Contacts of the helix formed by residues 124 - 143 (chain T) in PDB entry 5FLX
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 124 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111T LYS* 2.4 31.1 + - - +
112T MET* 3.4 6.7 + - - -
113T VAL 3.4 33.2 - - - +
114T GLU* 3.4 12.8 - - + +
122T LYS 3.6 0.6 + - - -
123T LEU* 1.3 76.6 - - - +
125T PRO* 1.3 67.6 - - + +
126T GLN* 4.0 2.5 - - - -
127T GLY* 2.8 18.4 + - - +
128T GLN* 2.8 29.8 + - - +
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Residues in contact with PRO 125 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14141 A 3.9 44.9 - - - +
14151 C 3.8 5.8 - - - +
114T GLU* 4.7 7.9 - - - +
123T LEU* 4.6 3.1 - - + +
124T THR* 1.3 87.9 - - + +
126T GLN* 1.3 55.5 + - - +
128T GLN* 3.4 1.8 + - + +
129T ARG* 2.9 42.4 + - - +
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Residues in contact with GLN 126 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110T LEU 4.8 4.7 - - - +
111T LYS* 3.6 32.8 - - + +
112T MET* 5.6 0.4 - - + -
124T THR* 3.2 1.5 + - - -
125T PRO* 1.3 76.5 - - - +
127T GLY* 1.3 61.7 + - - +
129T ARG* 2.4 44.3 + - - +
130T ASP* 2.9 60.4 + - - +
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Residues in contact with GLY 127 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111T LYS 3.9 0.4 + - - -
112T MET* 4.2 25.4 - - - -
123T LEU* 5.5 2.2 - - - -
124T THR* 2.8 24.0 + - - -
126T GLN* 1.3 73.3 - - - +
128T GLN* 1.3 57.6 + - - +
130T ASP* 4.0 2.9 - - - +
131T LEU* 2.9 44.3 + - - +
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Residues in contact with GLN 128 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14141 A 4.2 13.0 - - - +
14151 C 3.3 31.1 + - - +
14231 C 5.8 1.7 + - - -
6T VAL* 5.3 4.2 - - - +
65T TYR* 3.2 37.0 + - - -
123T LEU* 3.3 26.0 - - + +
124T THR 2.8 20.3 + - - +
125T PRO 3.7 4.7 - - - +
127T GLY* 1.3 69.4 - - - +
129T ARG* 1.3 55.3 + - - +
131T LEU* 4.8 3.4 - - - +
132T ASP* 2.7 60.5 + - - +
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Residues in contact with ARG 129 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14151 C 3.1 42.8 + - - +
14161 C 3.2 15.5 - - - +
125T PRO* 2.9 26.0 + - - +
126T GLN* 2.4 55.5 + - - +
128T GLN* 1.3 76.6 - - - +
130T ASP* 1.3 58.1 + - - +
132T ASP* 3.9 0.2 - - - +
133T ARG* 2.9 50.2 + - - +
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Residues in contact with ASP 130 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27T LYS* 3.6 23.4 + - - +
110T LEU 5.6 0.2 - - - +
112T MET* 4.6 13.6 - - + +
126T GLN* 2.9 45.6 + - - +
127T GLY* 4.0 4.5 - - - +
129T ARG* 1.3 76.9 - - - +
131T LEU* 1.3 60.5 + - + +
132T ASP 3.2 0.3 + - - -
133T ARG* 3.8 10.2 + - - +
134T ILE* 2.9 43.7 + - + +
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Residues in contact with LEU 131 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6T VAL* 3.4 22.7 - - + +
14T PHE* 3.7 8.6 - - + -
18T LEU* 4.2 27.6 - - + -
61T ALA* 3.9 42.8 - - + +
62T ARG* 5.6 0.9 - - - -
64T LEU* 4.8 10.3 - - + -
65T TYR* 5.2 11.2 - - + -
112T MET* 4.4 19.7 - - + +
123T LEU* 6.0 1.8 - - + -
127T GLY* 2.9 27.7 + - - +
128T GLN* 4.5 5.2 - - - +
130T ASP* 1.3 74.8 - - - +
132T ASP* 1.3 57.6 + - - +
134T ILE* 4.4 4.0 - - + -
135T ALA* 3.0 19.2 + - - +
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Residues in contact with ASP 132 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14151 C 2.4 34.4 + - - +
14161 C 2.8 26.2 + - - +
14221 G 4.9 2.6 + - - -
4T VAL 2.7 27.6 - - - +
5T THR* 4.6 2.4 - - - -
6T VAL* 4.5 2.7 - - - -
128T GLN* 2.7 35.6 + - - +
129T ARG 3.9 0.9 - - - +
131T LEU* 1.3 76.2 - - - +
133T ARG* 1.3 60.9 + - - +
135T ALA* 3.1 7.1 + - - +
136T GLY* 2.9 23.2 + - - -
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Residues in contact with ARG 133 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14161 C 3.6 47.3 + - - +
14171 C 5.0 7.2 + - - +
129T ARG* 2.9 32.4 + - - +
130T ASP* 3.9 9.8 + - - +
