Contacts of the strand formed by residues 14 - 17 (chain M) in PDB entry 1FD4
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 ILE 14 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8M CYS* 3.3 9.1 - - - -
9M LEU* 4.6 0.2 - - - -
12M GLY 5.5 0.2 - - - +
13M ALA* 1.3 76.1 - - - +
15M CYS* 1.3 59.6 + - - +
16M HIS* 4.2 19.3 - - + -
21M PRO* 4.2 18.8 - - + -
24M TYR* 3.7 31.0 - - + +
36M LYS 3.4 0.7 - - - +
37M CYS* 3.4 1.0 - - - -
38M CYS* 2.8 53.9 + - + +
14N ILE* 5.8 0.4 - - + -
15N CYS 3.4 11.0 - - - +
16N HIS* 3.6 41.3 - - + +
17N PRO* 3.8 11.4 - - + -
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Residues in contact with CYS 15 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5M PRO* 3.6 24.0 - - - -
8M CYS* 3.7 9.6 - - - -
9M LEU* 4.6 6.2 - - - +
14M ILE* 1.3 70.8 - - - +
16M HIS* 1.3 59.8 + - - +
30M CYS* 2.0 48.7 - - + -
35M THR* 5.4 0.4 - - - -
36M LYS 3.4 3.8 - - - -
9N LEU* 3.8 18.0 - - + +
14N ILE* 3.4 9.0 - - - +
15N CYS* 3.0 36.4 + - + +
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Residues in contact with HIS 16 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14M ILE* 3.9 14.3 + - + -
15M CYS* 1.3 73.5 - - - +
17M PRO* 1.3 90.8 + - + +
19M PHE* 2.8 49.0 + + - +
21M PRO* 3.8 25.1 - - + +
35M THR* 4.5 2.2 - - - -
36M LYS* 2.8 39.3 + - - +
38M CYS* 4.2 13.9 - - - -
9N LEU* 5.0 0.2 - - - -
14N ILE* 3.8 20.1 - - + +
16N HIS* 6.0 0.4 - - - -
24N TYR* 4.8 10.6 + - - -
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Residues in contact with PRO 17 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15M CYS 4.4 0.4 - - - +
16M HIS* 1.3 106.4 + - + +
18M VAL* 1.3 63.9 + - + +
19M PHE* 2.7 18.7 + - - -
34M GLY 4.1 3.8 - - - +
35M THR* 4.3 12.3 - - + -
9N LEU* 4.6 7.8 - - + +
12N GLY* 5.6 6.3 - - - +
13N ALA 4.0 11.7 - - - +
14N ILE* 3.4 24.9 - - + -
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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