Contacts of the strand formed by residues 33 - 40 (chain Y) in PDB entry 5GAG
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 LEU 33 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2229A U 4.9 8.7 + - - -
2230A G 4.9 1.2 + - - -
3Y ARG* 3.7 34.5 - - + -
4Y VAL 3.7 14.6 - - - +
5Y CYS* 3.7 24.2 - - + +
31Y PRO* 3.2 21.0 + - + +
32Y ASN* 1.3 74.1 + - - +
34Y HIS* 1.3 79.2 + - - +
50Y ARG* 3.9 28.0 - - + +
51Y VAL 3.5 4.0 - - - -
52Y SER* 3.6 24.7 - - - +
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Residues in contact with HIS 34 (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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2090A A 4.3 0.6 - + - -
2091A C 3.1 51.3 + + - +
2228A G 3.6 11.6 + - - -
2229A U 3.2 25.4 - + - -
32Y ASN* 2.9 34.6 + - - -
33Y LEU* 1.3 93.1 + - - +
35Y SER* 1.3 71.9 + - - +
36Y HIS 3.5 0.9 + - - -
50Y ARG* 3.4 4.8 - - - -
51Y VAL* 2.9 39.1 + - - +
53Y ALA* 5.1 4.9 - - + -
56Y MET* 5.1 4.5 - - + -
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Residues in contact with SER 35 (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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2200A C 4.1 18.0 + - - +
2201A G 4.8 13.6 + - - -
34Y HIS* 1.3 82.3 - - - +
36Y HIS* 1.3 63.3 + - - +
48Y THR* 4.7 10.8 - - - -
49Y LEU 3.2 10.1 - - - -
50Y ARG* 4.3 12.4 - - - +
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Residues in contact with HIS 36 (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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2091A C 5.2 0.4 - - - -
2092A U 3.8 9.0 + - - -
2199A A 3.5 23.8 + - - -
2200A C 3.3 7.9 - - - -
27H ARG* 4.3 8.9 - - + -
28H ASN* 3.3 24.9 + - - -
34Y HIS 4.4 3.1 - - - +
35Y SER* 1.3 78.8 - - - +
37Y ARG* 1.3 94.5 + - - +
38Y PHE* 3.4 40.0 - + + -
47Y VAL 3.6 1.2 - - - +
48Y THR* 3.3 4.3 - - - +
49Y LEU 2.9 30.8 + - - -
51Y VAL* 4.4 1.8 - - + -
56Y MET* 3.5 25.8 - - + -
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Residues in contact with ARG 37 (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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2199A A 3.5 32.5 + - - +
2200A C 3.0 30.7 + - - +
2217A G 6.0 1.1 - - - -
2218A G 4.8 8.7 + - - -
36Y HIS* 1.3 93.5 + - - +
38Y PHE* 1.3 61.4 + - - +
46Y PHE* 3.1 61.7 - - + +
47Y VAL 3.4 4.0 - - - +
48Y THR* 3.6 25.1 - - + +
101Y MG 4.5 3.8 - - - -
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Residues in contact with PHE 38 (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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27H ARG* 4.7 9.9 - - + -
36Y HIS* 3.4 46.9 - + + -
37Y ARG* 1.3 74.3 - - - +
39Y TRP* 1.3 61.8 + - - +
40Y VAL* 3.5 2.6 + - + +
45Y ARG 3.4 0.5 - - - +
46Y PHE* 3.1 8.2 - - - -
47Y VAL* 2.9 37.9 + - + +
49Y LEU* 4.3 23.1 - - + -
51Y VAL* 4.1 4.3 - - + -
56Y MET* 3.7 26.2 - - + -
59Y ILE* 3.4 37.5 - - + -
60Y ASP* 5.5 0.2 - - - -
64Y ILE* 4.0 28.9 - - + -
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Residues in contact with TRP 39 (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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31H VAL* 4.2 16.0 + - + +
32H PRO* 3.5 47.8 + - + +
37Y ARG 4.2 0.2 + - - -
38Y PHE* 1.3 72.3 - - - +
40Y VAL* 1.3 65.8 + - - +
41Y GLU* 3.5 24.3 + - + +
44Y LYS* 3.1 42.0 - - + -
45Y ARG* 3.0 48.9 - - - -
46Y PHE* 3.7 36.8 - + + -
64Y ILE* 4.4 8.2 - - - +
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Residues in contact with VAL 40 (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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38Y PHE* 4.4 2.5 - - + +
39Y TRP* 1.3 75.0 - - - +
41Y GLU* 1.3 61.7 + - - +
42Y SER* 3.8 3.1 - - - +
43Y GLU* 3.8 35.4 - - + +
44Y LYS* 3.0 6.8 + - - -
45Y ARG 2.8 34.5 + - - +
47Y VAL* 3.6 31.6 - - + -
64Y ILE* 4.1 24.9 - - + -
65Y ASP* 3.5 21.8 - - - +
68Y LEU* 4.5 8.7 - - + -
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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