Contacts of the strand formed by residues 39 - 48 (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 GLN 39 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39G GLN* 4.1 14.1 - - + +
40G TYR* 3.5 43.5 + - - +
151G PHE* 4.1 27.3 - - - -
34Z TYR* 3.4 4.0 - - - -
35Z ARG* 2.9 44.6 + - + +
38Z THR* 1.3 80.1 - - - +
40Z TYR* 1.3 66.0 + - - +
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Residues in contact with TYR 40 (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* 3.7 33.7 + - + +
39G GLN* 4.3 19.3 + - + +
32Z ALA* 4.2 14.8 - - + -
33Z VAL 4.6 1.1 - - - -
34Z TYR* 3.6 31.1 - + + -
39Z GLN* 1.3 78.7 - - - +
41Z LEU* 1.3 64.2 + - - +
42Z CYS* 3.6 32.6 + - - -
43Z GLY* 3.8 3.8 + - - -
73Z LEU* 4.5 1.6 - - + -
140Z GLY* 5.2 0.5 - - - -
141Z TRP* 3.8 36.3 + + + +
151Z PHE* 4.2 26.2 - + - -
193Z GLY* 3.0 28.3 + - - -
194Z ASP* 5.1 0.2 - - - -
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Residues in contact with LEU 41 (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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74Y LYS* 4.8 14.8 - - + +
33Z VAL* 2.9 23.4 + - + +
34Z TYR 4.3 5.2 - - - +
35Z ARG* 4.1 18.4 - - + +
39Z GLN 4.4 0.9 - - - +
40Z TYR* 1.3 83.0 - - - +
42Z CYS* 1.3 75.5 + - - +
58Z CYS* 3.3 34.3 - - + +
60Z ASP* 3.6 26.9 - - + +
64Z TYR* 4.0 22.7 - - + -
193Z GLY* 5.4 3.6 - - - -
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Residues in contact with CYS 42 (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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118Y ARG* 5.0 6.3 - - - -
32Z ALA* 3.7 0.5 - - - -
33Z VAL* 2.8 30.2 + - + +
40Z TYR* 3.6 21.3 + - - -
41Z LEU* 1.3 95.3 - - - +
43Z GLY* 1.3 65.1 + - - +
54Z THR* 4.0 2.2 - - - +
57Z HIS* 5.0 1.3 - - - -
58Z CYS* 2.0 55.0 - - + -
193Z GLY 4.7 3.8 - - - -
195Z SER* 3.3 17.3 - - - +
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Residues in contact with GLY 43 (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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30Z HIS* 4.5 8.7 - - - -
31Z VAL 3.2 11.7 - - - -
33Z VAL* 3.8 4.3 - - - +
40Z TYR* 3.8 8.9 + - - -
42Z CYS* 1.3 75.2 - - - +
44Z GLY* 1.3 57.4 + - - -
54Z THR* 2.8 23.4 + - - -
141Z TRP* 5.8 0.2 - - - -
193Z GLY 4.7 0.6 + - - -
194Z ASP 4.7 3.0 + - - -
195Z SER 2.7 13.0 + - - -
196Z GLY* 3.2 12.4 - - - -
197Z GLY* 4.4 3.4 - - - -
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Residues in contact with GLY 44 (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 3.2 1.7 - - - +
30Z HIS* 3.5 7.7 + - - -
31Z VAL* 2.7 44.4 + - - -
33Z VAL* 4.8 2.0 - - - -
43Z GLY* 1.3 74.6 - - - -
45Z VAL* 1.3 62.4 + - - +
52Z VAL* 4.9 0.7 - - - -
53Z LEU 3.3 10.3 - - - -
54Z THR* 4.4 2.0 - - - -
196Z GLY 3.0 13.7 + - - -
197Z GLY* 4.1 3.3 - - - +
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Residues in contact with VAL 45 (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* 3.0 9.2 - - + +
31Z VAL* 4.3 0.9 - - - -
44Z GLY* 1.3 73.9 - - - -
46Z LEU* 1.3 58.8 + - - +
47Z LEU* 3.8 17.5 - - + -
52Z VAL* 3.5 5.1 - - - +
53Z LEU* 2.8 60.3 + - + +
121Z ILE* 4.3 10.5 - - + -
196Z GLY 4.3 3.6 - - - +
198Z PRO* 3.4 44.4 - - + -
209Z LEU* 4.3 15.0 - - + -
212Z ILE* 4.7 4.7 - - + -
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Residues in contact with LEU 46 (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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28Z PRO 4.7 2.9 - - - +
29Z TRP* 2.8 21.2 + - - +
31Z VAL* 4.1 7.6 - - + +
45Z VAL* 1.3 71.9 - - - +
47Z LEU* 1.3 61.0 + - - +
48Z ASP 3.4 24.2 - - - +
51Z TRP 3.6 7.0 - - - +
52Z VAL* 3.8 12.1 - - + +
68Z LEU* 3.8 22.0 - - + -
108Z LEU* 4.5 8.3 - - + -
112Z ALA* 4.5 8.7 - - + -
114Z ILE* 4.6 6.1 - - + -
118Z VAL* 3.5 31.6 - - + -
119Z LYS 4.4 14.8 - - - +
120Z PRO* 3.2 6.5 - - + +
121Z ILE* 3.0 27.0 + - - +
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Residues in contact with LEU 47 (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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45Z VAL* 3.8 20.6 - - + -
46Z LEU* 1.3 73.5 - - - +
48Z ASP* 1.3 63.3 + - + +
51Z TRP* 3.0 13.9 + - + +
53Z LEU* 3.8 33.2 - - + +
105Z LEU* 4.0 18.2 - - + -
120Z PRO* 3.3 18.2 - - - +
121Z ILE* 4.1 17.5 - - + +
123Z LEU* 3.8 24.2 - - + -
209Z LEU* 4.5 6.3 - - + -
238Z ILE* 4.1 17.7 - - + -
242Z MET* 4.2 11.1 - - + +
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Residues in contact with ASP 48 (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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46Z LEU* 3.4 11.2 - - - +
47Z LEU* 1.3 79.5 - - - +
49Z PRO* 1.3 82.2 - - - +
50Z ASN* 3.8 11.6 + - - +
51Z TRP* 2.9 43.0 + - + +
120Z PRO* 4.7 2.2 - - - -
242Z MET* 3.6 25.7 - - + +
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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