Contacts of the helix formed by residues 99 - 120 (chain D) in PDB entry 3HSR
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 THR 99 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80D ASP* 2.7 49.2 + - - +
81D TYR 2.9 9.3 + - - -
82D VAL 3.7 24.9 - - - +
83D VAL* 4.2 9.9 - - + +
98D LEU* 1.3 77.7 - - - +
100D GLU* 1.3 67.2 + - - +
101D GLN 3.3 2.8 + - - -
102D GLY 2.9 12.8 + - - -
103D LYS* 3.1 19.9 + - - +
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Residues in contact with GLU 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D LEU 5.3 0.2 - - - +
99D THR* 1.3 73.9 - - - +
101D GLN* 1.3 62.0 + - - +
103D LYS* 3.4 36.8 + - - +
104D ALA* 3.0 23.0 + - - +
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Residues in contact with GLN 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D LYS 4.6 2.3 + - - +
80D ASP* 3.1 41.2 + - - +
81D TYR* 4.1 21.9 + - + -
99D THR* 3.2 2.4 + - - -
100D GLU* 1.3 79.4 - - - +
102D GLY* 1.3 60.6 + - - +
104D ALA* 3.1 17.5 + - + +
105D ILE* 3.2 20.9 + - + +
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Residues in contact with GLY 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D LEU* 5.6 1.7 - - - +
80D ASP 4.0 1.2 + - - -
81D TYR* 3.6 28.9 - - - -
98D LEU* 4.4 13.3 - - - +
99D THR* 2.9 12.0 + - - -
101D GLN* 1.3 77.8 - - - +
103D LYS* 1.3 59.8 + - - +
105D ILE* 3.3 21.0 + - - +
106D LYS* 3.3 12.6 + - - +
109D LEU* 5.6 0.3 - - - +
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Residues in contact with LYS 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D ASN* 3.2 50.9 + - + +
50D ASP* 4.3 21.7 + - - +
98D LEU* 3.8 30.6 + - + +
99D THR 3.1 11.4 + - - +
100D GLU* 3.4 38.3 + - - +
102D GLY* 1.3 73.9 - - - +
104D ALA* 1.3 62.2 + - - +
105D ILE 3.2 0.7 + - - -
106D LYS* 3.3 15.7 + - - +
107D SER 4.6 1.2 + - - -
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Residues in contact with ALA 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D GLU 3.0 13.8 + - - +
101D GLN* 3.1 14.7 + - + +
103D LYS* 1.3 77.1 - - - +
105D ILE* 1.3 65.0 + - + +
107D SER* 4.6 1.9 + - - -
108D PRO* 3.8 11.3 - - - +
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Residues in contact with ILE 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D TYR* 4.0 30.1 - - + -
36D LEU* 4.6 0.7 - - + -
44D LEU* 4.3 5.4 - - + -
81D TYR* 3.5 39.5 - - + +
101D GLN* 3.2 20.5 + - + +
102D GLY* 3.4 13.9 - - - +
103D LYS 3.2 0.4 - - - -
104D ALA* 1.3 80.3 - - + +
106D LYS* 1.3 64.4 + - - +
107D SER 3.3 2.7 - - - -
108D PRO* 2.9 9.8 - - + +
109D LEU* 2.8 46.8 + - + +
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Residues in contact with LYS 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D LEU* 2.8 29.2 + - + +
45D MET* 2.9 40.1 + - + +
47D ILE 2.9 18.5 + - - +
48D GLU* 4.6 8.5 + - - +
49D ASN* 3.3 30.3 - - - +
98D LEU* 4.3 9.4 - - + -
102D GLY 3.3 9.1 + - - +
103D LYS* 3.3 15.2 + - - +
105D ILE* 1.3 76.4 - - - +
107D SER* 1.3 62.7 + - - +
109D LEU* 3.6 8.1 - - + +
110D ALA* 3.0 25.1 + - + +
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Residues in contact with SER 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D LYS 4.6 2.0 + - - -
104D ALA 4.6 2.0 + - - -
106D LYS* 1.3 81.4 - - - +
108D PRO* 1.4 72.6 - - - +
110D ALA* 3.1 5.8 + - - +
111D GLU* 3.0 41.7 + - - +
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Residues in contact with PRO 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D TYR* 3.2 25.8 - - + +
104D ALA 3.8 7.2 - - - +
105D ILE* 2.9 36.1 - - + +
107D SER* 1.4 89.8 - - - +
109D LEU* 1.3 60.8 + - - +
111D GLU* 3.0 25.7 + - + +
112D ILE* 3.0 16.3 + - - +
115D LYS* 5.9 0.5 - - - -
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Residues in contact with LEU 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D LEU* 4.0 7.9 - - + -
34D TYR* 4.1 16.4 - - + -
36D LEU* 4.1 10.1 - - + -
41D TYR* 2.8 37.2 + - + -
44D LEU* 3.9 24.7 - - + -
45D MET* 3.5 23.3 - - + -
102D GLY 5.6 0.4 - - - +
105D ILE* 2.8 51.0 + - + +
106D LYS* 4.8 2.0 - - + +
108D PRO* 1.3 72.0 - - - +
110D ALA* 1.3 62.9 + - - +
112D ILE* 3.1 32.5 + - + +
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Residues in contact with ALA 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C MET* 4.1 17.7 - - + +
10C LYS* 4.2 19.3 - - - +
41D TYR* 4.4 1.1 - - - -
45D MET* 3.9 13.3 - - + -
106D LYS* 3.0 13.9 + - + +
