Contacts of the helix formed by residues 116 - 131 (chain B) in PDB entry 1FO4
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 CYS 116 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B CYS 6.0 0.2 - - - +
50B ALA* 4.9 9.7 - - + -
114B GLY 3.2 0.4 - - - -
115B PHE* 1.3 77.7 - - - +
117B THR* 1.3 70.9 + - - +
118B PRO* 3.5 1.1 - - - -
119B GLY* 3.3 5.7 + - - -
120B ILE* 3.1 40.5 + - + +
147B LEU 3.3 22.0 - - - +
148B CYS* 3.7 7.6 - - - -
156B ILE* 5.2 2.2 - - - -
744B LEU* 4.2 7.0 - - + -
4001B FES 2.3 42.4 - - - -
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Residues in contact with THR 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ILE* 4.1 17.0 - - + -
110B GLY 4.9 0.5 + - - -
111B SER* 2.7 30.4 + - - +
114B GLY* 3.1 13.3 - - - -
116B CYS* 1.3 83.5 - - - +
118B PRO* 1.3 72.3 - - - +
120B ILE* 3.1 5.8 + - - +
121B VAL* 2.8 31.6 + - + +
585B GLN 3.6 3.4 - - - -
586B ALA* 3.3 37.0 - - + +
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Residues in contact with PRO 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B GLY 3.2 27.8 - - - +
39B THR* 5.1 1.6 - - - -
40B LYS* 4.4 7.6 - - + -
50B ALA 5.0 3.1 - - - +
52B THR 5.2 0.4 - - - -
88B VAL* 4.1 18.6 - - + -
114B GLY 3.4 10.8 - - - +
115B PHE* 3.7 7.6 - - - +
116B CYS 3.6 2.9 - - - -
117B THR* 1.3 92.9 - - - +
119B GLY* 1.3 57.4 - - - +
121B VAL* 3.1 9.3 + - + +
122B MET* 3.0 34.7 + - - +
585B GLN 3.6 13.7 - - - +
588B GLY* 4.2 11.7 - - - +
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Residues in contact with GLY 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLY 3.3 19.7 - - - -
50B ALA 4.0 12.4 + - - -
52B THR* 3.4 17.1 - - - -
116B CYS 3.3 6.7 + - - -
117B THR 3.3 0.4 - - - -
118B PRO* 1.3 80.3 - - - +
120B ILE* 1.3 55.9 + - - +
122B MET 3.5 0.5 + - - -
123B SER* 3.1 23.0 + - - -
146B ASN* 3.3 13.5 - - - +
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Residues in contact with ILE 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ILE* 4.0 12.1 - - + -
116B CYS* 3.1 35.7 + - + +
117B THR* 3.1 8.1 + - - +
119B GLY* 1.3 74.3 - - - +
121B VAL* 1.3 67.0 + - - +
123B SER* 3.3 1.6 + - - +
124B MET* 3.0 19.9 + - - +
143B PHE* 3.4 19.9 - - + -
146B ASN* 3.7 28.0 - - + +
147B LEU 4.6 1.6 - - - +
148B CYS* 4.4 4.9 - - + -
156B ILE* 3.9 15.9 - - + -
160B PHE* 3.8 17.7 - - + -
1232B PHE* 3.7 23.6 - - + -
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Residues in contact with VAL 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B VAL* 4.5 1.8 - - + -
91B ILE* 3.7 28.0 - - + -
101B VAL* 3.5 18.3 - - + +
102B GLN* 3.7 15.9 - - + +
105B ILE* 4.1 18.8 - - + -
117B THR* 2.8 28.9 + - + +
118B PRO* 3.1 10.3 + - + +
120B ILE* 1.3 78.0 - - - +
122B MET* 1.3 56.6 + - - +
124B MET 3.3 1.4 + - - -
125B TYR* 2.7 32.2 + - - +
160B PHE* 5.0 0.4 - - - -
586B ALA 3.7 18.6 - - - +
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Residues in contact with MET 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B THR* 3.6 32.5 - - + +
53B VAL* 4.3 2.9 - - - -
54B MET* 4.0 12.8 - - + +
86B THR* 3.2 31.4 - - + +
87B THR* 3.7 4.5 - - - +
88B VAL* 3.7 31.9 - - + +
91B ILE* 4.4 14.1 - - + -
118B PRO 3.0 19.7 + - - +
119B GLY 3.9 3.1 - - - +
120B ILE 3.2 0.2 - - - -
121B VAL* 1.3 77.6 - - - +
123B SER* 1.3 58.7 + - - +
125B TYR* 3.7 24.2 - - + +
126B THR* 2.8 34.5 + - - -
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Residues in contact with SER 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B THR* 3.7 6.2 - - - +
69B SER* 5.0 4.7 + - - -
119B GLY 3.1 9.4 + - - -
