Contacts of the helix formed by residues 112 - 127 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B VAL* 3.8 12.5 - - + +
22B LEU* 3.5 45.5 - - + -
23B PRO 3.6 16.4 - - - +
24B LYS* 4.1 6.7 - - - +
26B TYR* 3.2 21.1 - - + +
28B ILE* 4.0 16.6 - - + -
111B THR* 1.3 86.7 - - - +
113B GLU* 1.3 61.1 + - - +
115B PHE* 4.4 0.2 - - + -
116B PHE* 3.0 31.8 + - + +
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Residues in contact with GLU 113 (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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19B VAL* 4.0 21.4 - - + +
111B THR* 3.2 7.8 + - - +
112B PRO* 1.3 81.0 - - - +
114B GLU* 1.3 65.7 + - - +
116B PHE* 4.0 0.9 - - - +
117B ARG* 3.1 54.7 + - - +
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Residues in contact with GLU 114 (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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27B MSE 5.1 1.6 - - - +
109B LEU 4.7 1.6 - - - +
110B PHE* 3.8 23.0 - - + -
111B THR* 3.1 39.5 + - - +
113B GLU* 1.3 84.9 - - - +
115B PHE* 1.3 65.6 + - - +
117B ARG* 3.3 9.4 + - - +
118B ILE* 3.1 29.2 + - - +
249B 1PE 4.0 25.8 + - - +
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Residues in contact with PHE 115 (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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28B ILE* 3.9 31.4 - - + -
30B LEU* 3.8 40.8 - - + -
52B LEU* 3.4 26.9 - - + -
55B SER* 3.8 22.2 - - - -
56B LEU* 3.9 28.0 - - + -
59B LEU* 5.6 0.4 - - + -
110B PHE* 3.9 11.3 - - + +
111B THR 3.1 13.2 + - - +
112B PRO 3.8 3.8 - - - +
114B GLU* 1.3 77.9 - - - +
116B PHE* 1.3 82.2 - + + +
118B ILE* 3.1 9.6 + - - +
119B PHE* 2.8 24.4 + - + +
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Residues in contact with PHE 116 (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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15B VAL* 3.5 28.0 - - + -
18B LEU* 3.5 18.8 - - + -
19B VAL* 3.8 15.0 - - + -
22B LEU* 3.6 24.2 - - + -
28B ILE* 4.1 6.1 - - + -
56B LEU* 3.9 17.7 - - + -
59B LEU* 4.3 7.0 - - + -
79B LEU* 3.5 24.7 - - + -
112B PRO 3.0 26.6 + - - +
113B GLU 4.0 1.1 - - - +
115B PHE* 1.3 95.2 - + - +
117B ARG* 1.3 59.2 + - - +
119B PHE* 3.7 18.5 - + + +
120B ASN* 2.8 37.4 + - - -
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Residues in contact with ARG 117 (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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113B GLU* 3.1 52.6 + - - +
114B GLU* 3.5 16.1 - - - +
115B PHE 3.3 0.2 - - - -
116B PHE* 1.3 73.5 - - - +
118B ILE* 1.3 61.8 + - + +
120B ASN* 3.9 6.3 - - - +
121B ARG* 3.1 26.9 + - - +
249B 1PE 2.7 31.4 + - - +
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Residues in contact with ILE 118 (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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30B LEU* 4.0 9.9 - - + -
32B TYR* 4.1 13.9 - - + -
36B MSE 3.9 24.2 - - + +
48B MSE 3.8 30.1 - - + -
52B LEU* 4.8 0.9 - - + -
110B PHE* 3.7 35.7 - - + -
114B GLU 3.1 15.1 + - - +
115B PHE* 3.3 8.7 - - - +
117B ARG* 1.3 76.3 - - + +
119B PHE* 1.3 66.4 + - - +
121B ARG* 3.1 7.2 + - - +
122B SER* 3.0 27.1 + - - +
249B 1PE 4.1 15.3 - - - +
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Residues in contact with PHE 119 (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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15B VAL* 4.2 6.1 - - + -
52B LEU* 4.0 28.5 - - + +
56B LEU* 3.6 31.4 - - + -
79B LEU* 4.1 33.9 - - + -
82B ILE* 5.0 5.2 - - + -
83B VAL* 4.3 10.5 - - + -
115B PHE* 2.8 19.6 + - + +
116B PHE* 3.7 25.8 - + + +
118B ILE* 1.3 71.7 - - - +
120B ASN* 1.3 73.4 + - - +
