Contacts of the helix formed by residues 106 - 124 (chain H) in PDB entry 5T0J
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 106 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105H ILE* 1.3 97.9 - - + +
107H THR* 1.3 60.4 + - + +
108H ALA* 3.0 16.8 + - + +
109H GLN* 3.1 17.2 + - + +
110H LEU* 3.6 5.7 + - - +
139H TRP 5.5 0.4 - - - +
140H ASN* 3.6 24.2 - - + -
141H GLU* 5.1 8.5 - - + +
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Residues in contact with THR 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71H HIS* 4.3 5.2 - - + +
72H ILE* 3.7 26.9 - - + -
105H ILE 5.0 0.2 - - - +
106H PRO* 1.3 69.2 - - + +
108H ALA* 1.3 61.2 + - - +
109H GLN 3.2 0.4 - - - -
110H LEU* 3.0 11.6 + - - +
111H VAL* 2.8 37.0 + - - +
137H CYS 4.8 3.1 - - - -
138H GLY* 3.8 7.7 - - - -
139H TRP 3.5 36.6 - - - +
140H ASN* 3.4 4.1 + - - +
145H TYR* 3.5 27.9 - - - +
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Residues in contact with ALA 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106H PRO* 3.0 9.5 + - + +
107H THR* 1.3 81.1 + - - +
109H GLN* 1.3 57.2 + - - +
111H VAL* 3.5 7.9 + - - +
112H GLN* 3.1 31.5 + - - +
140H ASN* 4.8 1.2 - - - +
145H TYR* 5.0 14.1 - - + +
147H PHE* 5.1 9.0 - - + -
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Residues in contact with GLN 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97H TYR* 3.1 35.0 - - + +
105H ILE* 4.5 7.0 - - + -
106H PRO* 3.1 10.6 + - + +
108H ALA* 1.3 75.8 - - - +
110H LEU* 1.3 61.1 + - - +
112H GLN* 3.1 28.6 + - - +
113H ARG* 2.9 45.6 + - - +
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Residues in contact with LEU 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69H THR* 6.0 0.7 - - - +
71H HIS* 5.3 2.2 - - + +
72H ILE* 4.1 23.3 - - + -
94H ALA* 4.4 15.5 - - + +
97H TYR* 3.6 26.5 - - + -
98H TYR* 6.3 0.4 - - + -
104H PRO* 3.3 26.9 - - + +
105H ILE 3.4 13.5 - - - +
106H PRO 3.6 4.7 - - - +
107H THR* 3.0 15.4 + - + +
109H GLN* 1.3 77.5 - - - +
111H VAL* 1.3 57.9 + - + +
113H ARG* 5.1 0.2 - - - -
114H VAL* 2.8 56.8 + - + +
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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
----------------------------------------------------------
107H THR* 2.8 28.8 + - - +
108H ALA 3.8 4.9 - - - +
110H LEU* 1.3 72.8 - - + +
112H GLN* 1.3 63.8 + - - +
114H VAL* 5.1 1.3 - - - -
115H ALA* 3.2 25.2 - - + +
136H ILE* 3.7 41.1 - - + -
137H CYS 5.6 0.7 - - - +
145H TYR* 6.2 0.2 - - + -
147H PHE* 3.5 40.4 - - + -
155H TYR* 5.1 15.0 - - + -
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Residues in contact with GLN 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108H ALA 3.1 21.0 + - - +
109H GLN* 3.2 30.7 - - - +
110H LEU 3.1 0.2 - - - -
111H VAL* 1.3 79.2 - - - +
113H ARG* 1.3 59.2 + - + +
115H ALA 4.1 0.2 - - - -
116H SER* 3.2 26.7 + - - -
155H TYR* 4.8 19.2 + - - -
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Residues in contact with ARG 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93H LEU* 3.8 15.1 - - + +
97H TYR* 3.5 47.8 - - + -
101H TYR* 4.1 17.5 + - - -
109H GLN* 2.9 33.3 + - - +
110H LEU* 4.4 1.6 - - - +
112H GLN* 1.3 71.7 - - - +
114H VAL* 1.3 69.0 + - + +
116H SER* 2.4 28.7 + - - +
117H VAL 3.6 1.9 + - - -
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Residues in contact with VAL 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90H ALA* 4.1 25.4 - - + -
93H LEU* 3.4 30.3 - - + +
94H ALA* 3.9 30.3 - - + -
97H TYR* 6.0 0.9 - - + -
110H LEU* 2.8 41.1 + - + +
111H VAL* 5.1 1.1 - - - -
113H ARG* 1.3 72.6 - - + +
115H ALA* 1.3 59.0 + - - +
118H MET* 3.5 15.4 + - + +
136H ILE* 6.6 0.2 - - + -
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Residues in contact with ALA 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111H VAL* 3.2 23.4 + - + +
112H GLN 4.1 0.4 - - - -
113H ARG 3.3 0.2 - - - -
114H VAL* 1.3 77.3 - - - +
116H SER* 1.3 54.7 + - - +
117H VAL 3.5 0.2 - - - -
118H MET* 3.8 16.6 - - + -
119H GLN* 2.7 34.5 + - - +
136H ILE* 4.7 18.8 - - + -