120B ILE 3.3 2.9 + - - -
122B MET* 1.3 75.1 - - - +
124B MET* 1.3 62.6 + - - +
126B THR* 3.5 6.1 + - - -
127B LEU* 3.2 20.3 + - - +
142B ALA* 3.6 20.0 + - - +
143B PHE* 3.7 11.7 - - - -
146B ASN* 2.5 34.9 + - - -
341B GLN* 3.2 14.2 + - - -
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Residues in contact with MET 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B VAL* 3.7 22.9 - - + -
120B ILE 3.0 16.6 + - - +
121B VAL 3.6 3.4 - - - +
123B SER* 1.3 77.0 - - - +
125B TYR* 1.3 65.2 + - - +
127B LEU* 3.2 16.5 + - + +
128B LEU* 3.1 46.0 + - + +
139B ILE* 4.2 22.7 - - + -
142B ALA* 5.2 0.4 - - - -
143B PHE* 3.8 11.8 - - + -
160B PHE* 3.8 35.7 - - + -
163B PHE* 3.5 31.9 - - + -
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Residues in contact with TYR 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B MET* 3.7 33.4 - - + +
86B THR* 4.3 4.3 - - + +
91B ILE* 3.5 40.8 - - + +
99B HIS* 3.3 35.0 - + - -
101B VAL* 4.1 8.2 - - + +
121B VAL 2.7 21.9 + - - +
122B MET* 3.7 22.0 - - + +
124B MET* 1.3 74.2 - - - +
126B THR* 1.3 64.1 + - - +
128B LEU* 3.3 4.6 + - + +
129B ARG* 2.9 49.7 + - - +
209B GLU* 2.8 23.7 + - - +
210B PRO* 3.6 8.1 - - - +
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Residues in contact with THR 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B MET* 3.6 31.1 - - + +
68B PHE* 3.7 9.9 - - - +
69B SER* 3.5 36.3 - - - +
122B MET 2.8 21.3 + - - -
123B SER 3.7 5.2 - - - -
124B MET 3.2 0.2 - - - -
125B TYR* 1.3 75.1 - - - +
127B LEU* 1.3 66.3 + - - +
129B ARG* 3.2 8.3 + - - +
130B ASN* 2.9 35.2 + - - +
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Residues in contact with LEU 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B SER 3.2 10.6 + - - +
124B MET* 3.2 17.2 + - + +
126B THR* 1.3 79.5 - - - +
128B LEU* 1.3 52.1 + - - +
130B ASN* 2.8 11.3 + - + +
131B GLN* 2.6 40.9 + - + +
134B PRO* 3.9 22.9 - - + -
138B GLU* 3.6 41.1 - - + +
139B ILE* 3.6 21.3 - - + +
142B ALA* 3.9 13.0 - - + -
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Residues in contact with LEU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B HIS* 4.9 0.4 - - + -
101B VAL* 3.6 31.2 - - + -
124B MET* 3.1 28.3 + - + +
125B TYR* 3.7 7.9 - - + +
127B LEU* 1.3 79.3 - - - +
129B ARG* 1.3 61.9 + - - +
131B GLN 3.3 4.9 - - - +
132B PRO* 3.1 35.5 - - - +
134B PRO* 3.7 29.4 - - + -
163B PHE* 3.7 30.3 - - + -
204B LEU* 4.0 21.1 - - + +
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Residues in contact with ARG 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B MET* 4.0 23.0 - - - +
67B HIS* 3.5 46.4 + - + -
125B TYR* 2.9 45.1 + - - +
126B THR 3.3 11.2 - - - +
127B LEU 3.1 0.2 - - - -
128B LEU* 1.3 78.2 - - - +
130B ASN* 1.3 59.8 + - - +
132B PRO* 5.4 1.1 - - - +
209B GLU* 3.0 33.6 - - - +
210B PRO* 3.2 25.3 + - - +
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Residues in contact with ASN 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B HIS* 3.2 38.2 + - - +
126B THR* 2.9 31.1 + - - +
127B LEU* 2.8 9.6 + - + +
128B LEU 4.1 0.2 - - - -
129B ARG* 1.3 77.9 - - - +
131B GLN* 1.3 65.4 + - + +
132B PRO* 4.2 4.6 - - - +
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Residues in contact with GLN 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B LEU* 2.6 22.8 + - + +
128B LEU* 3.2 16.4 - - - +
130B ASN* 1.3 78.4 - - + +
132B PRO* 1.3 73.5 - - - +
133B GLU* 2.8 41.5 + - - +
134B PRO* 3.3 30.2 - - + +
138B GLU* 3.8 14.9 - - - +
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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