Contacts of the helix formed by residues 95 - 106 (chain F) in PDB entry 5TJG
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 95 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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572D ARG* 4.7 18.2 + - + +
576D GLU* 3.6 34.1 - - - +
587D ARG* 5.5 3.6 - - - +
94F ASP* 1.3 86.7 - - - +
96F VAL* 1.3 69.7 + - + +
98F GLN* 3.4 10.6 + - + +
99F TYR* 3.1 23.4 + - - +
225F LEU* 3.9 23.7 - - + +
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Residues in contact with VAL 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F ASP* 3.2 3.2 - - - +
95F PRO* 1.3 81.7 - - + +
97F ARG* 1.3 60.5 + - - +
99F TYR* 3.4 3.2 + - + +
100F LEU* 3.0 50.4 + - + +
224F PHE* 4.1 27.8 - - + -
225F LEU* 3.7 26.9 - - + -
228F ILE* 5.5 2.2 - - + -
8G G 3.3 39.5 - - + +
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Residues in contact with ARG 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F ASP* 3.5 26.1 + - - +
95F PRO 3.4 0.2 - - - -
96F VAL* 1.3 78.2 - - - +
98F GLN* 1.3 61.8 + - - +
100F LEU* 4.2 4.7 - - - +
101F HIS* 3.2 24.5 + - + +
7G G 5.0 10.2 + - - +
8G G 3.2 27.5 - - - +
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Residues in contact with GLN 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D TYR 4.4 4.2 + - - -
129D PHE 3.6 13.6 + - - -
130D ASN* 3.2 32.9 + - - +
572D ARG* 3.4 29.6 - - - +
94F ASP 3.5 10.1 + - - +
95F PRO* 3.4 13.2 + - + +
96F VAL 3.2 0.4 - - - -
97F ARG* 1.3 78.9 - - - +
99F TYR* 1.3 60.3 + - - +
101F HIS* 3.4 11.9 + - - +
102F GLU* 3.1 43.1 + - - +
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Residues in contact with TYR 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565D ILE* 4.1 12.6 - - + -
566D ILE* 5.2 0.4 - - - -
569D ASN* 3.4 44.0 - - + +
572D ARG* 3.9 9.9 - - - +
95F PRO 3.1 13.5 + - - +
96F VAL* 4.0 3.8 - - + +
98F GLN* 1.3 77.0 - - - +
100F LEU* 1.3 72.8 + - + +
102F GLU* 3.1 9.5 + - - +
103F ILE* 3.0 49.6 + - + +
207F LEU* 3.9 12.8 + - - +
211F VAL* 3.9 15.7 - - + -
225F LEU* 5.2 3.8 - - + -
228F ILE* 3.5 36.9 - - + +
229F GLN* 4.3 2.0 - - - -
232F ASN* 3.2 23.9 + - - -
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Residues in contact with LEU 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96F VAL* 3.0 36.1 + - + +
97F ARG* 4.2 4.5 - - - +
99F TYR* 1.3 81.3 - - + +
101F HIS* 1.3 57.0 + - - +
103F ILE* 3.3 15.7 - - + +
104F GLY 3.0 19.6 + - - -
211F VAL* 3.7 31.9 - - + -
228F ILE* 5.4 1.3 - - + -
7G G 3.5 48.6 - - + +
8G G 3.8 42.0 - - + +
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Residues in contact with HIS 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D THR* 6.3 2.9 - - + -
155D ASP* 5.6 5.8 - - - -
97F ARG* 3.2 21.2 + - + +
98F GLN* 3.6 13.8 + - - +
100F LEU* 1.3 77.9 - - - +
102F GLU* 1.3 67.4 + - - +
104F GLY* 3.0 9.0 + - - -
105F GLN* 3.2 45.5 + - + +
7G G 4.0 21.2 - - - +
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Residues in contact with GLU 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D PHE 3.7 2.6 - - - +
155D ASP* 4.7 6.1 - - - +
565D ILE* 4.5 25.1 - - + +
568D ARG* 2.5 39.5 + - - +
572D ARG* 2.9 43.8 + - - -
98F GLN* 3.1 27.5 + - - +
99F TYR* 3.1 12.3 + - - +
101F HIS* 1.3 77.5 - - - +
103F ILE* 1.3 61.0 + - - +
104F GLY 3.0 4.7 + - - -
105F GLN* 3.1 22.2 + - - +
106F VAL* 3.9 7.6 + - - +
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Residues in contact with ILE 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565D ILE* 3.9 13.5 - - + -
99F TYR* 3.0 44.9 + - + +
100F LEU* 3.3 26.7 - - + +
102F GLU* 1.3 74.4 - - - +
104F GLY* 1.3 58.0 + - - +
105F GLN 3.4 0.2 - - - -
106F VAL* 3.4 16.9 + - - +
204F GLU 5.3 2.4 - - - +
207F LEU* 3.9 16.4 - - + +
208F ARG* 3.1 41.5 + - + +
211F VAL* 3.8 28.5 - - + -
7G G 4.3 9.9 - - + +
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Residues in contact with GLY 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100F LEU 3.0 8.9 + - - -
101F HIS 3.0 4.5 + - - -
102F GLU 3.0 1.8 - - - -
103F ILE* 1.3 77.4 - - - +
105F GLN* 1.3 64.9 + - - +
106F VAL 3.5 1.6 + - - +
107F PRO* 4.7 1.0 - - - +
208F ARG* 3.5 10.3 + - - -
7G G 3.2 42.7 - - - +
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Residues in contact with GLN 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D ASP* 5.1 10.3 + - - +
156D GLU* 5.2 12.1 + - - +
159D ARG* 4.3 23.1 - - - +
101F HIS* 3.2 44.7 + - + +
102F GLU* 3.1 11.6 + - - +
104F GLY* 1.3 80.2 - - - +
106F VAL* 1.3 61.9 + - + +
107F PRO* 3.2 11.3 - - - +
7G G 4.9 2.1 - - - +
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Residues in contact with VAL 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D ARG* 6.3 1.1 - - - +
565D ILE* 4.7 14.4 - - + -
102F GLU 3.9 8.2 + - - +
103F ILE* 3.4 10.0 + - - +
104F GLY 3.3 1.3 - - - -
105F GLN* 1.3 76.8 - - + +
107F PRO* 1.3 79.6 - - + +
201F HIS 5.5 0.4 - - - +
204F GLU* 3.6 48.0 - - + +
205F ALA* 3.7 10.8 - - + +
207F LEU* 6.2 0.7 - - + -
208F ARG* 3.2 23.6 + - - -
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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
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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