Contacts of the helix formed by residues 94 - 103 (chain I) 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 ARG 94 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91I ALA* 4.3 21.3 - - - +
92I ALA* 3.3 0.4 - - - +
93I ALA* 1.3 80.0 - - - +
95I LEU* 1.3 59.5 + - - +
97I LYS* 3.8 3.8 + - - +
98I GLU* 3.2 40.4 + - - +
126I LEU 3.4 23.3 + - - +
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Residues in contact with LEU 95 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41I LEU* 3.5 29.4 - - + -
44I ALA* 3.1 45.1 - - + +
45I GLY* 4.2 4.7 - - - +
48I ALA* 4.3 6.5 - - + -
50I VAL* 4.8 4.9 - - + -
52I MET* 5.4 3.1 - - - -
91I ALA 3.4 22.8 + - - +
92I ALA* 3.4 5.5 + - - +
94I ARG* 1.3 77.6 - - - +
96I PHE* 1.3 61.1 + - + +
98I GLU* 3.7 5.3 + - + +
99I PHE* 2.9 33.3 + - + +
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Residues in contact with PHE 96 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I VAL* 4.1 21.5 - - + -
28I ALA* 3.5 32.1 - - + -
41I LEU* 3.4 33.4 - - + -
52I MET* 3.6 12.8 - - + -
81I LEU* 3.7 26.0 - - + -
83I ALA* 3.6 27.1 - - + -
92I ALA* 3.0 18.6 + - - +
93I ALA* 4.8 2.7 - - - -
94I ARG 3.5 0.2 - - - -
95I LEU* 1.3 77.8 - - + +
97I LYS* 1.3 59.4 + - - +
98I GLU 3.5 0.2 - - - -
99I PHE* 3.9 2.9 - + - +
100I ALA* 2.9 29.3 + - - +
106I PHE* 4.2 3.6 - + - -
108I VAL* 3.2 26.1 - - + +
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Residues in contact with LYS 97 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93I ALA* 2.4 41.9 + - - +
94I ARG* 3.8 6.0 + - - +
95I LEU 3.4 0.4 - - - -
96I PHE* 1.3 76.9 - - - +
98I GLU* 1.3 61.5 + - + +
100I ALA* 3.9 4.3 - - - +
101I LYS* 2.9 43.7 + - + +
108I VAL* 4.8 12.8 - - + +
120I ALA 4.8 6.3 - - - +
123I ILE* 3.1 49.6 + - - +
124I ASP* 3.6 26.3 + - - +
126I LEU 4.9 1.6 - - - -
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Residues in contact with GLU 98 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94I ARG* 3.2 29.9 + - - +
95I LEU* 4.2 4.7 - - + +
97I LYS* 1.3 73.8 - - + +
99I PHE* 1.3 62.3 + - - +
101I LYS* 4.3 19.7 - - - +
102I ALA* 3.0 32.3 + - - +
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Residues in contact with PHE 99 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33I VAL* 4.4 1.6 - - + -
37I LYS* 2.9 37.9 - - + -
38I MET* 4.1 13.0 - - - -
40I GLU* 4.7 5.4 - - + -
41I LEU* 3.4 48.2 - - + -
95I LEU* 2.9 22.6 + - + +
96I PHE* 3.9 7.2 - - - +
98I GLU* 1.3 76.8 - - - +
100I ALA* 1.3 55.5 + - - +
102I ALA* 4.7 2.2 - - - -
103I ASN* 3.0 56.9 + - - +
106I PHE* 3.3 27.4 - + - -
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Residues in contact with ALA 100 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96I PHE 2.9 19.9 + - - +
97I LYS* 4.1 5.2 - - - +
99I PHE* 1.3 75.7 - - - +
101I LYS* 1.3 58.1 + - + +
104I ALA* 3.4 19.6 + - - +
105I LYS 3.4 14.2 - - - +
106I PHE* 3.4 28.4 - - + +
107I GLU* 4.1 8.3 - - - +
108I VAL* 3.9 9.9 - - + -
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Residues in contact with LYS 101 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97I LYS* 2.9 27.3 + - + +
98I GLU* 4.3 22.1 - - - +
100I ALA* 1.3 77.3 - - + +
102I ALA* 1.3 62.6 + - - +
104I ALA* 3.7 10.3 + - - +
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Residues in contact with ALA 102 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98I GLU 3.0 21.5 + - - +
99I PHE* 4.2 2.7 - - - +
101I LYS* 1.3 77.0 - - - +
103I ASN* 1.3 65.6 + - - +
104I ALA* 3.5 1.9 + - - +
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Residues in contact with ASN 103 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33I VAL* 3.8 9.7 - - - +
37I LYS* 2.9 45.8 + - - +
99I PHE* 3.0 52.1 + - - +
102I ALA* 1.3 77.6 - - - +
104I ALA* 1.3 66.6 + - - +
105I LYS* 3.1 34.8 + - + +
106I PHE* 4.3 3.7 - - + -
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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