Contacts of the strand formed by residues 25 - 29 (chain A) in PDB entry 5FQU
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 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A ARG* 4.9 8.1 - - - +
23A PRO* 3.1 28.7 - - + +
24A LYS* 1.3 75.0 - - - +
26A GLY* 1.3 66.3 + - - +
51A ILE* 4.9 4.3 - - + -
52A GLN* 3.4 28.7 - - + +
53A ILE* 3.8 8.2 - - + -
54A ASP* 2.9 37.1 + - - +
55A ALA 3.5 2.4 + - - -
224A VAL* 4.2 2.0 - - - -
226A VAL* 3.6 13.0 - - + +
228A ILE* 3.9 33.2 - - + -
311A LEU* 4.4 33.4 - - + -
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Residues in contact with GLY 26 (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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25A ILE* 1.3 76.3 - - - +
27A LEU* 1.3 60.5 + - - -
28A VAL* 4.8 0.9 - - - -
55A ALA* 3.2 9.9 - - - -
219A ALA* 5.1 3.1 - - - -
224A VAL* 3.8 22.2 - - - +
226A VAL 2.9 12.7 + - - -
227A VAL* 3.2 10.8 - - - +
228A ILE 2.9 24.9 + - - -
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Residues in contact with LEU 27 (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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25A ILE 4.2 0.6 + - - -
26A GLY* 1.3 71.7 - - - -
28A VAL* 1.3 60.8 + - - +
29A LEU* 3.6 33.0 - - + -
42A VAL* 5.1 0.7 - - + -
43A LEU* 3.6 32.1 - - + -
46A LEU* 4.1 17.0 - - + -
53A ILE* 3.9 23.3 - - + -
55A ALA 2.7 9.6 + - - +
56A ILE* 3.3 16.8 - - + +
57A ALA 3.0 25.1 + - - +
219A ALA* 5.1 0.6 - - - +
228A ILE* 3.4 34.8 - - + +
230A VAL* 4.1 6.5 - - + -
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Residues in contact with VAL 28 (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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27A LEU* 1.3 77.4 - - - +
29A LEU* 1.3 69.1 + - - +
30A SER 4.0 0.4 + - - -
57A ALA 3.3 4.7 - - - +
214A ILE* 4.0 11.7 - - + -
215A PRO* 3.5 45.3 - - + +
216A VAL* 4.0 7.2 - - - +
219A ALA* 3.8 25.6 - - + -
227A VAL* 4.3 9.9 - - + -
228A ILE 2.8 14.0 + - - +
229A VAL* 4.1 19.1 - - + -
230A VAL* 3.0 24.6 + - - +
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Residues in contact with LEU 29 (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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27A LEU* 3.6 33.4 - - + +
28A VAL* 1.3 84.9 - - - +
30A SER* 1.3 66.3 + - - +
39A HIS* 3.5 36.6 - - + +
42A VAL* 5.7 1.3 - - + -
43A LEU* 5.2 4.0 - - + -
56A ILE* 4.7 2.5 - - + -
57A ALA 2.9 12.8 + - - +
58A GLY* 3.4 2.1 - - - -
59A THR 3.3 20.8 + - - -
62A GLY* 3.4 30.6 - - - +
65A VAL* 4.5 3.4 - - + -
66A GLY* 3.6 22.4 - - - +
215A PRO* 4.5 1.3 - - - +
230A VAL* 3.7 11.9 - - + -
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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