Contacts of the helix formed by residues 112 - 127 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A VAL* 4.2 11.7 - - + +
22A LEU* 4.0 31.6 - - + +
23A PRO 3.4 22.0 - - - +
24A LYS* 3.8 9.0 - - - +
26A TYR* 2.9 24.7 - - + +
28A ILE* 3.8 18.4 - - + -
111A THR* 1.3 88.4 - - - +
113A GLU* 1.3 56.8 + - - +
115A PHE* 3.2 0.5 + - - +
116A PHE* 2.9 38.2 + - + -
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Residues in contact with GLU 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A VAL* 4.0 23.1 - - + +
111A THR* 3.3 6.8 + - - +
112A PRO* 1.3 77.6 - - - +
114A GLU* 1.3 71.8 + - - +
116A PHE* 3.3 2.5 + - - +
117A ARG* 3.0 52.0 + - - +
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Residues in contact with GLU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A MSE 5.2 0.9 - - - +
109A LEU 5.1 0.5 - - - +
110A PHE* 3.9 18.7 - - + -
111A THR* 2.9 44.1 + - - +
113A GLU* 1.3 82.9 - - - +
115A PHE* 1.3 63.2 + - - +
117A ARG* 3.3 26.6 + - - +
118A ILE* 3.2 28.4 + - - +
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Residues in contact with PHE 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ILE* 3.7 31.4 - - + -
30A LEU* 4.0 22.4 - - + -
52A LEU* 3.5 29.2 - - + +
55A SER* 3.8 26.7 - - - -
56A LEU* 4.1 22.9 - - + -
59A LEU* 5.5 0.2 - - + -
110A PHE* 3.9 14.9 - + + +
111A THR 3.0 15.5 + - - +
112A PRO 3.6 3.1 - - - +
114A GLU* 1.3 76.6 - - - +
116A PHE* 1.3 95.3 + + - +
118A ILE* 3.3 7.7 + - - +
119A PHE* 3.0 24.1 + - + +
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Residues in contact with PHE 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A VAL* 3.6 28.7 - - + -
18A LEU* 3.5 27.6 - - + -
19A VAL* 3.4 18.8 - - + -
22A LEU* 4.0 15.5 - - + -
28A ILE* 4.5 5.6 - - + -
56A LEU* 3.9 11.0 - - + -
59A LEU* 5.2 2.5 - - + -
79A LEU* 3.6 23.6 - - + -
112A PRO 2.9 27.1 + - - +
113A GLU 4.0 2.0 - - - +
115A PHE* 1.3 104.1 - + - +
117A ARG* 1.3 58.7 + - - +
118A ILE 3.4 0.2 - - - -
119A PHE* 3.8 17.8 - + + +
120A ASN* 2.9 36.7 + - - -
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Residues in contact with ARG 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A GLU* 3.0 46.8 + - - +
114A GLU* 3.4 36.1 - - - +
115A PHE 3.2 0.2 - - - -
116A PHE* 1.3 77.0 - - - +
118A ILE* 1.3 63.5 + - + +
120A ASN* 3.4 4.8 + - - +
121A ARG* 3.0 29.5 + - + +
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Residues in contact with ILE 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LEU* 3.8 21.8 - - + -
32A TYR* 3.9 16.4 - - + -
36A MSE 3.7 23.1 - - + -
48A MSE 3.9 10.8 - - + -
52A LEU* 4.8 1.6 - - + -
110A PHE* 3.5 38.4 - - + -
114A GLU 3.2 14.4 + - - +
115A PHE* 3.3 6.0 + - - +
117A ARG* 1.3 77.0 - - + +
119A PHE* 1.3 58.9 + - - +
121A ARG* 3.5 9.8 - - - +
122A SER* 2.8 35.5 + - - +
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Residues in contact with PHE 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ASN 5.9 4.5 - - - -
15A VAL* 4.1 17.9 - - + -
52A LEU* 3.9 26.1 - - + +
56A LEU* 3.7 21.3 - - + -
79A LEU* 3.9 24.5 - - + -
82A ILE* 4.5 7.2 - - + -
83A VAL* 3.3 31.2 - - + -
115A PHE* 3.0 18.1 + - + +
116A PHE* 3.8 21.8 - + + +
117A ARG 3.3 0.2 - - - -
118A ILE* 1.3 74.8 - - - +
120A ASN* 1.3 74.6 + - - +
121A ARG 3.2 0.2 + - - -
122A SER* 3.3 2.8 + - - -
123A ILE* 3.0 50.3 + - + +
