Contacts of the strand formed by residues 80 - 87 (chain U) 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 TRP 80 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1339A G 5.8 1.1 - - - -
15U HIS* 4.2 22.4 - + - -
33U LYS* 3.5 46.0 - - + -
34U VAL 5.2 3.4 - - - +
36U LYS* 4.2 13.1 - - + +
62U VAL* 3.3 8.2 - - - +
63U VAL* 2.8 70.1 + - + +
65U GLY* 5.6 2.2 - - - -
78U SER 3.9 9.2 - - - -
79U ASP* 1.3 81.2 - - - +
81U LYS* 1.3 79.3 + - - +
82U LYS* 3.8 32.3 - - + -
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Residues in contact with LYS 81 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1599A U 4.4 1.6 + - - -
1600A C 2.4 36.2 + - - -
32U LEU 3.6 0.2 - - - +
33U LYS* 3.7 2.8 - - - -
34U VAL* 2.9 53.9 + - + +
35U ALA 4.4 0.7 - - - +
36U LYS* 3.0 34.6 + - + +
37U ASP* 4.1 4.2 + - - +
38U ALA 3.1 27.3 + - - +
43U ILE* 5.2 0.2 - - + -
60U THR* 4.2 17.9 + - + +
61U LEU 3.2 17.3 - - - +
62U VAL* 3.8 15.0 - - + +
80U TRP* 1.3 80.6 - - - +
82U LYS* 1.3 62.9 - - - +
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Residues in contact with LYS 82 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1339A G 3.2 35.4 + - - -
1340A U 3.2 26.8 + - - +
15U HIS* 3.5 21.4 + - - -
31U VAL* 4.0 15.4 - - + +
32U LEU 3.4 5.2 - - - +
60U THR* 3.5 3.3 - - - -
61U LEU* 2.9 55.9 + - + +
62U VAL* 4.7 0.2 - - - +
63U VAL* 4.3 11.2 - - + +
80U TRP* 3.8 22.0 + - + -
81U LYS* 1.3 74.5 - - - +
83U ALA* 1.3 66.0 + - - +
84U TYR* 3.8 15.6 + - + +
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Residues in contact with ALA 83 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30U ILE 3.6 1.2 - - - +
31U VAL* 3.5 2.9 - - - -
32U LEU* 2.9 37.2 + - + +
34U VAL* 4.2 8.5 - - + -
43U ILE* 4.2 16.6 - - + -
58U VAL* 4.2 7.0 - - + -
59U ASN 3.5 5.2 - - - +
60U THR* 3.8 21.8 - - + -
82U LYS* 1.3 77.5 - - - +
84U TYR* 1.3 63.9 + - - +
85U VAL* 3.6 9.1 + - + +
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Residues in contact with TYR 84 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1339A G 4.9 0.2 + - - -
1340A U 2.6 29.8 + - - -
1341A G 3.2 65.3 - + + +
19U LYS* 3.4 26.8 - - + +
23U ALA* 5.3 5.6 - - + -
29U THR* 3.9 15.0 - - + -
30U ILE 3.6 2.5 - - - -
31U VAL* 3.5 38.4 - - + -
57U VAL 4.2 0.2 - - - +
58U VAL* 3.6 2.6 - - - +
59U ASN* 2.9 37.5 + - + +
61U LEU* 3.9 14.1 - - + -
82U LYS* 3.8 10.7 + - + +
83U ALA* 1.3 70.7 - - - +
85U VAL* 1.3 60.4 + - - +
86U THR* 4.0 3.0 + - - -
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Residues in contact with VAL 85 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29U THR* 3.2 6.4 - - - +
30U ILE* 2.9 44.6 + - + +
32U LEU* 4.7 14.1 - - + -
43U ILE* 4.2 16.4 - - + -
47U VAL* 4.5 10.8 - - + -
55U VAL* 3.8 25.8 - - + -
57U VAL 4.0 2.2 - - - -
58U VAL* 3.6 29.4 - - + -
83U ALA* 4.0 11.2 - - + +
84U TYR* 1.3 74.4 - - - +
86U THR* 1.3 62.8 + - - +
87U LEU* 3.7 12.4 + - + +
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Residues in contact with THR 86 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1341A G 4.5 11.8 + - - -
1399A C 4.7 13.2 + - - +
27U SER* 4.6 7.2 - - - +
28U ASN 4.5 1.6 - - - +
29U THR* 3.9 17.9 + - - +
55U VAL* 3.4 7.1 - - - +
56U GLU* 2.7 52.5 + - + +
57U VAL* 2.9 31.7 + - + +
59U ASN* 5.8 1.4 + - - -
84U TYR 4.8 1.7 + - - -
85U VAL* 1.3 71.4 - - - +
87U LEU* 1.3 66.4 + - - +
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Residues in contact with LEU 87 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27U SER 5.1 0.2 - - - +
28U ASN* 3.2 32.2 + - - +
30U ILE* 3.7 14.8 - - + -
47U VAL* 4.6 2.5 - - + -
53U VAL* 4.0 28.3 - - + -
54U GLU 3.6 11.4 - - - +
55U VAL* 4.3 11.4 - - + -
56U GLU* 4.5 1.7 - - - +
85U VAL* 4.2 13.9 - - + +
86U THR* 1.3 86.4 - - - +
88U LYS* 1.3 69.9 + - - +
89U GLU* 3.6 1.0 + - - -
91U GLN* 4.2 13.2 - - + +
93U LEU* 3.5 39.9 - - + -
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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