Contacts of the helix formed by residues 15 - 25 (chain A) in PDB entry 3FTF
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 SER 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A LEU* 3.5 4.8 + - - -
14A VAL* 1.3 77.8 - - - +
16A GLU* 1.3 64.6 + - - +
17A GLY* 4.0 6.1 + - - -
18A VAL* 3.5 22.5 + - - +
19A LEU* 3.2 28.2 + - - +
165A PHE* 3.7 35.0 - - - -
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Residues in contact with GLU 16 (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 SER* 1.3 70.4 + - - +
17A GLY* 1.3 63.5 - - - +
19A LEU* 3.2 13.1 + - - +
20A LYS* 3.0 31.8 + - + +
47A VAL* 5.8 1.0 - - - +
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Residues in contact with GLY 17 (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 SER* 3.3 4.3 + - - -
16A GLU* 1.3 79.2 - - - +
18A VAL* 1.3 56.9 + - - +
20A LYS* 3.4 18.3 - - - -
21A LYS* 3.2 26.5 + - - +
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Residues in contact with VAL 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 3.4 29.6 - - + -
15A SER* 3.5 18.7 + - - +
17A GLY* 1.3 72.4 - - - +
19A LEU* 1.3 59.6 + - - +
21A LYS* 3.5 5.6 - - - +
22A ILE* 2.9 36.8 + - + +
127A MET* 3.9 13.9 - - + -
159A MET* 3.8 25.1 - - + -
161A VAL* 3.6 32.1 - - + -
165A PHE* 4.9 3.6 - - + -
176A VAL* 4.2 0.9 - - + -
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Residues in contact with LEU 19 (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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13A LEU* 3.4 44.0 - - + +
14A VAL* 4.9 1.1 - - - -
15A SER 3.2 31.9 + - - +
16A GLU* 3.2 12.3 + - - +
18A VAL* 1.3 78.6 - - - +
20A LYS* 1.3 60.2 + - - +
22A ILE* 3.6 3.5 + - - -
23A ALA 3.5 13.7 + - - -
43A ASN* 3.8 17.0 - - + +
44A LEU* 3.5 50.1 - - + +
47A VAL* 3.7 16.8 - - + +
501A SAH 5.4 1.1 - - - +
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Residues in contact with LYS 20 (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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16A GLU* 3.0 20.2 - - + +
17A GLY* 3.4 20.6 + - - -
19A LEU* 1.3 73.3 - - + +
21A LYS* 1.3 63.3 + - - +
22A ILE 3.3 0.7 - - - -
23A ALA* 3.8 1.6 - - - +
24A GLU* 2.9 72.7 + - + +
47A VAL* 3.6 20.8 - - + +
51A HIS* 5.0 2.4 + - - +
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Residues in contact with LYS 21 (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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17A GLY 3.2 19.4 + - - +
18A VAL* 3.1 9.1 + - - +
20A LYS* 1.3 81.6 - - - +
22A ILE* 1.3 64.9 + - + +
24A GLU* 4.2 8.4 + - - +
25A GLU* 3.5 35.1 + - - +
158A VAL* 4.5 18.5 - - + +
159A MET* 3.6 31.9 - - + -
176A VAL* 5.8 1.5 - - + +
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Residues in contact with ILE 22 (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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13A LEU* 3.8 27.1 - - + -
18A VAL* 2.9 21.0 + - + +
19A LEU* 3.7 6.3 - - - +
20A LYS 3.3 0.2 - - - -
21A LYS* 1.3 79.4 - - + +
23A ALA* 1.3 61.0 + - - +
25A GLU* 3.7 11.1 + - - +
26A LEU* 4.0 10.9 + - - +
44A LEU* 3.8 21.8 - - + -
99A VAL* 3.7 26.0 - - + -
100A GLY 5.4 2.0 - - - +
101A ASN* 5.7 2.2 - - + -
125A VAL* 4.1 16.5 - - + +
126A PHE 6.1 1.6 - - - -
127A MET* 3.8 23.1 - - + +
176A VAL* 3.9 23.3 - - + -
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Residues in contact with ALA 23 (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 LEU 3.5 3.8 + - - +
20A LYS 3.9 2.7 - - - +
21A LYS 3.3 0.4 - - - -
22A ILE* 1.3 77.0 - - - +
24A GLU* 1.3 65.2 + - - +
26A LEU* 3.1 20.5 + - - +
27A ASN 4.1 1.2 + - - -
28A ILE* 3.8 8.4 + - + +
44A LEU* 5.0 0.7 - - + -
47A VAL* 3.7 25.4 - - + -
48A LEU* 4.0 23.8 - - + -
51A HIS* 3.5 26.8 - - + +
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Residues in contact with GLU 24 (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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20A LYS* 2.9 48.3 + - + +
21A LYS* 4.2 10.5 + - - +
23A ALA* 1.3 75.7 - - - +
25A GLU* 1.3 63.1 + - - +
27A ASN* 3.2 22.5 + - - -
51A HIS* 4.2 20.2 - - + +
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Residues in contact with GLU 25 (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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21A LYS* 3.5 30.5 + - - +
22A ILE* 3.8 7.6 - - - +
23A ALA 3.2 1.2 - - - -
24A GLU* 1.3 79.7 - - - +
26A LEU* 1.3 59.5 - - - +
27A ASN* 3.2 3.9 + - - +
125A VAL* 4.2 13.6 - - + +
158A VAL* 4.1 34.9 - - + +
176A VAL* 5.9 0.2 - - + -
178A LYS* 3.1 54.2 + - + +
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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