149H SER* 5.7 4.0 - - - -
155H TYR* 5.9 6.3 - - + -
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Residues in contact with SER 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112H GLN 3.2 18.8 + - - -
113H ARG* 2.4 27.7 + - - +
115H ALA* 1.3 77.8 - - - +
117H VAL* 1.3 72.0 + - - +
119H GLN* 3.2 19.1 - - - +
120H GLU* 3.2 8.7 + - - +
88I ASN* 5.8 5.6 - - - -
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Residues in contact with VAL 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89H ARG* 4.6 22.7 - - + +
93H LEU* 3.6 28.9 - - + -
113H ARG 3.6 2.9 + - - +
114H VAL 3.9 0.2 + - - -
116H SER* 1.3 88.3 + - - +
118H MET* 1.3 56.3 + - - +
119H GLN 3.2 0.2 - - - -
120H GLU* 3.2 13.9 + - + +
121H TYR* 2.6 35.7 + - + +
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Residues in contact with MET 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86H LEU* 4.2 20.4 - - + -
89H ARG* 6.1 2.6 - - + +
93H LEU* 4.7 1.0 - - - +
114H VAL* 3.5 19.7 + - + +
115H ALA* 3.8 14.4 - - - +
116H SER 3.4 0.4 - - - -
117H VAL* 1.3 78.6 - - - +
119H GLN* 1.3 49.9 + - - +
121H TYR* 4.1 8.1 - - + -
122H THR* 2.6 48.7 + - + +
132H VAL 4.5 10.5 - - - +
134H LEU* 3.6 33.7 - - + +
136H ILE* 5.6 2.2 - - - -
149H SER* 3.4 31.6 - - - +
150H ASP 4.3 12.6 - - - +
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Residues in contact with GLN 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115H ALA 2.7 23.4 + - - +
116H SER* 3.2 10.1 - - - +
118H MET* 1.3 72.0 - - - +
120H GLU* 1.3 56.1 + - - +
122H THR* 3.0 5.8 + - - -
123H GLN* 2.6 77.0 + - - +
152H SER 3.7 0.5 - - - +
153H GLY* 2.7 43.0 + - - -
155H TYR* 5.9 0.6 - - - -
81I SER* 3.3 26.6 + - - +
84I ASN* 4.7 10.0 + - + +
85I VAL* 5.1 7.9 - - + -
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Residues in contact with GLU 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H LEU* 5.3 8.8 - - + +
116H SER 3.2 8.3 + - - +
117H VAL* 3.2 18.5 + - + +
119H GLN* 1.3 81.8 - - - +
121H TYR* 1.3 62.2 + - - +
123H GLN* 4.5 2.5 - - - -
124H SER* 2.4 64.1 + - - +
85I VAL* 6.2 4.9 - - + -
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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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127G GLN* 3.8 9.6 + - - -
82H ASP 5.5 3.6 - - - -
85H VAL* 3.2 31.4 - - + +
86H LEU* 5.7 11.9 - - + -
89H ARG* 3.6 36.8 - - + +
117H VAL* 2.6 23.3 + - + +
118H MET* 3.8 8.5 - - + +
120H GLU* 1.3 84.0 + - - +
122H THR* 1.3 69.9 + - + +
124H SER* 3.7 8.8 + - - +
126H GLY* 5.3 0.5 - - - -
130H PHE* 3.2 63.3 - + - -
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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
----------------------------------------------------------
22H ILE* 5.1 9.9 - - - +
86H LEU* 5.7 4.3 - - + -
118H MET* 2.6 44.0 + - + +
119H GLN* 3.0 10.6 + - - -
121H TYR* 1.3 85.0 - - + +
123H GLN* 1.3 64.7 + - - +
124H SER 3.7 4.7 - - - +
129H PRO* 6.2 0.2 - - - +
130H PHE* 4.2 26.7 + - + +
132H VAL 5.0 4.7 - - - +
150H ASP 4.4 3.3 + - - +
151H PRO* 3.3 35.6 + - + +
153H GLY* 4.8 1.0 + - - -
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Residues in contact with GLN 123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H LEU* 2.7 30.5 - - + +
11H THR* 2.9 26.9 + - + +
22H ILE* 5.1 3.1 - - - +
119H GLN* 2.6 48.4 + - - +
120H GLU* 4.4 2.7 - - - +
122H THR* 1.3 73.4 + - - +
124H SER* 1.3 55.3 + - - +
151H PRO 4.7 3.1 - - - -
152H SER* 5.2 3.4 - - - +
79I ILE* 5.1 1.8 - - - +
81I SER* 3.2 20.3 - - - +
82I ASP* 3.4 24.5 + - - +
85I VAL* 4.6 5.6 - - - +
128I ARG* 3.1 28.7 - - - +
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Residues in contact with SER 124 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H LEU* 3.3 33.8 - - - +
120H GLU* 2.4 52.5 + - - +
121H TYR* 3.7 9.7 + - - +
122H THR 3.7 8.0 - - - +
123H GLN* 1.3 78.9 - - - +
125H GLY* 1.3 70.1 + - - +
126H GLY 3.1 3.8 + - - -
130H PHE* 4.9 0.7 - - - -
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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