107D SER* 3.4 10.3 - - - +
109D LEU* 1.3 76.9 - - - +
111D GLU* 1.3 58.5 + - + +
113D SER* 2.9 34.5 + - - -
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Residues in contact with GLU 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C MET* 4.4 15.7 - - + -
107D SER* 3.0 34.1 + - - +
108D PRO* 3.0 17.1 + - + +
110D ALA* 1.3 76.0 - - + +
112D ILE* 1.3 63.5 + - - +
114D VAL* 3.1 15.6 + - - +
115D LYS* 3.1 21.0 + - - +
144D GOL 4.1 35.5 + - - +
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Residues in contact with ILE 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D TYR* 3.6 27.4 - - + +
30D TYR* 3.7 41.1 - - + +
31D LEU* 3.8 27.6 - - + -
34D TYR* 3.9 16.8 - - + -
41D TYR* 4.1 2.2 - - + +
108D PRO 3.0 16.1 + - - +
109D LEU* 3.2 27.1 - - + +
110D ALA 3.0 0.6 - - - -
111D GLU* 1.3 76.5 - - - +
113D SER* 1.3 55.0 + - - +
115D LYS* 3.2 13.3 + - + +
116D VAL* 2.9 27.4 + - + +
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Residues in contact with SER 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C BT6 4.6 1.3 - - - -
6C MET* 3.8 21.8 + - - +
9C SER* 2.7 28.3 + - - -
10C LYS* 3.9 18.3 - - - +
27D TYR* 3.4 26.0 - - - -
41D TYR* 4.0 5.1 + - - -
109D LEU 3.9 1.0 + - - -
110D ALA 2.9 17.1 + - - -
112D ILE* 1.3 78.3 - - - +
114D VAL* 1.3 59.1 + - - +
116D VAL* 3.4 0.7 + - - +
117D PHE 3.0 16.1 + - - -
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Residues in contact with VAL 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C HIS* 3.8 18.8 - - + -
6C MET* 3.7 49.1 - - + +
111D GLU* 3.1 8.9 + - - +
113D SER* 1.3 79.1 + - - +
115D LYS* 1.3 61.2 + - - +
117D PHE* 3.2 1.4 + - - +
118D ASN* 2.8 55.2 + - - +
144D GOL 3.7 28.7 - - - +
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Residues in contact with LYS 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D TYR* 3.8 41.1 + - + +
108D PRO 5.9 0.4 - - - -
111D GLU* 3.1 17.8 + - - +
112D ILE* 3.3 14.8 - - + +
114D VAL* 1.3 79.5 - - - +
116D VAL* 1.3 60.9 + - - +
118D ASN* 3.3 6.2 + - - +
119D GLU* 3.2 25.1 + - - +
144D GOL 2.7 43.5 + - - +
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Residues in contact with VAL 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C SER* 4.7 2.0 - - - +
23D ILE* 4.3 4.3 - - + +
26D LYS* 3.9 16.2 - - + -
27D TYR* 3.5 49.4 - - + +
30D TYR* 3.7 27.4 - - + -
112D ILE* 2.9 26.2 + - + +
113D SER 3.8 4.0 - - - +
115D LYS* 1.3 71.3 - - - +
117D PHE* 1.3 64.8 + - - +
119D GLU* 2.9 22.4 + - - +
120D PHE* 3.5 21.3 - - + -
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Residues in contact with PHE 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C HIS* 3.6 54.3 - + + +
8C LEU* 4.3 15.3 - - + -
9C SER* 3.5 26.4 + - - +
12C LEU* 4.5 7.9 - - + -
113D SER 3.0 17.3 + - - +
114D VAL* 3.5 4.3 - - - +
116D VAL* 1.3 78.3 - - - +
118D ASN* 1.3 63.0 + - - +
119D GLU 3.2 1.0 + - - -
120D PHE* 3.2 26.2 + - - +
122D ILE* 3.7 38.9 - - + +
123D SER 4.4 11.2 - - - -
124D GLU* 4.8 1.8 - - + -
127D ALA* 3.9 20.2 - - + -
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Residues in contact with ASN 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C HIS* 2.8 37.4 + - - -
114D VAL* 2.8 40.2 + - - +
115D LYS* 3.8 6.4 + - - +
116D VAL 3.2 0.2 - - - -
117D PHE* 1.3 74.1 - - - +
119D GLU* 1.3 63.1 + - - +
120D PHE 3.3 5.0 + - - +
144D GOL 4.5 6.4 - - - -
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Residues in contact with GLU 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C ASN* 4.6 1.9 + - - -
26D LYS* 2.9 42.0 + - + +
29D ASN* 5.8 2.4 + - - -
30D TYR* 2.4 38.0 + - - +
115D LYS 3.2 10.4 + - - +
116D VAL 2.9 10.7 + - - +
118D ASN* 1.3 79.8 - - - +
120D PHE* 1.3 61.4 + - - +
121D ASN 4.2 0.2 + - - -
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Residues in contact with PHE 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C PHE* 3.6 23.3 - + + -
141C ASN* 3.4 17.3 - - + +
142C PHE* 4.3 19.5 - + - -
22D GLU* 3.9 16.6 - - + -
23D ILE* 3.8 26.5 - - + -
26D LYS* 3.6 36.6 - - + -
116D VAL* 3.5 29.8 - - + -
117D PHE* 3.2 13.4 + - - +
118D ASN* 4.0 4.7 - - - +
119D GLU* 1.3 81.1 - - - +
121D ASN* 1.3 60.0 + - - +
122D ILE* 3.3 26.2 + - + +
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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
------------------------------------------------------------
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