Contacts of the strand formed by residues 17 - 22 (chain l) 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 ILE 17 (chain l).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16l HIS* 1.3 74.4 - - - +
18l VAL* 1.3 58.8 + - - +
30l GLY* 3.4 16.4 - - - +
31l LYS* 4.3 2.4 - - + +
73l LEU 5.0 0.5 - - - -
74l PRO* 4.4 17.7 - - - +
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Residues in contact with VAL 18 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13l ALA* 5.7 6.5 - - + -
16l HIS* 3.6 5.4 + - + +
17l ILE* 1.3 73.7 - - - +
19l THR* 1.3 64.4 + - - +
28l TYR 3.8 1.0 - - - +
29l ARG* 3.4 3.8 - - - +
30l GLY 2.8 32.9 + - - +
32l LEU* 4.6 13.5 - - + -
71l LEU* 5.7 3.8 - - + -
72l ILE 3.5 15.0 - - - +
73l LEU* 4.9 4.9 - - + -
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Residues in contact with THR 19 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18l VAL* 1.3 76.0 - - - +
20l CYS* 1.3 62.0 + - - +
27l VAL* 6.4 1.3 - - - -
28l TYR 3.4 5.6 - - - -
29l ARG* 4.3 10.8 - - - +
71l LEU* 3.2 6.8 - - - +
72l ILE* 2.8 51.4 + - - +
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Residues in contact with CYS 20 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19l THR* 1.3 76.4 - - - +
21l GLU* 1.3 61.6 + - - +
22l THR 4.2 0.2 + - - -
26l GLU 3.6 1.6 - - - +
27l VAL* 3.4 4.3 - - - -
28l TYR* 2.7 50.1 + - + +
68l ILE* 6.1 3.4 - - + -
70l PHE 3.6 7.4 - - - +
71l LEU* 5.2 3.8 - - + -
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Residues in contact with GLU 21 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19l THR 4.4 0.4 - - - -
20l CYS* 1.3 74.6 - - - +
22l THR* 1.3 65.0 + - - +
25l GLY* 5.2 6.5 - - - +
26l GLU 3.4 8.5 - - - +
27l VAL* 5.0 5.8 - - + -
68l ILE* 3.8 3.7 - - - +
69l ARG* 2.9 24.8 + - + -
70l PHE* 3.1 22.3 + - + +
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Residues in contact with THR 22 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68k ILE* 6.1 4.0 - - - -
20l CYS 4.1 0.6 - - - -
21l GLU* 1.3 78.2 - - - +
23l ASN* 1.3 65.6 + - - +
24l THR* 3.1 12.3 - - - -
25l GLY* 3.2 12.9 + - - +
26l GLU* 3.1 21.9 + - - -
67l LYS* 3.3 13.7 - - - -
68l ILE* 4.3 1.3 - - - +
69l ARG* 3.5 12.4 - - - +
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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