Contacts of the strand formed by residues 16 - 21 (chain k) in PDB entry 6FF7
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 LYS 16 (chain k).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15k LYS* 1.3 74.9 - - - +
17k LEU* 1.3 61.4 + - - +
29k GLY* 3.7 8.7 - - - +
30k ILE* 4.3 5.6 - - + +
72k ALA* 3.9 2.6 - - - -
73k LEU* 2.9 36.5 + - + +
74k GLU* 3.8 9.5 + - + +
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Residues in contact with LEU 17 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12k PHE* 6.6 0.7 - - + -
15k LYS* 4.5 4.7 - - + +
16k LYS* 1.3 75.9 - - - +
18k SER* 1.3 62.5 + - - +
19k LEU* 4.2 2.2 - - + -
28k GLN* 3.2 9.0 - - - +
29k GLY 2.9 35.5 + - - +
31k LEU* 5.5 6.1 - - + +
70k LEU* 5.2 9.2 - - + -
71k GLU 3.4 11.9 - - - +
72k ALA* 4.8 2.5 - - - -
73k LEU* 4.3 5.2 - - - +
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Residues in contact with SER 18 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17k LEU* 1.3 73.0 - - - +
19k LEU* 1.3 60.1 + - - +
20k LYS 4.0 1.2 + - - -
27k VAL 3.8 4.9 - - - -
28k GLN* 4.6 4.9 - - - +
70k LEU* 3.4 3.2 - - - -
71k GLU* 2.7 48.4 + - - +
73k LEU* 5.6 5.2 - - - -
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Residues in contact with LEU 19 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17k LEU* 4.2 3.1 - - + -
18k SER* 1.3 71.6 - - - +
20k LYS* 1.3 63.3 + - - +
21k LEU* 3.7 3.5 + - + +
26k HIS* 3.3 8.3 - - - +
27k VAL* 2.8 43.1 + - + +
28k GLN* 5.7 0.2 - - - -
69k MET 3.7 4.9 - - - +
70k LEU* 4.6 6.3 - - + +
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Residues in contact with LYS 20 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18k SER 4.0 1.6 + - - +
19k LEU* 1.3 71.8 - - - +
21k LEU* 1.3 59.9 + - - +
25k ARG 3.7 4.7 - - - +
26k HIS* 4.7 4.3 - - + +
67k ILE* 4.0 2.3 - - - -
68k ILE* 3.0 28.3 + - + +
69k MET* 2.8 32.9 + - + +
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Residues in contact with LEU 21 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85j THR* 6.2 3.1 - - - -
19k LEU* 3.7 4.6 + - + +
20k LYS* 1.3 75.4 - - - +
22k ASN* 1.3 71.2 + - - +
24k GLY* 3.6 4.7 + - - -
25k ARG* 2.7 35.3 + - + +
26k HIS* 5.5 0.4 - - - -
66k SER* 3.4 15.7 - - - +
67k ILE* 4.9 1.1 - - - +
68k ILE* 4.6 5.1 - - - +
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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