Contacts of the helix formed by residues 112 - 125 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19D VAL* 4.4 14.4 - - + +
22D LEU* 3.7 36.3 - - + +
23D PRO 3.5 23.8 - - - +
24D LYS* 4.1 4.5 - - - +
26D TYR* 3.1 21.1 - - + +
28D ILE* 4.0 17.2 - - + -
111D THR* 1.3 85.7 - - - +
113D GLU* 1.4 56.9 + - + +
115D PHE 3.2 0.3 + - - -
116D PHE* 2.8 38.6 + - + +
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Residues in contact with GLU 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D VAL* 3.8 27.6 - - + +
111D THR* 3.7 14.5 + - - +
112D PRO* 1.4 76.1 - - + +
114D GLU* 1.3 66.3 + - + +
116D PHE 3.9 0.3 - - - -
117D ARG* 3.0 30.0 + - - +
1021D CA 2.5 30.2 - - - -
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Residues in contact with GLU 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B 1PE 3.6 31.9 + - - +
27D MSE 5.0 1.4 - - - +
109D LEU 4.3 2.1 - - - +
110D PHE* 3.4 17.3 - - + -
111D THR* 3.1 37.0 + - - +
112D PRO 3.3 0.6 - - - -
113D GLU* 1.3 83.1 - - + +
115D PHE* 1.3 66.1 + - - +
117D ARG* 3.4 6.9 + - - +
118D ILE* 3.2 27.4 + - - +
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Residues in contact with PHE 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D ILE* 3.7 31.6 - - + -
30D LEU* 3.8 31.6 - - + -
52D LEU* 3.9 13.8 - - + +
55D SER* 3.7 32.1 - - - -
56D LEU* 4.0 21.3 - - + -
59D LEU* 5.4 0.7 - - + -
110D PHE* 3.8 13.4 - + + +
111D THR 2.9 20.7 + - - +
112D PRO 3.7 2.9 - - - +
114D GLU* 1.3 73.1 - - - +
116D PHE* 1.3 91.1 + + - +
118D ILE* 3.3 7.9 + - - +
119D PHE* 2.9 29.1 + - + -
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Residues in contact with PHE 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D VAL* 3.7 25.6 - - + -
18D LEU* 3.6 19.5 - - + -
19D VAL* 4.2 15.3 - - + -
22D LEU* 3.8 22.9 - - + -
28D ILE* 4.3 7.2 - - + -
56D LEU* 3.9 10.8 - - + -
59D LEU* 4.1 8.3 - - + -
79D LEU* 3.7 22.4 - - + -
112D PRO* 2.8 34.1 + - + +
113D GLU 4.5 0.7 - - - +
115D PHE* 1.3 98.8 - + - +
117D ARG* 1.3 62.6 + - - +
119D PHE* 3.7 20.5 - + - +
120D ASN* 3.0 29.5 + - - -
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Residues in contact with ARG 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B GLU* 2.8 43.0 + - - -
249B 1PE 5.4 7.5 + - - -
113D GLU 3.0 20.0 + - - +
114D GLU* 3.4 6.7 + - - +
116D PHE* 1.3 75.3 - - - +
118D ILE* 1.4 58.5 + - + +
120D ASN* 3.5 8.4 + - + +
121D ARG* 2.9 29.8 + - + +
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Residues in contact with ILE 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B 1PE 4.2 11.0 - - - +
30D LEU* 4.1 9.4 - - + -
32D TYR* 4.0 15.3 - - + -
36D MSE 3.6 19.3 - - + -
48D MSE 3.3 32.3 - - + -
52D LEU* 4.7 0.2 - - + -
110D PHE* 3.6 39.5 - - + -
114D GLU 3.2 15.1 + - - +
115D PHE* 3.5 5.6 - - - +
117D ARG* 1.4 74.8 - - + +
119D PHE* 1.3 65.6 + - - +
121D ARG* 3.2 6.4 + - - +
122D SER* 2.9 27.8 + - - +