122B SER* 3.5 1.6 + - - -
123B ILE* 3.1 67.0 + - + +
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Residues in contact with ASN 120 (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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12B VAL* 5.3 14.0 - - - +
15B VAL* 3.9 23.9 - - - +
116B PHE* 2.8 23.6 + - - +
117B ARG* 4.0 7.1 - - - +
118B ILE 3.2 0.2 - - - -
119B PHE* 1.3 89.5 - - - +
121B ARG* 1.3 64.9 + - - +
123B ILE* 3.5 5.5 + - - +
124B ASP* 3.0 36.6 + - - +
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Residues in contact with ARG 121 (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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36B MSE 4.1 39.9 + - + -
37B ASP 5.6 1.4 + - - -
39B LEU 6.0 0.2 + - - -
41B SER* 4.2 7.9 + - - +
44B TRP* 4.0 16.4 - - + -
117B ARG 3.1 17.8 + - - +
118B ILE 3.1 4.4 + - - +
120B ASN* 1.3 74.0 - - - +
122B SER* 1.3 51.8 + - - +
124B ASP* 3.4 10.7 + - - +
125B ALA* 2.8 54.1 + - - +
128B ASP* 6.0 3.4 - - - +
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Residues in contact with SER 122 (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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36B MSE 4.4 2.3 - - - -
44B TRP* 3.8 6.5 - - - -
45B ILE* 3.1 32.5 - - - +
48B MSE 3.1 26.2 - - - +
49B VAL* 5.2 3.1 - - - -
52B LEU* 3.7 17.0 - - - +
118B ILE 3.0 17.0 + - - -
119B PHE 3.7 4.5 - - - -
121B ARG* 1.3 74.7 - - - +
123B ILE* 1.3 65.7 + - - +
125B ALA* 3.1 11.7 + - - +
126B PHE* 3.4 7.9 - - - -
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Residues in contact with ILE 123 (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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49B VAL* 5.9 0.2 - - + -
52B LEU* 6.1 0.2 - - + -
82B ILE* 3.7 22.2 - - + -
83B VAL* 4.2 8.3 - - + -
86B LEU* 3.4 28.9 - - + +
119B PHE* 3.1 48.5 + - + +
120B ASN* 3.9 7.2 - - - +
122B SER* 1.3 79.2 - - - +
124B ASP* 1.3 67.4 + - - +
126B PHE* 3.6 21.3 + - - +
127B LYS* 4.3 9.1 + - - +
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Residues in contact with ASP 124 (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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120B ASN* 3.0 32.2 + - - +
121B ARG* 3.5 13.2 - - - +
123B ILE* 1.3 78.7 - - - +
125B ALA* 1.3 63.6 + - - +
126B PHE 3.0 3.1 - - - -
127B LYS* 3.2 51.2 + - + +
128B ASP* 3.7 8.7 + - - +
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Residues in contact with ALA 125 (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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41B SER* 3.4 21.5 + - - -
44B TRP* 3.6 25.8 - - + -
45B ILE* 3.8 8.1 - - + -
121B ARG* 2.8 26.2 + - - +
122B SER 3.1 13.4 + - - +
124B ASP* 1.3 76.1 - - - +
126B PHE* 1.3 58.0 + - - +
128B ASP* 4.1 8.9 - - - +
129B PHE* 3.1 18.1 - - - -
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Residues in contact with PHE 126 (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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45B ILE* 3.2 34.5 - - + -
49B VAL* 3.6 22.9 - - + -
86B LEU* 3.8 34.5 - - + -
89B CYS* 4.9 7.9 - - - -
90B VAL* 3.3 33.9 - - + -
98B LEU* 6.4 0.2 - - + -
122B SER 3.4 11.7 - - - -
123B ILE 3.7 10.5 - - - +
124B ASP 3.0 0.6 - - - -
125B ALA* 1.3 77.1 - - - +
127B LYS* 1.4 63.2 + - - +
129B PHE* 3.1 35.8 - + - +
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Residues in contact with LYS 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 ILE* 4.9 7.4 - - - +
124B ASP* 3.2 44.4 + - + +
126B PHE* 1.4 75.7 - - + +
128B ASP* 1.3 57.0 + - + +
129B PHE 3.4 3.2 + - - -
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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