Contacts of the strand formed by residues 55 - 63 (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 VAL 55 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44U LYS* 3.8 31.1 + - + +
47U VAL* 3.8 27.1 - - + -
48U GLN* 3.3 35.3 + - + +
53U VAL 4.7 0.4 - - - +
54U GLU* 1.3 74.5 - - - +
56U GLU* 1.3 66.5 + - - +
57U VAL 3.6 13.9 - - - +
58U VAL* 4.0 5.8 - - + -
85U VAL* 3.8 19.1 - - + -
86U THR 3.4 11.7 - - - +
87U LEU* 4.3 3.6 - - + +
88U LYS* 3.4 14.9 + - - -
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Residues in contact with GLU 56 (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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1399A C 4.9 6.2 + - - -
44U LYS* 4.1 13.2 + - - -
55U VAL* 1.3 77.6 - - - +
57U VAL* 1.3 75.8 + - + +
86U THR* 2.7 31.9 + - + +
87U LEU 4.7 0.9 - - - +
88U LYS* 3.9 33.7 - - + +
89U GLU 5.3 0.3 + - - -
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Residues in contact with VAL 57 (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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1343A G 5.5 4.7 - - - +
1399A C 5.7 2.7 - - - +
3119A MG 4.2 16.6 - - - -
40U LYS* 5.9 0.7 - - - +
44U LYS* 5.4 2.9 - - - +
55U VAL* 3.6 2.9 - - - +
56U GLU* 1.3 101.3 - - + +
58U VAL* 1.3 68.6 + - - +
59U ASN* 3.8 19.2 + - - +
84U TYR 4.2 0.3 - - - +
86U THR* 2.9 41.6 + - + +
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Residues in contact with VAL 58 (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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40U LYS* 3.2 36.5 + - + +
43U ILE* 4.2 18.4 - - + -
44U LYS* 4.4 13.4 - - + +
55U VAL* 4.0 8.3 - - + -
57U VAL* 1.3 82.8 - - - +
59U ASN* 1.3 66.7 + - - +
60U THR* 3.7 23.6 - - + -
83U ALA* 4.2 10.1 - - + -
84U TYR 3.6 7.4 - - - +
85U VAL* 3.6 31.2 - - + -
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Residues in contact with ASN 59 (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 2.6 52.1 + - + +
1342A A 3.5 16.6 - - - +
1343A G 5.1 1.0 + - - -
1398A C 2.9 31.7 + - - -
3119A MG 4.1 3.2 - - - -
40U LYS* 4.1 1.9 + - - -
57U VAL* 3.8 16.3 - - - +
58U VAL* 1.3 80.3 - - - +
60U THR* 1.3 60.8 + - - +
82U LYS 4.4 0.2 - - - +
83U ALA* 3.5 1.4 - - - -
84U TYR* 2.9 39.2 + - + +
86U THR* 5.8 1.3 + - - -
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Residues in contact with THR 60 (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 3.8 2.9 - - - +
1342A A 3.1 26.5 + - - -
1599A U 4.7 1.7 + - - +
1600A C 4.2 14.4 + - - -
3090A MG 3.6 5.2 - - - -
38U ALA 5.6 0.7 - - - +
40U LYS* 3.8 25.7 - - + +
43U ILE* 4.2 11.9 - - + -
58U VAL* 3.7 21.1 - - + -
59U ASN* 1.3 76.7 - - - +
61U LEU* 1.3 62.3 + - - +
81U LYS* 4.2 16.6 + - + +
82U LYS 3.5 6.3 - - - -
83U ALA* 3.8 12.3 - - + -
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Residues in contact with LEU 61 (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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1340A U 3.3 50.7 - - + +
1341A G 3.8 25.1 - - - +
1601A G 5.6 1.3 - - - -
1602A U 5.9 3.6 - - + -
60U THR* 1.3 76.4 - - - +
62U VAL* 1.3 89.7 + - - +
63U VAL* 4.1 12.3 - - + +
81U LYS* 3.2 6.5 - - - +
82U LYS* 2.9 58.0 + - + +
84U TYR* 3.9 15.5 - - + -
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Residues in contact with VAL 62 (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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1340A U 4.6 7.9 + - - -
1600A C 4.5 9.9 - - - +
1601A G 3.7 35.2 + - - +
1602A U 4.8 1.9 + - - -
36U LYS* 4.6 20.2 - - - +
61U LEU* 1.3 90.7 - - - +
63U VAL* 1.3 68.0 + - - +
64U LYS* 3.6 20.7 + - + +
79U ASP* 5.0 1.6 - - + -
80U TRP 3.3 16.4 - - - +
81U LYS* 3.8 26.2 - - + -
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Residues in contact with VAL 63 (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 5.7 8.3 - - + +
1340A U 5.9 8.1 - - + +
61U LEU* 4.4 8.1 - - + -
62U VAL* 1.3 74.1 - - - +
64U LYS* 1.3 72.6 - - - +
65U GLY* 5.3 1.1 - - - -
79U ASP* 3.2 7.1 - - - +
80U TRP* 2.8 87.5 + - + +
82U LYS* 4.3 17.7 - - + +
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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