Contacts of the strand formed by residues 40 - 45 (chain D) in PDB entry 1FSK
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 SER 40 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31D PRO* 4.0 8.1 - - - -
38D ILE* 3.7 1.0 - - - -
39D SER* 1.3 86.5 + - - +
41D VAL* 1.3 65.4 + - - +
42D GLU* 5.7 0.7 + - - -
55D LYS 3.8 1.3 - - - +
56D ILE* 3.7 0.5 - - - -
57D SER* 2.7 49.3 + - - +
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Residues in contact with VAL 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D ASP* 3.2 46.6 - - + +
30D PHE* 5.5 0.2 - - + -
31D PRO* 4.4 5.7 - - + +
38D ILE* 3.8 23.8 - - + -
40D SER* 1.3 81.1 - - - +
42D GLU* 1.3 66.7 + - - +
43D ASN* 5.2 1.3 - - - +
54D LYS* 4.1 18.8 - - + -
55D LYS 3.5 2.9 - - - -
56D ILE* 4.0 28.0 - - + -
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Residues in contact with GLU 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D SER* 5.7 0.3 + - - -
41D VAL* 1.3 77.7 - - - +
43D ASN* 1.3 64.0 + - - +
44D ILE* 3.2 16.1 + - + +
54D LYS* 3.2 2.8 - - - -
55D LYS* 2.8 69.7 + - + +
57D SER* 5.5 1.8 + - - +
101F ARG* 3.7 39.8 + - - +
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Residues in contact with ASN 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D VAL* 5.2 1.6 - - - +
42D GLU* 1.3 72.7 - - - +
44D ILE* 1.3 64.6 + - - +
45D GLU 3.1 3.3 + - - -
46D GLY 3.6 12.8 + - - +
47D ASN* 3.5 4.9 - - - +
48D GLY* 3.1 36.6 - - - +
52D THR* 3.6 9.2 - - + -
53D ILE 3.6 5.4 - - - -
54D LYS* 3.8 20.7 + - - +
101F ARG* 3.5 13.0 - - - +
102F ASP* 3.2 32.0 + - - +
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Residues in contact with ILE 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D GLU* 3.2 15.7 + - - +
43D ASN* 1.3 70.3 - - - +
45D GLU* 1.3 58.2 + - - +
53D ILE* 2.8 28.5 + - + +
55D LYS* 3.4 49.1 - - + +
68D LYS* 4.7 17.0 - - + +
31F SER* 5.4 3.8 - - - +
32F TYR* 3.7 33.1 + - + +
101F ARG* 3.4 20.7 + - - +
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Residues in contact with GLU 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D ASN 3.1 0.8 + - - -
44D ILE* 1.3 80.6 - - + +
46D GLY* 1.3 67.2 + - - +
52D THR* 3.5 4.0 - - - +
53D ILE* 2.9 36.8 + - + +
31F SER 4.3 0.9 - - - +
32F TYR* 3.0 30.3 - - + -
33F TRP* 2.6 44.6 + - + +
35F ASN* 4.9 0.5 + - - -
52F PHE* 4.7 0.5 - - - -
99F GLY 3.0 24.9 + - - -
100F ALA 3.8 9.9 - - - +
103F THR 4.4 2.2 - - - +
104F TRP* 3.2 27.5 - - + -
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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