Contacts of the helix formed by residues 103 - 123 (chain H) in PDB entry 5X7X
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 PRO 103 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92G GLU* 3.4 44.9 - - + +
95G LYS* 4.3 22.4 - - + -
96G LEU* 4.4 18.2 - - + +
101H LEU 3.9 5.2 - - - +
102H LEU* 1.3 87.8 - - + +
104H GLY* 1.3 67.4 + - - +
105H GLU 3.3 0.9 + - - -
106H LEU* 3.1 20.2 + - + +
107H ALA 3.5 0.2 + - - -
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Residues in contact with GLY 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92G GLU* 3.3 6.1 - - - -
102H LEU 3.8 3.0 + - - -
103H PRO* 1.3 68.3 - - - +
105H GLU* 1.3 65.7 + - - -
107H ALA* 3.1 16.6 + - - +
108H LYS* 3.2 22.5 + - - +
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Residues in contact with GLU 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92G GLU* 2.7 23.0 + - - +
104H GLY* 1.3 68.5 - - - -
106H LEU* 1.3 64.9 + - + +
108H LYS* 3.2 11.0 + - - +
109H HIS* 2.7 60.1 + - + +
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Residues in contact with LEU 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57G TYR* 3.9 19.8 - - + +
58G LEU* 4.2 13.0 - - + -
61G GLU* 5.0 9.6 - - + -
90G ASP* 5.2 2.2 - - - +
92G GLU* 3.0 43.6 + - + +
93G LEU* 3.7 31.6 - - + -
96G LEU* 4.5 12.1 - - + -
102H LEU* 3.8 11.6 - - + +
103H PRO* 3.1 15.9 + - + +
105H GLU* 1.3 78.7 - - + +
107H ALA* 1.3 56.9 + - - +
110H ALA* 2.9 33.4 + - - +
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Residues in contact with ALA 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98H VAL* 4.2 8.0 - - - +
99H ARG* 4.6 15.3 - - + +
102H LEU* 3.6 36.9 - - + +
103H PRO 3.5 2.0 + - - -
104H GLY 3.1 12.0 + - - +
106H LEU* 1.3 77.1 - - - +
108H LYS* 1.3 63.3 + - + +
110H ALA* 3.9 0.5 - - - +
111H VAL* 2.9 37.4 + - - +
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Residues in contact with LYS 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99H ARG* 3.7 26.2 - - - +
104H GLY* 3.2 19.4 + - - +
105H GLU* 3.2 15.7 + - - +
107H ALA* 1.3 78.9 - - - +
109H HIS* 1.3 65.1 + - + +
111H VAL* 3.4 6.0 + - - +
112H SER* 2.9 28.1 + - - -
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Residues in contact with HIS 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57G TYR* 3.1 32.9 + + + +
105H GLU* 2.7 55.9 + - + +
106H LEU* 5.9 0.2 - - - +
108H LYS* 1.3 77.6 - - + +
110H ALA* 1.3 59.5 + - - +
112H SER* 3.2 8.6 + - - -
113H GLU* 2.9 35.4 + - + +
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Residues in contact with ALA 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54G VAL* 3.7 23.7 - - + +
57G TYR* 3.8 21.6 - - + -
98H VAL* 4.0 7.4 - - + -
102H LEU* 3.7 21.8 - - + -
106H LEU 2.9 19.7 + - - +
107H ALA 3.9 1.6 - - - +
109H HIS* 1.3 76.6 - - - +
111H VAL* 1.3 57.1 + - - +
113H GLU* 3.3 3.4 + - - +
114H GLY* 2.9 25.1 + - - -
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Residues in contact with VAL 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50G TYR* 3.2 18.6 + - - +
95H GLN* 3.4 22.9 - - + +
98H VAL* 4.0 15.7 - - + -
99H ARG* 3.5 46.7 - - + +
107H ALA 2.9 20.8 + - - +
108H LYS* 3.6 5.6 - - - +
110H ALA* 1.3 75.6 - - - +
112H SER* 1.3 64.8 + - - +
114H GLY 3.3 0.2 + - - -
115H THR* 3.0 26.9 + - + +
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Residues in contact with SER 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108H LYS 2.9 14.2 + - - -
109H HIS* 3.2 13.9 + - - -
111H VAL* 1.3 77.4 - - - +
113H GLU* 1.3 62.3 + - - +
115H THR* 2.9 21.2 + - - -
116H LYS* 2.9 24.7 + - - +
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Residues in contact with GLU 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G LEU* 6.1 1.0 - - - +
53G ALA* 3.7 12.4 - - + +
57G TYR* 4.0 34.9 - - + +
