Contacts of the strand formed by residues 36 - 40 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34N LEU 3.8 0.2 + - - -
35N ASN* 1.3 72.3 - - - +
37N LEU* 1.3 62.5 + - - +
38N GLU* 5.9 0.4 - - - +
47N VAL* 4.6 7.6 - - + -
48N LEU 3.3 7.4 - - - +
49N GLU* 4.6 0.7 - - - +
78N ASP* 3.6 2.6 - - - +
79N THR* 2.7 46.7 + - + +
81N GLY 2.9 8.9 + - - -
82N PRO 3.9 1.1 - - - +
83N ILE* 3.7 39.9 - - + +
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Residues in contact with LEU 37 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23N VAL* 3.8 32.5 - - + -
25N PHE* 4.0 8.7 - - + -
31N PRO* 3.9 13.5 - - + -
36N ALA* 1.3 72.2 - - - +
38N GLU* 1.3 72.9 + - - +
39N ILE* 5.0 0.2 - - - -
47N VAL* 3.4 4.0 - - - +
48N LEU* 2.7 39.2 + - + +
50N VAL* 4.2 12.3 - - + -
59N VAL* 4.6 4.0 - - + -
61N THR* 3.9 21.1 - - + -
76N VAL* 3.5 13.0 - - + -
77N LEU 3.4 4.5 - - - +
78N ASP* 3.4 37.7 - - + +
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Residues in contact with GLU 38 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36N ALA* 5.8 0.6 - - + +
37N LEU* 1.3 82.2 - - - +
39N ILE* 1.3 66.0 + - - +
40N LYS 4.3 0.4 - - - -
45N LYS* 4.0 35.9 + - + +
46N LEU 3.3 5.8 - - - +
47N VAL* 4.2 16.0 - - + +
75N LYS 4.0 0.3 - - - +
76N VAL* 3.5 4.0 - - - +
77N LEU* 2.8 59.7 + - + +
79N THR* 3.5 25.1 - - + +
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Residues in contact with ILE 39 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13N VAL* 5.4 2.2 - - + -
21N VAL* 6.0 0.2 - - + -
38N GLU* 1.3 82.4 - - - +
40N LYS* 1.3 70.2 + - + +
41N THR* 3.1 9.4 + - + +
45N LYS* 3.4 4.7 - - - -
46N LEU* 2.8 66.5 + - + +
48N LEU* 3.7 34.1 - - + -
70N LEU* 4.7 9.2 - - + -
74N GLU* 4.1 26.0 - - + +
75N LYS 3.6 13.5 - - - +
76N VAL* 3.8 22.2 - - + -
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Residues in contact with LYS 40 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38N GLU 4.3 0.4 - - - -
39N ILE* 1.3 76.5 - - + +
41N THR* 1.3 62.3 + - - +
42N PRO* 4.5 1.2 - - - +
44N GLY 4.2 5.6 - - - +
45N LYS* 4.7 3.1 - - - +
75N LYS* 3.6 49.3 + - + +
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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