Contacts of the helix formed by residues 104 - 121 (chain D) in PDB entry 4YYJ
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 104 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D ASN* 3.5 9.9 - - + +
101D ARG* 2.7 35.5 + - + +
102D PRO 3.1 0.4 - - - -
103D ASP* 1.3 91.6 - - - +
105D VAL* 1.3 65.3 + - - +
106D TYR* 3.8 16.0 + - + +
107D TYR* 3.2 15.2 + - - +
108D LYS* 3.1 26.3 + - - +
60E ILE* 6.0 3.4 - - + -
8F BTK 6.2 0.2 - - - +
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Residues in contact with VAL 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D HIS* 5.9 0.7 - - + -
44D PHE* 3.3 35.9 - - + -
103D ASP 3.9 0.6 + - - -
104D THR* 1.3 71.7 - - - +
106D TYR* 1.3 64.5 + - + +
108D LYS* 3.9 7.6 - - + +
109D LEU* 3.0 34.8 + - + +
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Residues in contact with TYR 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D PHE* 3.7 45.9 - + + -
45D PHE* 4.6 2.4 - - - -
96D ALA* 4.5 2.4 - - - +
100D ASN* 3.5 36.1 - - - +
104D THR* 3.2 15.0 - - + +
105D VAL* 1.3 78.7 - - + +
107D TYR* 1.3 60.4 + - - +
109D LEU* 3.8 4.1 - - - +
110D ALA* 3.0 30.0 + - - +
8F BTK 3.8 65.4 - - + +
9F GLY* 4.7 8.3 + - - -
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Residues in contact with TYR 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D ALA 4.5 3.8 - - - -
97D MET* 3.5 41.4 - - + +
100D ASN* 3.3 23.8 - - + +
101D ARG 3.2 20.0 - - - +
102D PRO* 3.4 43.2 - - + +
104D THR* 3.2 5.6 + - - +
106D TYR* 1.3 78.8 - - - +
108D LYS* 1.3 64.8 + - + +
110D ALA* 3.2 5.3 + - - +
111D LYS* 3.0 51.5 + - + +
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Residues in contact with LYS 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D PRO 3.8 10.3 - - - +
103D ASP* 2.5 38.3 + - - +
104D THR 3.1 17.0 + - - +
105D VAL* 4.0 6.7 - - + +
107D TYR* 1.3 83.8 - - + +
109D LEU* 1.3 61.2 + - - +
111D LYS* 3.7 5.9 + - + +
112D LYS* 3.1 27.0 + - - +
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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
----------------------------------------------------------
39D LYS 3.7 18.8 - - - +
40D ASP* 3.5 30.7 - - + +
41D PRO* 5.8 2.0 - - + -
42D HIS* 6.5 0.2 - - + -
44D PHE* 3.9 17.5 - - + -
45D PHE* 3.7 21.1 - - + -
105D VAL* 3.0 21.4 + - + +
106D TYR* 3.8 4.7 - - - +
108D LYS* 1.3 75.1 - - - +
110D ALA* 1.3 60.3 + - - +
112D LYS* 3.2 18.1 + - - +
113D ILE* 2.8 39.7 + - + +
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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
----------------------------------------------------------
45D PHE* 3.6 15.4 - - + -
93D CYS* 3.7 17.7 - - - +
96D ALA* 3.5 32.1 - - + -
97D MET* 4.0 6.7 - - + -
106D TYR 3.0 13.5 + - - +
107D TYR 3.7 3.4 - - - +
109D LEU* 1.3 77.6 - - - +
111D LYS* 1.3 61.7 + - - +
113D ILE* 4.2 2.9 - - - -
114D LEU* 2.9 26.9 + - - +
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Residues in contact with LYS 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D MET* 3.6 23.0 - - - -
107D TYR* 3.0 40.9 + - + +
108D LYS* 4.0 6.3 - - - +
110D ALA* 1.3 72.2 - - - +
112D LYS* 1.3 66.0 + - - +
114D LEU* 3.7 2.4 - - - +
115D HIS* 3.3 50.1 + - + +
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Residues in contact with LYS 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D LYS* 5.7 2.0 - - - -
108D LYS 3.1 17.4 + - - +
109D LEU* 3.2 21.1 + - + +
111D LYS* 1.3 83.0 - - - +
113D ILE* 1.3 68.4 + - + +
115D HIS* 4.2 1.6 - - - +
116D ALA* 3.2 27.1 + - + +
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Residues in contact with ILE 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D LEU* 4.9 4.0 - - + +