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Residues in contact with PHE 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D ASN* 4.4 9.9 - - + -
15D VAL* 4.0 19.3 - - + -
52D LEU* 4.1 23.2 - - + +
56D LEU* 3.8 21.1 - - + -
79D LEU* 4.0 26.5 - - + -
82D ILE* 5.6 3.6 - - + -
83D VAL* 3.5 27.8 - - + -
115D PHE* 2.9 17.8 + - + +
116D PHE* 3.7 26.0 - + + +
118D ILE* 1.3 75.4 - - - +
120D ASN* 1.3 74.9 + - - +
122D SER* 3.2 2.1 + - - -
123D ILE* 3.0 48.2 + - + +
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Residues in contact with ASN 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D ASN* 5.0 1.4 - - - +
12D VAL* 3.6 28.5 + - + +
15D VAL* 3.6 25.2 - - - +
16D THR* 5.9 0.4 + - - -
116D PHE 3.0 24.6 + - - +
117D ARG* 3.8 7.1 - - + +
119D PHE* 1.3 87.4 - - - +
121D ARG* 1.3 61.7 + - - +
123D ILE* 3.5 6.7 + - - +
124D ASP* 3.2 23.7 + - - +
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Residues in contact with ARG 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D MSE 2.9 52.1 + - + +
37D ASP* 3.8 18.7 + - - +
39D LEU 4.6 5.7 + - - -
41D SER* 5.6 1.0 + - - -
44D TRP* 3.8 16.0 - - + -
117D ARG* 2.9 19.3 + - + +
118D ILE* 3.2 8.5 + - - +
120D ASN* 1.3 77.2 - - - +
122D SER* 1.3 60.3 + - - +
124D ASP* 3.4 6.6 + - - +
125D ALA* 3.2 25.4 + - - +
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Residues in contact with SER 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D MSE 4.3 0.7 - - - -
44D TRP* 3.7 9.5 - - - -
45D ILE* 3.1 34.5 - - - +
48D MSE 3.5 22.6 - - - +
49D VAL* 5.1 1.8 - - - -
52D LEU* 3.5 23.9 - - - +
118D ILE* 2.9 21.4 + - - +
119D PHE 3.8 0.7 - - - -
121D ARG* 1.3 71.3 - - - +
123D ILE* 1.3 66.2 + - - +
125D ALA 3.3 7.3 + - - -
126D PHE* 3.5 5.4 + - - +
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Residues in contact with ILE 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D ASN* 5.5 9.4 - - + -
49D VAL* 4.6 3.6 - - + -
52D LEU* 4.5 8.1 - - + -
82D ILE* 4.8 11.7 - - + -
83D VAL* 4.0 11.4 - - + -
86D LEU* 3.8 28.5 - - + +
119D PHE* 3.0 54.5 + - + +
120D ASN* 4.0 7.9 - - - +
122D SER* 1.3 78.9 - - - +
124D ASP* 1.3 62.8 + - + +
126D PHE* 3.4 17.0 - - - +
127D LYS* 4.3 2.1 + - - +
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Residues in contact with ASP 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D ASN 3.2 16.9 + - - +
121D ARG* 3.7 7.4 - - - +
122D SER 3.3 0.2 - - - -
123D ILE* 1.3 78.4 - - + +
125D ALA* 1.3 59.7 + - - +
126D PHE 3.1 0.2 - - - -
127D LYS* 3.0 32.7 + - - +
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Residues in contact with ALA 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D SER* 3.4 32.8 + - - +
44D TRP* 3.8 18.4 - - + -
45D ILE* 4.1 8.1 - - + +
121D ARG* 3.2 17.4 + - - +
122D SER 3.3 6.4 + - - +
124D ASP* 1.3 79.4 + - - +
126D PHE* 1.3 59.2 + - - +
127D LYS 3.4 6.5 + - - -
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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