132T ASP* 1.3 75.2 - - - +
134T ILE* 1.3 59.4 + - + +
136T GLY* 3.0 4.3 + - - +
137T GLN* 2.9 30.3 + - - +
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Residues in contact with ILE 134 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14T PHE* 3.5 21.1 - - + -
18T LEU* 3.6 34.8 - - + -
21T PHE* 4.4 15.0 - - + -
22T LEU* 5.8 2.9 - - + -
27T LYS* 6.1 2.0 - - - +
130T ASP* 2.9 32.4 + - + +
131T LEU* 3.9 6.5 - - + +
133T ARG* 1.3 78.1 - - + +
135T ALA* 1.3 57.4 + - - +
137T GLN* 3.1 26.7 - - - +
138T VAL* 2.9 40.9 + - + +
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Residues in contact with ALA 135 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4T VAL* 3.3 12.1 - - + +
5T THR 4.0 7.0 - - - +
6T VAL* 3.6 35.7 - - + +
9T VAL* 4.5 4.0 - - + +
14T PHE* 3.4 13.6 - - + -
131T LEU 3.0 16.2 + - - +
132T ASP* 3.1 11.2 + - - +
134T ILE* 1.3 77.7 - - - +
136T GLY* 1.3 56.8 + - - +
138T VAL* 3.4 1.2 + - - +
139T ALA* 2.9 23.6 + - - +
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Residues in contact with GLY 136 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14161 C 5.7 3.8 - - - -
2T PRO 5.7 0.7 - - - -
4T VAL* 3.8 22.2 - - - +
132T ASP 2.9 12.7 + - - -
133T ARG* 3.0 5.3 + - - -
135T ALA* 1.3 78.0 - - - +
137T GLN* 1.3 56.3 + - - +
139T ALA* 3.3 4.3 + - - +
140T ALA* 2.9 25.6 + - - +
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Residues in contact with GLN 137 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21T PHE* 3.2 54.2 - - + -
133T ARG* 2.9 13.4 + - - +
134T ILE* 3.1 34.5 - - + +
136T GLY* 1.3 73.1 - - - +
138T VAL* 1.3 62.2 + - + +
140T ALA* 3.3 10.1 + - - +
141T ALA* 2.9 26.2 + - - +
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Residues in contact with VAL 138 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9T VAL* 3.7 26.2 - - + -
13T GLU* 4.0 12.7 - - + +
14T PHE* 3.6 32.8 - - + +
17T ALA* 3.6 29.6 - - + -
134T ILE* 2.9 26.4 + - + +
135T ALA 3.8 3.6 - - - +
137T GLN* 1.3 76.8 - - + +
139T ALA* 1.3 58.1 + - - +
141T ALA* 3.1 9.6 + - + +
142T ASN* 2.9 24.9 + - - +
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Residues in contact with ALA 139 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4T VAL* 3.7 25.4 - - + -
8T ASP* 6.1 0.2 - - + -
9T VAL* 3.8 17.9 - - + +
135T ALA 2.9 17.4 + - - +
136T GLY 3.5 5.6 - - - +
138T VAL* 1.3 77.8 - - - +
140T ALA* 1.3 56.6 + - - +
142T ASN* 2.9 6.5 + - - +
143T LYS* 2.9 30.5 + - - +
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Residues in contact with ALA 140 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136T GLY 2.9 13.8 + - - +
137T GLN* 3.5 13.2 - - - +
138T VAL 3.2 0.4 - - - -
139T ALA* 1.3 76.3 - - - +
141T ALA* 1.3 59.4 + - - +
143T LYS* 3.2 39.9 + - - +
144T LYS* 3.5 12.6 + - - +
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Residues in contact with ALA 141 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13T GLU* 5.4 6.9 - - - +
16T ARG* 5.9 2.9 - - - +
137T GLN 2.9 13.4 + - - +
138T VAL* 3.1 12.8 + - + +
140T ALA* 1.3 74.3 - - - +
142T ASN* 1.3 63.6 + - - +
144T LYS* 3.6 20.5 + - - +
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Residues in contact with ASN 142 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41Q MET* 6.0 5.1 - - - +
8T ASP 5.6 1.4 + - - -
9T VAL* 4.8 20.1 - - + +
13T GLU* 5.3 13.4 - - + +
138T VAL 2.9 12.5 + - - +
139T ALA* 2.9 13.0 + - - +
141T ALA* 1.3 76.2 - - - +
143T LYS* 1.3 63.4 + - - +
144T LYS 3.1 5.0 + - - -
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Residues in contact with LYS 143 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2T PRO* 6.3 3.6 - - - -
139T ALA 2.9 11.3 + - - +
140T ALA* 3.2 35.7 + - - +
142T ASN* 1.3 76.5 - - - +
144T LYS* 1.3 59.7 + - + +
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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
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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