Contacts of the strand formed by residues 30 - 35 (chain Z) in PDB entry 1SGF
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 HIS 30 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27Z GLN* 3.3 24.7 + - + +
28Z PRO 3.0 7.6 - - - +
29Z TRP* 1.3 82.3 - - + +
31Z VAL* 1.3 74.1 + - - +
43Z GLY* 4.5 5.2 - - - -
44Z GLY 3.5 4.7 + - - -
67Z TRP 4.5 0.7 - - - +
68Z LEU* 5.3 0.2 - - - +
69Z GLY* 4.2 14.0 + - - -
70Z LYS 5.0 3.8 + - - +
139Z SER* 3.0 47.6 + - - -
140Z GLY* 3.6 8.8 - - - -
141Z TRP* 3.2 38.3 - + + -
155Z LEU* 3.4 18.0 - - + +
194Z ASP 5.7 0.2 - - - -
197Z GLY* 4.3 6.5 - - - -
198Z PRO* 3.6 18.6 - - + +
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Residues in contact with VAL 31 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29Z TRP 3.8 10.5 - - - +
30Z HIS* 1.3 86.6 - - - +
32Z ALA* 1.3 70.3 + - - +
33Z VAL* 4.2 8.7 - - + -
43Z GLY* 3.2 5.9 - - - -
44Z GLY 2.7 38.3 + - - +
46Z LEU* 4.1 7.6 - - + +
52Z VAL* 4.0 24.0 - - + -
66Z VAL* 3.2 27.4 - - + -
67Z TRP 4.0 4.0 - - - +
68Z LEU* 3.5 28.0 - - + -
141Z TRP* 4.3 0.4 - - - -
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Residues in contact with ALA 32 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31Z VAL* 1.3 75.1 - - - +
33Z VAL* 1.3 61.4 + - - +
34Z TYR* 3.6 24.8 - - + -
40Z TYR* 4.2 5.4 - - + -
42Z CYS 3.8 4.5 - - - -
66Z VAL* 3.6 3.5 - - - -
67Z TRP* 3.1 36.1 + - + +
70Z LYS* 5.9 0.4 - - + -
73Z LEU* 4.4 5.2 - - + -
141Z TRP* 3.6 28.7 - - + -
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Residues in contact with VAL 33 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31Z VAL* 4.2 13.0 - - + -
32Z ALA* 1.3 72.8 - - - +
34Z TYR* 1.3 64.5 + - - +
40Z TYR* 4.2 1.0 - - - -
41Z LEU* 2.9 30.6 + - + +
42Z CYS* 2.8 29.0 + - + +
43Z GLY 3.8 19.7 - - - +
44Z GLY* 4.6 1.1 - - - +
52Z VAL* 5.1 1.6 - - + -
54Z THR* 4.1 16.2 - - + +
58Z CYS* 5.8 1.3 - - + -
64Z TYR* 3.9 27.8 - - + -
65Z LYS 3.6 9.6 - - - +
66Z VAL* 4.9 1.6 - - + -
106Z LEU* 4.0 16.8 - - + -
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Residues in contact with TYR 34 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38G THR* 4.4 7.8 + - - +
74G PHE* 3.5 28.5 - + + -
32Z ALA* 3.6 28.9 - - + -
33Z VAL* 1.3 79.9 - - - +
35Z ARG* 1.3 60.0 + - - +
36Z TYR 4.3 2.9 - - - +
38Z THR 3.8 11.7 - - - -
39Z GLN 3.4 21.3 - - - -
40Z TYR* 3.6 23.4 - + + -
41Z LEU* 4.3 3.1 - - - +
63Z ASN 3.5 0.7 - - - +
64Z TYR* 3.2 8.1 - - - -
65Z LYS* 2.8 46.0 + - + -
67Z TRP* 3.5 30.7 - + + -
73Z LEU* 3.4 30.3 - - - +
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Residues in contact with ARG 35 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148G LYS* 5.8 3.2 - - - +
149G PHE* 3.5 28.5 + - - +
151G PHE* 5.4 6.1 - - - -
74Y LYS* 6.1 1.8 - - - +
34Z TYR* 1.3 73.3 - - - +
36Z TYR* 1.3 79.1 + - + +
38Z THR 2.9 9.9 + - - -
39Z GLN* 2.9 29.7 + - + +
41Z LEU* 4.1 16.6 - - + -
60Z ASP* 3.2 31.7 + - + +
61Z ASP* 2.7 38.3 + - - -
63Z ASN 3.4 20.9 - - - +
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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