Contacts of the strand formed by residues 116 - 123 (chain I) in PDB entry 6ALG
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 ASP 116 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102I LEU 3.8 0.9 - - - +
103I VAL* 3.6 4.7 - - - +
104I ILE* 3.4 43.5 + - + +
114I VAL* 3.6 0.9 - - - +
115I LYS* 1.3 105.8 - - - +
117I ILE* 1.3 67.8 + - - +
118I LYS* 5.5 2.1 - - - -
485I ASP* 3.0 28.8 - - - +
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Residues in contact with ILE 117 (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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101I ARG* 5.0 12.6 - - + +
102I LEU 3.5 6.5 - - - +
103I VAL* 3.7 22.4 - - + -
114I VAL* 3.9 14.1 - - + -
115I LYS 5.8 0.2 - - - -
116I ASP* 1.3 80.1 - - - +
118I LYS* 1.3 68.4 + - - +
119I GLU* 5.4 9.4 - - + +
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Residues in contact with LYS 118 (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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101I ARG* 3.4 6.5 - - - +
102I LEU* 3.0 64.4 + - + +
104I ILE* 5.4 3.5 - - - +
116I ASP* 5.5 2.7 - - - -
117I ILE* 1.3 80.0 - - - +
119I GLU* 1.3 63.2 + - - +
484I LEU 4.4 1.0 + - - -
485I ASP* 3.1 42.4 + - - +
487I LEU 2.9 23.4 + - - +
488I MET* 4.4 8.1 - - + +
489I PRO* 3.9 22.2 - - + +
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Residues in contact with GLU 119 (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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71I VAL* 4.3 11.0 - - + +
99I LYS* 5.2 9.1 - - + +
100I LEU 3.8 14.6 - - - +
101I ARG* 3.2 39.2 + - + +
117I ILE* 5.4 7.9 - - + +
118I LYS* 1.3 78.1 - - - +
120I GLN* 1.3 70.1 + - - +
489I PRO* 5.5 1.9 - - - +
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Residues in contact with GLN 120 (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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99I LYS* 3.3 9.2 - - - +
100I LEU* 3.3 26.4 + - + +
119I GLU* 1.3 78.8 - - - +
121I GLU* 1.3 64.6 + - - +
122I VAL* 3.8 5.2 + - + +
488I MET* 4.9 6.6 - - - +
489I PRO* 3.2 41.0 + - + +
490I GLN* 2.4 41.9 + - - +
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Residues in contact with GLU 121 (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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74I ARG* 2.4 54.5 + - - +
97I ARG* 3.4 28.3 + - + +
98I VAL 3.3 5.6 - - - +
99I LYS* 3.5 37.4 + - + +
120I GLN* 1.3 77.3 - - - +
122I VAL* 1.3 62.3 + - - +
123I TYR 4.0 0.3 + - - -
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Residues in contact with VAL 122 (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 ARG* 3.4 5.7 - - - -
98I VAL* 2.5 56.4 + - + +
100I LEU* 3.7 27.6 - - + -
120I GLN* 3.8 8.0 + - + +
121I GLU* 1.3 74.8 - - - +
123I TYR* 1.3 68.6 + - - +
124I MET* 4.3 9.6 - - + -
489I PRO 3.3 23.8 - - - +
490I GLN* 3.6 21.5 - - + -
493I ILE* 3.7 15.5 - - + -
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Residues in contact with TYR 123 (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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95I PRO* 3.9 16.8 - - + -
96I LEU 3.9 8.1 - - - -
97I ARG* 3.4 33.8 - - - +
121I GLU 4.0 0.4 + - - -
122I VAL* 1.3 86.0 - - - +
124I MET* 1.3 66.0 + - - +
125I GLY* 3.2 24.7 + - - -
126I GLU* 3.3 28.8 + - + +
493I ILE* 4.6 6.4 - - - +
494I ASN 5.3 1.9 - - - +
495I ALA* 3.9 27.2 - - + +
499I SER* 5.8 1.2 - - - -
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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