Contacts of the strand formed by residues 36 - 41 (chain X) in PDB entry 3FKS
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 ALA 36 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35X ASN* 1.3 75.0 - - - +
37X LEU* 1.3 65.6 + - - +
38X GLU* 6.0 0.9 - - + -
47X VAL* 6.0 2.7 - - + -
48X LEU 3.2 11.0 - - - +
78X ASP* 3.1 22.0 - - - +
79X THR* 3.3 25.7 + - + +
81X GLY 2.8 18.1 + - - +
82X PRO 4.2 2.7 - - - +
83X ILE* 3.8 25.1 - - + -
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Residues in contact with LEU 37 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23X VAL* 4.5 9.9 - - + -
25X PHE* 4.4 14.8 - - + -
31X PRO* 4.5 3.4 - - + -
36X ALA* 1.3 74.3 - - - +
38X GLU* 1.3 70.6 + - - +
47X VAL* 3.2 2.4 - - - +
48X LEU* 2.7 49.4 + - + +
50X VAL* 3.8 14.6 - - + -
59X VAL* 4.9 1.3 - - + -
61X THR* 3.8 27.8 - - + -
76X VAL* 4.0 24.9 - - + -
77X LEU 3.5 5.8 - - - +
78X ASP* 3.1 39.3 - - + +
79X THR* 4.4 0.9 - - - -
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Residues in contact with GLU 38 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36X ALA* 6.0 0.2 - - + -
37X LEU* 1.3 82.8 - - - +
39X ILE* 1.3 69.5 + - - +
40X LYS* 5.9 0.5 - - - +
45X LYS* 3.3 45.3 + - + +
46X LEU 3.6 5.6 - - - +
47X VAL* 3.7 16.7 - - + +
75X LYS 4.3 0.3 - - - +
76X VAL* 4.0 0.2 - - - -
77X LEU* 2.9 50.3 + - + +
79X THR* 4.3 15.3 + - - +
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Residues in contact with ILE 39 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13X VAL* 4.6 10.1 - - + -
21X VAL* 6.2 0.4 - - + -
38X GLU* 1.3 83.9 - - - +
40X LYS* 1.3 69.8 + - - +
41X THR* 3.2 9.4 + - - +
45X LYS* 3.5 6.9 - - - +
46X LEU* 3.1 45.7 + - + +
48X LEU* 4.3 16.8 - - + -
70X LEU* 4.8 14.8 - - + -
74X GLU* 4.2 22.0 - - + +
75X LYS 3.3 22.9 - - - +
76X VAL* 3.6 25.8 - - + -
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Residues in contact with LYS 40 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38X GLU 5.9 0.2 - - - +
39X ILE* 1.3 79.5 - - - +
41X THR* 1.3 60.2 + - - +
42X PRO* 4.4 3.0 - - - +
44X GLY 4.7 2.2 - - - -
45X LYS* 5.9 0.4 - - - -
74X GLU* 4.8 8.0 - - - +
75X LYS* 4.6 34.8 + - + +
77X LEU* 5.5 18.4 - - + -
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Residues in contact with THR 41 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39X ILE* 3.2 3.3 + - - +
40X LYS* 1.3 74.1 - - - +
42X PRO* 1.3 70.6 - - - +
43X GLN* 3.0 22.9 + - + +
44X GLY 2.8 55.1 + - - +
45X LYS 3.5 5.2 - - - +
46X LEU* 3.5 26.2 - - + +
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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
------------------------------------------------------------
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