39D LYS* 3.5 43.2 - - + +
40D ASP* 5.0 2.9 - - + -
45D PHE* 3.8 31.6 - - + -
67D PHE* 4.4 12.1 - - + -
89D PHE* 3.3 21.8 - - + -
92D MET* 4.7 0.4 - - + -
93D CYS* 4.0 8.5 - - - -
109D LEU* 2.8 34.1 + - + +
110D ALA* 3.9 5.2 - - - +
112D LYS* 1.3 77.1 - - + +
114D LEU* 1.3 60.5 + - - +
116D ALA* 4.2 5.2 - - + -
117D GLY* 2.7 32.7 + - - -
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Residues in contact with LEU 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D PHE* 3.9 6.9 - - + -
90D LYS* 4.0 20.2 - - + -
93D CYS* 3.8 18.6 - - + -
94D ASP* 4.0 9.6 - - - +
97D MET* 3.8 27.8 - - + -
110D ALA 2.9 19.1 + - - +
111D LYS 3.7 4.0 - - - +
112D LYS 3.3 0.2 - - - -
113D ILE* 1.3 77.4 - - - +
115D HIS* 1.3 82.4 + - + +
118D PHE* 3.1 52.3 + - + +
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Residues in contact with HIS 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D MET* 6.2 0.9 - - + -
111D LYS* 3.3 46.3 + - + +
112D LYS* 4.4 1.3 - - - +
114D LEU* 1.3 98.0 - - + +
116D ALA* 1.3 64.2 + - - +
118D PHE* 4.0 4.1 - - - +
119D LYS* 3.2 32.9 + - + +
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Residues in contact with ALA 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D LYS* 3.9 23.8 + - + +
112D LYS* 3.2 22.6 + - + +
113D ILE* 4.0 5.4 - - + +
115D HIS* 1.3 78.1 - - - +
117D GLY* 1.3 56.6 + - - +
119D LYS* 3.4 11.5 + - - +
120D MET* 3.0 29.2 + - - +
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Residues in contact with GLY 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D LEU* 3.5 25.6 - - - -
39D LYS* 4.6 1.1 - - - +
89D PHE* 3.9 3.4 - - - -
113D ILE 2.7 23.4 + - - -
116D ALA* 1.3 70.2 - - - +
118D PHE* 1.3 59.5 + - - +
120D MET* 3.2 5.3 + - - +
121D MET* 2.9 41.0 + - - +
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Residues in contact with PHE 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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86D LYS* 3.6 58.4 + - + -
87D ALA* 5.3 0.4 - - - -
89D PHE* 3.8 17.9 - + - -
90D LYS* 3.9 18.6 - - + -
114D LEU* 3.1 38.9 + - + +
115D HIS* 4.0 4.9 - - - +
116D ALA 3.4 0.2 - - - -
117D GLY* 1.3 74.3 - - - +
119D LYS* 1.3 62.4 + - + +
121D MET* 3.4 14.2 + - + -
122D SER* 3.3 19.2 + - - -
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Residues in contact with LYS 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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115D HIS* 3.2 23.0 + - + +
116D ALA* 3.6 11.7 - - - +
118D PHE* 1.3 76.8 - - + +
120D MET* 1.3 62.0 + - - +
122D SER* 3.2 21.7 + - - +
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Residues in contact with MET 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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31A HIS* 4.1 16.0 - - + -
35A GLN* 6.5 0.2 - - - -
32D PHE* 4.1 14.6 - - - +
35D GLN* 3.4 51.8 - - + +
36D LEU* 3.4 38.8 - - + +
39D LYS* 4.5 11.0 - - - +
116D ALA 3.0 16.8 + - - +
117D GLY* 3.2 1.5 + - - +
119D LYS* 1.3 76.9 - - - +
121D MET* 1.3 64.2 + - + +
122D SER 3.2 7.1 + - - -
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Residues in contact with MET 121 (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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31A HIS* 6.0 0.4 - - - -
32D PHE* 3.7 43.3 - - + -
36D LEU* 4.3 8.1 - - + -
82D VAL* 4.7 3.5 - - - +
85D PHE* 3.7 30.1 - - - -
86D LYS* 2.9 49.5 + - + +
89D PHE* 3.9 24.7 - - + -
117D GLY 2.9 28.7 + - - +
118D PHE* 3.6 7.0 - - + +
119D LYS 3.3 0.4 - - - -
120D MET* 1.3 81.9 - - + +
122D SER* 1.3 58.6 + - - +
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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