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Residues in contact with ASN 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ASN 5.4 1.7 + - - -
12A VAL* 3.9 23.3 + - - +
15A VAL* 3.5 31.8 - - - +
116A PHE 2.9 31.1 + - - +
117A ARG* 4.2 4.3 - - - +
119A PHE* 1.3 79.4 - - - +
121A ARG* 1.3 57.2 + - - +
123A ILE* 3.4 9.3 + - - +
124A ASP* 2.9 41.0 + - - +
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Residues in contact with ARG 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A MSE 3.3 36.4 + - - +
37A ASP* 3.6 30.5 + - - +
39A LEU 4.8 4.2 + - - -
44A TRP* 3.6 27.8 - - - +
117A ARG* 3.0 22.0 + - + +
118A ILE* 3.5 8.1 - - - +
120A ASN* 1.3 75.1 - - - +
122A SER* 1.3 63.9 + - - +
123A ILE 3.2 0.4 - - - -
124A ASP* 3.4 4.8 + - - +
125A ALA* 3.0 25.1 + - - +
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Residues in contact with SER 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A MSE 4.1 4.5 - - - +
44A TRP* 3.7 15.2 - - - -
45A ILE* 3.3 33.3 - - - +
48A MSE 4.0 8.1 - - - +
49A VAL* 4.7 6.1 - - - -
52A LEU* 3.4 25.7 - - - +
118A ILE* 2.8 19.4 + - - +
119A PHE 3.7 1.6 - - - -
121A ARG* 1.3 75.7 - - - +
123A ILE* 1.3 63.0 + - - +
125A ALA 3.6 3.1 + - - -
126A PHE* 3.4 11.8 - - - -
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Residues in contact with ILE 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ASN 5.4 9.9 - - - +
49A VAL* 5.4 1.1 - - + -
52A LEU* 6.1 0.4 - - + -
82A ILE* 3.9 20.6 - - + -
83A VAL* 4.7 7.0 - - + -
86A LEU* 3.4 29.2 - - + +
119A PHE* 3.0 47.3 + - + +
120A ASN* 3.5 13.2 - - - +
122A SER* 1.3 78.5 - - - +
124A ASP* 1.3 73.2 + - - +
125A ALA 3.3 0.7 + - - -
126A PHE* 3.4 20.1 + - - +
127A LYS* 4.4 1.4 + - - +
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Residues in contact with ASP 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A ASN* 2.9 29.2 + - - +
121A ARG* 3.4 6.0 + - - +
122A SER 3.4 0.2 - - - -
123A ILE* 1.3 84.2 - - - +
125A ALA* 1.3 56.7 + - - +
126A PHE 2.9 7.7 + - - -
127A LYS* 2.9 23.9 + - + +
128A ASP* 3.3 23.7 + - - +
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Residues in contact with ALA 125 (chain A).
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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41A SER* 3.9 19.1 + - - -
44A TRP* 3.9 21.5 - - + -
45A ILE* 3.9 5.7 - - + +
121A ARG 3.0 17.8 + - - +
122A SER 3.7 9.2 - - - +
123A ILE 3.2 0.8 - - - -
124A ASP* 1.3 74.2 - - - +
126A PHE* 1.3 59.9 + - - +
128A ASP* 3.9 23.6 - - - +
129A PHE* 3.6 15.1 - - - -
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Residues in contact with PHE 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ILE* 3.8 21.3 - - + -
49A VAL* 3.9 8.3 - - + -
86A LEU* 3.6 52.3 - - + -
89A CYS* 5.3 8.1 - - + -
90A VAL* 3.8 27.8 - - + -
122A SER 3.4 21.5 - - - -
123A ILE 3.7 9.0 - - - +
124A ASP 2.9 1.6 + - - -
125A ALA* 1.3 80.4 - - - +
127A LYS* 1.3 66.3 + - - +
129A PHE* 3.5 38.4 - + + +
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Residues in contact with LYS 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A ILE 4.4 1.9 + - - +
124A ASP* 2.9 18.9 + - - +
126A PHE* 1.3 79.4 - - - +
128A ASP* 1.3 60.5 + - - +
129A PHE* 2.9 9.2 + - - +
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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