Contacts of the helix formed by residues 112 - 124 (chain C) in PDB entry 1SCF
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 112 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19C VAL* 4.5 14.8 - - + +
22C LEU* 3.7 36.1 - - + -
23C PRO 3.4 23.6 - - - +
24C LYS* 4.0 5.8 - - - +
26C TYR* 3.0 25.8 - - + +
28C ILE* 4.0 17.0 - - + -
111C THR* 1.4 80.1 - - - +
113C GLU* 1.3 56.3 + - - +
115C PHE* 3.2 0.5 + - - +
116C PHE* 2.8 36.7 + - + -
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Residues in contact with GLU 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C VAL* 4.0 25.5 - - + +
111C THR* 3.3 7.7 + - - +
112C PRO* 1.3 76.4 - - - +
114C GLU* 1.3 58.9 + - + +
116C PHE* 3.3 2.1 + - - +
117C ARG* 2.8 58.9 + - - +
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Residues in contact with GLU 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C LEU 4.4 2.3 - - - +
110C PHE* 3.6 23.1 - - + -
111C THR* 3.2 42.4 + - - +
113C GLU* 1.3 76.2 - - + +
115C PHE* 1.3 67.7 + - - +
117C ARG* 3.5 27.5 - - - +
118C ILE* 3.5 26.4 + - + +
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Residues in contact with PHE 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C ILE* 3.8 30.3 - - + -
30C LEU* 3.8 23.6 - - + -
52C LEU* 3.6 29.8 - - + -
55C SER* 3.8 28.5 - - - -
56C LEU* 4.2 17.3 - - + -
59C LEU* 5.3 0.7 - - + -
110C PHE* 3.8 13.4 - + + +
111C THR 2.9 16.8 + - - +
112C PRO 3.5 2.5 - - - +
114C GLU* 1.3 77.8 - - - +
116C PHE* 1.3 101.1 + + - +
117C ARG 3.1 1.4 + - - -
118C ILE* 3.2 8.7 + - - +
119C PHE* 3.1 19.4 + - + +
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Residues in contact with PHE 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C VAL* 3.9 24.9 - - + -
18C LEU* 3.4 24.9 - - + -
19C VAL* 3.9 18.2 - - + -
22C LEU* 4.0 16.4 - - + -
28C ILE* 4.3 5.4 - - + -
56C LEU* 3.9 14.1 - - + -
59C LEU* 4.4 3.8 - - + -
79C LEU* 3.8 22.2 - - + -
112C PRO* 2.8 31.0 + - + +
113C GLU 3.3 2.0 + - - +
115C PHE* 1.3 102.8 - + - +
117C ARG* 1.3 55.2 + - - +
119C PHE* 3.5 22.5 - + - +
120C ASN* 2.9 35.4 + - - +
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Residues in contact with ARG 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C GLU* 2.8 47.1 + - - +
114C GLU* 3.5 39.1 - - - +
115C PHE 3.1 0.2 - - - -
116C PHE* 1.3 75.2 - - - +
118C ILE* 1.3 62.1 + - + +
120C ASN* 4.0 5.3 - - - +
121C ARG* 3.1 30.5 + - - +
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Residues in contact with ILE 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C LEU* 3.6 12.8 - - + -
32C TYR* 3.8 13.0 - - + -
36C MSE 4.0 19.5 - - + +
48C MSE 3.5 30.1 - - + -
52C LEU* 4.3 4.9 - - + -
110C PHE* 3.4 39.9 - - + -
114C GLU* 3.5 14.1 + - + +
115C PHE 3.2 6.7 + - - +
117C ARG* 1.3 76.3 - - + +
119C PHE* 1.3 55.3 + - - +
121C ARG* 3.5 8.7 + - - +
122C SER* 2.8 37.7 + - - +
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Residues in contact with PHE 119 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11C ASN* 5.8 3.8 - - + -
15C VAL* 4.0 17.3 - - + -
52C LEU* 3.8 27.8 - - + +
56C LEU* 3.8 20.6 - - + -
79C LEU* 3.9 24.7 - - + -
82C ILE* 5.4 3.8 - - + -
83C VAL* 3.6 26.9 - - + -
115C PHE* 3.1 14.8 + + + +
116C PHE* 3.5 26.9 - + + +
118C ILE* 1.3 76.5 - - - +
120C ASN* 1.3 75.7 + - - +
122C SER* 3.0 23.2 + - - -
123C ILE* 3.1 29.6 + - + +
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Residues in contact with ASN 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ASN* 6.2 1.0 - - - +
12C VAL* 4.4 21.5 - - - +
15C VAL* 4.1 19.9 - - - +
116C PHE 2.9 23.3 + - - +
117C ARG* 4.0 5.4 - - - +
119C PHE* 1.3 91.6 - - - +
121C ARG* 1.3 61.1 + - - +
123C ILE* 3.5 4.5 + - - +
124C ASP* 3.0 37.3 + - - +
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Residues in contact with ARG 121 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36C MSE 2.6 47.1 + - + +
37C ASP* 3.1 31.2 + - - +
38C VAL 4.8 1.0 + - - -
39C LEU 3.8 10.3 + - - -
40C PRO* 5.7 0.6 - - - +
41C SER 5.7 0.4 - - - +
44C TRP* 4.0 16.0 - - + -
117C ARG* 3.1 20.0 + - - +
118C ILE* 3.6 6.1 - - - +
120C ASN* 1.3 75.5 - - - +
122C SER* 1.3 55.3 + - - +
124C ASP* 3.6 4.5 + - - +
125C ALA* 3.1 27.2 + - - +
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Residues in contact with SER 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C TRP* 3.6 14.0 - - - -
45C ILE* 3.2 26.0 - - - +
48C MSE 4.0 5.8 - - - +
49C VAL* 5.0 4.3 - - - -
52C LEU* 3.3 23.6 - - - +
118C ILE* 2.8 16.5 + - - +
119C PHE 3.0 9.8 + - - -
121C ARG* 1.3 71.8 - - - +
123C ILE* 1.3 68.9 + - - -
124C ASP 3.2 1.6 - - - -
125C ALA 3.4 3.5 + - - -
126C PHE* 3.2 18.9 - - - -
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Residues in contact with ILE 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C VAL* 5.5 1.3 - - + -
52C LEU* 5.5 0.7 - - + -
82C ILE* 5.1 12.6 - - + -
83C VAL* 4.5 9.0 - - + -
86C LEU* 3.5 33.4 - - + -
119C PHE* 3.1 51.6 + - + +
120C ASN* 4.4 5.6 - - - +
122C SER* 1.3 81.3 - - - +
124C ASP* 1.3 61.8 + - - +
126C PHE* 3.3 26.5 - - + +
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Residues in contact with ASP 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C ASN* 3.0 34.6 + - - +
121C ARG* 3.8 5.6 - - - +
122C SER 3.2 0.2 - - - -
123C ILE* 1.3 79.2 - - - +
125C ALA* 1.3 54.9 - - - +
126C PHE* 2.9 17.5 + - - -
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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