Contacts of the helix formed by residues 109 - 120 (chain F) in PDB entry 3JSX
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 109 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10F ALA* 3.8 33.9 - - + +
42F TYR* 5.7 3.8 - - + +
101F PHE* 3.8 12.3 - - + -
102F PRO* 3.5 24.9 - - + +
104F GLN* 3.6 27.1 - - + +
107F GLY 3.8 0.2 - - - -
108F VAL* 1.3 90.7 - - + +
110F ALA* 1.3 66.4 + - - +
111F ILE* 4.1 10.5 - - + +
112F LEU* 2.9 16.8 + - + -
113F LYS 3.2 6.8 + - - -
117H GLU* 3.6 2.5 - - - +
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Residues in contact with ALA 110 (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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48F PRO* 4.0 4.1 - - - +
108F VAL 3.5 0.6 + - - -
109F PRO* 1.3 71.4 - - - +
111F ILE* 1.3 58.4 + - - +
113F LYS* 4.0 1.8 - - - -
114F GLY* 3.1 23.0 + - - -
48H PRO* 3.9 10.5 - - + +
49H ILE* 5.7 0.7 - - - -
110H ALA* 3.5 14.4 - - - +
113H LYS* 3.6 14.6 - - + -
114H GLY* 3.0 42.2 - - - +
117H GLU* 3.2 17.8 + - - +
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Residues in contact with ILE 111 (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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10F ALA* 4.0 19.5 - - + -
41F LEU* 3.4 45.0 - - + +
42F TYR* 4.0 34.5 - - + +
45F ASN* 5.8 0.2 - - - -
46F PHE* 3.9 18.3 - - + +
48F PRO* 4.2 9.6 - - + +
109F PRO* 2.9 6.5 + - + +
110F ALA* 1.3 78.6 - - - +
112F LEU* 1.3 59.7 + - - +
114F GLY* 4.2 1.4 - - - -
115F TRP* 3.4 15.9 + - - +
49H ILE* 3.5 40.7 - - + +
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Residues in contact with LEU 112 (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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8F VAL* 4.1 17.3 - - + +
10F ALA* 4.2 10.3 - - + -
41F LEU* 3.9 11.4 - - + -
99F PHE* 3.8 30.7 - - + -
100F GLN 5.7 0.4 - - - +
101F PHE* 3.6 38.8 - - + -
108F VAL* 3.8 18.6 - - + -
109F PRO* 2.9 9.2 + - + +
111F ILE* 1.3 79.5 - - - +
113F LYS* 1.3 67.9 + - - +
114F GLY 3.3 0.2 - - - -
115F TRP* 2.9 18.5 + - + +
116F PHE* 2.9 33.0 + - + -
144F LEU* 6.2 0.2 - - + -
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Residues in contact with LYS 113 (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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108F VAL* 3.6 21.7 - - + +
109F PRO 3.2 7.6 + - - +
110F ALA* 3.8 9.6 - - - +
112F LEU* 1.3 73.6 - - - +
114F GLY* 1.3 59.2 + - - +
116F PHE* 2.9 12.7 + - - +
117F GLU* 2.7 63.0 + - - +
175F ILE* 4.4 10.1 - - + -
104H GLN 2.7 25.2 + - - -
105H TRP* 3.7 24.2 - - - -
107H GLY* 4.1 4.6 - - - +
108H VAL 2.8 27.5 + - - +
110H ALA* 3.9 9.6 - - + +
113H LYS* 5.0 6.1 - - + -
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Residues in contact with GLY 114 (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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48F PRO* 2.9 33.4 - - - -
110F ALA 3.1 11.2 + - - -
113F LYS* 1.3 77.6 - - - +
115F TRP* 1.3 56.1 + - - +
117F GLU* 3.7 5.1 - - - -
118F ARG* 3.0 35.9 + - - +
110H ALA* 3.3 9.9 - - - +
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Residues in contact with TRP 115 (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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6F LEU* 4.7 5.6 - - + -
