Contacts of the strand formed by residues 17 - 22 (chain Y) 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 SER 17 (chain Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13Y SER* 5.3 4.4 + - - -
15Y CYS 3.9 2.9 + - - -
16Y ASP* 1.3 77.2 - - - +
18Y VAL* 1.3 71.9 + - - +
19Y SER* 5.3 0.3 + - - -
56Y THR* 3.7 18.0 - - - +
57Y LYS 3.2 15.0 - - - -
59Y ARG* 4.4 4.7 - - - +
108Y CYS* 4.1 13.5 - - - -
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Residues in contact with VAL 18 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17Y SER* 1.3 81.9 - - - +
19Y SER* 1.3 64.3 + - - +
20Y VAL* 4.1 8.0 + - + -
55Y GLU 3.6 1.0 - - - +
56Y THR* 3.2 21.2 - - - -
57Y LYS* 3.1 32.2 + - + +
58Y CYS 4.8 5.8 - - - +
59Y ARG* 3.8 32.1 - - + +
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Residues in contact with SER 19 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A ILE* 3.8 18.4 - - - +
190A THR* 4.4 0.9 - - - -
191A CYS* 3.4 29.6 + - - +
17Y SER* 5.3 0.7 + - - -
18Y VAL* 1.3 73.4 - - - +
20Y VAL* 1.3 66.9 + - - +
54Y PHE* 3.7 22.2 - - - -
55Y GLU 3.3 3.6 - - - -
56Y THR* 2.9 27.6 + - - +
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Residues in contact with VAL 20 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A SER* 4.2 11.7 - - - +
189A TYR 3.4 13.9 - - - +
190A THR* 4.6 14.8 - - + +
191A CYS* 4.7 1.1 - - - +
18Y VAL* 5.0 9.2 - - + -
19Y SER* 1.3 80.6 - - - +
21Y TRP* 1.3 63.8 + - - +
22Y VAL* 3.9 20.4 - - + -
53Y PHE 3.6 0.2 - - - +
54Y PHE* 3.6 5.9 - - - -
55Y GLU* 2.9 34.3 + - + +
57Y LYS* 3.9 26.5 - - - +
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Residues in contact with TRP 21 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A SER* 3.2 6.4 - - - -
189A TYR* 2.8 46.9 + - + +
190A THR 4.2 17.0 - - - -
191A CYS* 4.5 4.3 - - + -
220A CYS* 3.6 19.6 - - - +
221A GLY 3.8 18.6 + - - -
222A PRO* 3.8 29.4 - - - +
31B ILE* 3.9 16.2 - - + -
86B PHE* 3.9 18.2 - + + -
101B PHE* 3.6 35.4 - + - -
20Y VAL* 1.3 74.3 - - - +
22Y VAL* 1.3 62.1 + - - +
52Y TYR* 4.3 15.7 - - + -
53Y PHE 3.6 5.2 - - - -
54Y PHE* 3.6 45.5 - + + -
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Residues in contact with VAL 22 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A SER* 4.2 6.1 - - - -
20Y VAL* 3.9 18.8 - - + -
21Y TRP* 1.3 75.9 - - - +
23Y GLY* 1.3 56.9 + - - +
24Y ASP* 3.4 24.7 - - - +
25Y LYS* 4.1 19.5 - - + +
51Y GLN 3.8 1.7 - - - +
52Y TYR* 3.3 8.9 - - - -
53Y PHE* 2.9 40.5 + - + +
55Y GLU* 3.5 33.9 - - + +
57Y LYS* 4.8 3.1 - - - +
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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