109H HIS* 2.9 20.8 + - + +
110H ALA 3.7 4.5 - - - +
112H SER* 1.3 79.0 + - - +
114H GLY* 1.3 57.6 + - - +
116H LYS* 3.5 27.3 + - - +
117H ALA* 2.9 31.5 + - - +
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Residues in contact with GLY 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50G TYR* 3.5 34.0 - - - -
53G ALA* 3.9 12.9 - - - +
54G VAL* 4.8 0.2 - - - +
110H ALA 2.9 12.2 + - - -
113H GLU* 1.3 75.5 - - - +
115H THR* 1.3 62.2 + - - +
117H ALA* 3.2 3.3 + - - +
118H VAL* 2.9 27.9 + - - +
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Residues in contact with THR 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G TYR* 3.7 8.7 - - + -
95H GLN* 3.2 26.7 - - - +
111H VAL* 3.0 19.1 + - + +
112H SER* 2.9 22.3 + - - -
114H GLY* 1.3 74.2 - - - +
116H LYS* 1.3 55.8 + - - +
118H VAL* 3.3 5.4 + - - +
119H THR* 2.9 35.6 + - - -
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Residues in contact with LYS 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G ALA 5.8 1.8 + - - -
22G GLY 6.0 0.2 + - - -
112H SER* 2.9 23.1 + - - +
113H GLU* 3.6 28.4 + - - +
115H THR* 1.3 79.4 + - - +
117H ALA* 1.3 58.9 + - - +
119H THR* 3.4 7.0 + - - +
120H LYS* 2.9 37.9 + - + +
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Residues in contact with ALA 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21G ALA* 3.9 20.1 - - - +
23G LEU* 4.1 8.3 - - + -
49G VAL* 3.5 14.7 - - + +
53G ALA* 3.6 22.4 - - + -
113H GLU 2.9 17.9 + - - +
114H GLY 3.6 2.0 - - - +
116H LYS* 1.3 76.0 - - - +
118H VAL* 1.3 61.6 + - - +
120H LYS* 3.8 2.1 - - - +
121H TYR* 2.9 31.0 + - - +
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Residues in contact with VAL 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46G GLY* 3.7 35.9 - - - +
49G VAL* 3.8 6.7 - - + -
50G TYR* 3.8 24.0 - - + +
91H SER* 4.5 9.0 - - - +
114H GLY 2.9 20.3 + - - +
115H THR* 3.3 5.6 + - - +
117H ALA* 1.3 75.0 - - - +
119H THR* 1.3 55.5 + - - +
121H TYR* 3.4 3.5 + - + +
122H THR* 2.6 47.3 + - - +
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Residues in contact with THR 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115H THR* 2.9 20.8 + - - -
116H LYS* 3.6 7.6 - - - +
118H VAL* 1.3 79.1 - - - +
120H LYS* 1.3 62.0 + - - +
122H THR* 3.4 6.0 + - - -
123H SER* 3.0 23.3 + - - -
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Residues in contact with LYS 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G SER 5.2 1.8 - - - -
20G ARG* 3.5 19.6 - - - +
21G ALA 3.5 16.8 - - - +
22G GLY* 3.9 13.5 - - - -
116H LYS* 2.9 25.7 + - + +
117H ALA* 3.8 3.4 - - - +
119H THR* 1.3 76.3 - - - +
121H TYR* 1.3 64.0 + - - +
123H SER* 2.9 27.4 + - - +
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Residues in contact with TYR 121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G ARG* 3.3 55.5 + - + -
20G ARG* 3.6 48.7 + - + +
21G ALA* 3.9 8.5 - - + -
45G ALA* 4.4 22.1 + - + +
46G GLY* 5.6 2.9 - - - -
49G VAL* 3.7 27.8 - - + -
117H ALA 2.9 18.8 + - - +
118H VAL* 3.7 4.5 - - + +
120H LYS* 1.3 77.2 - - - +
122H THR* 1.3 70.9 + - - +
123H SER 4.5 2.6 - - - -
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Residues in contact with THR 122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118H VAL* 2.6 33.0 + - - +
119H THR* 3.6 6.7 - - - -
121H TYR* 1.3 84.0 - - - +
123H SER* 1.3 66.2 + - - +
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Residues in contact with SER 123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119H THR* 3.0 14.3 + - - -
120H LYS* 2.9 23.3 + - - +
121H TYR 4.5 2.5 - - - -
122H THR* 1.3 82.6 - - - +
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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
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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