -
94O GLY* 4.7 6.3 - - - -
95O SER 5.6 0.2 - - - +
109O VAL* 3.4 43.7 - - + +
110O GLU 5.4 0.4 - - - -
111O CYS* 3.4 45.5 - - + +
115O HIS 3.0 7.6 + - - +
116O VAL* 3.2 18.8 - - + +
118O THR* 1.3 72.3 - - + +
120O MET* 1.3 61.1 + - + +
122O TYR* 4.0 11.9 + - - +
123O LEU 3.6 4.7 + - - -
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Residues in contact with MET 120 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47O ILE* 3.2 50.0 - - + -
109O VAL* 5.2 1.8 - - + -
116O VAL* 2.8 35.2 + - + +
117O ASP* 3.4 9.9 - - - +
118O THR 2.6 6.5 + - - -
119O VAL* 1.3 72.9 - - - +
121O GLU* 1.3 68.8 + - - +
123O LEU* 2.8 25.6 + - - +
124O LEU* 2.8 18.2 + - + +
206O LEU* 5.2 3.8 - - - -
216O LEU* 4.7 11.9 - - + -
219O VAL* 4.1 33.0 - - + -
223O PHE* 5.7 2.5 - - + -
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Residues in contact with GLU 121 (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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79O GLY* 4.7 3.9 - - - +
80O ALA* 5.5 0.7 - - + -
84O ARG* 3.3 30.2 + - - -
117O ASP 3.6 5.6 + - - +
118O THR* 2.9 14.9 + - - +
120O MET* 1.3 78.3 - - - +
122O TYR* 1.3 74.5 + - + +
124O LEU* 3.2 12.3 + - + +
125O ASN* 2.8 47.4 + - - +
223O PHE* 6.5 0.7 - - - -
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Residues in contact with TYR 122 (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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107F TRP* 5.0 2.4 - - - -
80O ALA* 3.8 14.1 - - + -
84O ARG* 3.4 54.6 + - + +
85O ILE* 3.6 29.2 - - + -
88O GLY* 3.8 17.9 - - - -
89O ILE* 4.0 31.9 - - + -
96O LEU* 5.9 0.4 - - - -
118O THR* 3.7 34.3 - - + +
119O VAL* 4.4 4.7 - - - +
120O MET 3.1 0.8 - - - -
121O GLU* 1.3 84.4 + - + +
123O LEU* 1.3 57.6 + - - +
125O ASN* 3.2 4.4 + - - +
126O VAL* 2.7 42.4 + - + +
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Residues in contact with LEU 123 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47O ILE* 3.4 33.4 - - + -
48O GLY 4.3 0.7 - - - +
49O VAL* 4.1 14.4 - - + -
96O LEU* 4.7 7.4 - - + +
107O TYR* 3.3 42.6 - - + +
109O VAL* 3.3 39.3 - - + +
119O VAL 3.6 3.9 + - - +
120O MET* 2.8 17.3 + - - +
122O TYR* 1.3 74.6 - - - +
124O LEU* 1.3 60.5 + - - +
126O VAL* 4.1 4.2 - - + +
127O THR* 2.8 31.4 + - + +
206O LEU* 5.0 0.2 - - + -
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Residues in contact with LEU 124 (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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49O VAL* 6.2 0.7 - - - -
120O MET* 2.8 16.6 + - + +
121O GLU* 3.2 17.3 - - + +
123O LEU* 1.3 76.8 - - - +
125O ASN* 1.3 77.1 + - - +
126O VAL 3.0 1.4 + - - -
127O THR* 3.0 8.2 + - - -
128O THR* 3.0 43.6 + - - +
219O VAL* 5.6 1.8 - - + -
223O PHE* 4.2 36.3 - - + +
224O LEU* 4.0 30.7 - - + -
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Residues in contact with ASN 125 (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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77O THR* 3.0 34.2 + - + +
78O LYS* 4.1 0.9 - - - +
79O GLY* 3.2 32.0 + - - -
80O ALA* 4.5 4.2 - - + +
121O GLU* 2.8 45.3 + - - +
122O TYR* 3.9 5.4 - - - +
124O LEU* 1.3 86.5 - - - +
126O VAL* 1.3 57.4 + - - +
129O ALA* 3.1 36.7 + - - +
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Residues in contact with VAL 126 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73O SER* 3.3 34.8 - - - +
75O LEU 5.6 0.2 - - - +
77O THR* 3.9 6.1 - - + -
85O ILE* 4.3 22.4 - - + -
96O LEU* 4.5 16.2 - - + -
107O TYR* 4.0 27.8 - - + -
122O TYR* 2.7 34.0 + - - +
123O LEU* 4.1 4.9 - - - +
125O ASN* 1.3 75.1 - - - +
127O THR* 1.3 61.2 + - + +
128O THR 3.5 0.4 + - - -
130O PRO* 4.0 17.3 - - - +
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Residues in contact with THR 127 (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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49O VAL* 4.4 22.4 - - + +
51O ILE* 5.0 0.9 - - + -
107O TYR* 3.4 47.6 - - + -
123O LEU* 2.8 26.7 + - + +
124O LEU* 3.0 7.3 + - - -
126O VAL* 1.3 77.4 - - + +
128O THR* 1.3 69.5 + - - +
130O PRO* 4.5 2.7 - - - -
195O VAL* 4.7 2.4 - - - +
199O PHE* 3.5 28.6 - - - +
204O MET* 4.9 2.0 - - - +
224O LEU* 5.1 0.9 - - - +
226O ILE* 3.7 6.8 - - - +
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Residues in contact with THR 128 (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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78O LYS* 5.2 2.3 + - - -
124O LEU* 3.0 27.9 + - - +
127O THR* 1.3 96.8 - - - +
129O ALA* 1.3 63.4 + - - +
130O PRO* 3.4 6.5 - - - +
204O MET* 4.4 8.1 - - + -
224O LEU* 3.6 26.9 - - + -
225O ASN* 5.1 9.3 + - - +
226O ILE* 3.3 34.4 - - + +
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Residues in contact with ALA 129 (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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77O THR* 3.0 3.3 - - - -
78O LYS* 3.0 49.6 + - + +
125O ASN* 3.1 34.3 + - - +
128O THR* 1.3 85.2 + - - +
130O PRO* 1.3 67.4 - - - +
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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
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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