8F VAL* 4.2 17.7 - - + -
39F SER* 4.8 0.2 - - - -
41F LEU* 3.9 24.5 - - + +
46F PHE* 3.4 35.2 - + + -
87F GLU* 3.0 39.6 + - + +
91F LEU* 3.9 31.2 - - + -
99F PHE* 3.7 15.3 - + - -
111F ILE 3.4 17.0 + - - +
112F LEU* 2.9 19.3 + - + +
114F GLY* 1.3 72.4 - - - +
116F PHE* 1.3 94.4 + + - +
119F VAL* 2.9 41.5 + - + +
120F PHE* 3.7 10.5 - + - -
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Residues in contact with PHE 116 (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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99F PHE* 3.7 41.1 - + - -
108F VAL* 4.4 12.3 - - + -
112F LEU* 2.9 37.3 + - + -
113F LYS* 2.9 13.7 + - - +
115F TRP* 1.3 87.8 - + - +
117F GLU* 1.3 61.6 + - + +
120F PHE* 2.9 63.3 + + + +
144F LEU* 5.9 1.8 - - + -
171F ILE* 5.2 4.7 - - + -
175F ILE* 3.6 40.4 - - + -
176F LEU* 4.9 5.2 - - + -
105H TRP* 3.8 12.9 + - + -
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Residues in contact with GLU 117 (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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48F PRO 4.7 0.9 - - - +
50F ILE* 3.3 28.0 - - + +
67F TYR* 4.3 4.2 - - - -
113F LYS* 2.7 46.3 + - - +
114F GLY* 3.3 5.7 + - - +
116F PHE* 1.3 77.6 - - - +
118F ARG* 1.3 57.8 + - - +
120F PHE 4.8 2.3 - - - +
121F ILE* 4.1 10.4 - - - +
104H GLN* 3.1 31.6 - - + +
105H TRP* 3.8 23.0 + - + -
109H PRO* 3.4 3.8 - - - +
110H ALA* 2.9 31.7 + - - +
601H FAD 4.4 7.8 - - + +
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Residues in contact with ARG 118 (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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46F PHE* 3.5 19.1 - - + -
47F ASN* 2.5 62.6 + - - +
48F PRO 3.8 1.3 - - - +
49F ILE 3.6 19.2 + - - +
50F ILE* 3.2 25.1 - - + +
53F LYS 5.6 0.2 + - - -
54F ASP* 2.9 26.6 + - - -
67F TYR* 4.2 2.2 - - - -
81F SER* 3.8 5.5 + - - -
83F ASP* 3.3 33.5 + - - -
84F ILE* 3.6 29.0 - - + +
114F GLY 3.0 16.5 + - - +
117F GLU* 1.3 76.7 - - - +
119F VAL* 1.3 63.1 + - - +
121F ILE* 3.1 22.1 - - - +
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Residues in contact with VAL 119 (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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46F PHE* 4.1 10.3 - - + -
84F ILE* 4.4 7.4 - - - +
87F GLU* 3.7 22.7 - - + -
88F GLN* 3.0 44.7 + - + +
91F LEU* 4.0 20.4 - - + -
115F TRP* 2.9 47.3 + - + +
118F ARG* 1.3 80.1 - - + +
120F PHE* 1.3 62.0 + - + +
121F ILE 2.8 9.2 + - - -
124F PHE* 3.8 3.3 - - - -
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Residues in contact with PHE 120 (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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91F LEU* 3.3 30.1 - - + -
99F PHE* 4.9 3.6 - + - -
115F TRP* 3.7 17.0 - + - -
116F PHE* 2.9 55.5 + + + +
117F GLU 4.8 1.9 - - - +
119F VAL* 1.3 72.4 - - + +
121F ILE* 1.3 65.9 + - - +
124F PHE* 5.3 0.2 - + - -
125F ALA* 3.4 19.7 - - + -
126F TYR* 3.4 14.4 + - - -
137F PHE* 4.4 2.9 - + - -
175F ILE* 4.0 15.0 - - + -
176F LEU* 5.3 1.1 - - + -
179F CYS* 3.7 23.1 - - - -
181F PHE* 4.2 21.1 - + - -
105H TRP* 3.5 21.0 + + + -
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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