Contacts of the strand formed by residues 139 - 148 (chain H) 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 PHE 139 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69H ALA* 3.9 12.7 - - - +
73H ASN* 5.5 0.3 - - - +
116H ARG* 5.4 8.3 - - + -
131H SER* 5.2 7.6 - - - -
132H PHE 3.2 20.4 - - - +
133H GLN* 3.4 35.2 - - + -
134H VAL* 4.7 1.3 - - - +
136H SER 3.6 20.6 - - - -
137H GLU* 3.7 13.1 + - - -
138H VAL* 1.3 78.2 - - - +
140H ALA* 1.3 66.4 + - - +
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Residues in contact with ALA 140 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69H ALA* 4.0 7.9 - - - +
72H ILE* 3.6 30.5 - - + -
73H ASN* 3.6 26.0 - - + +
131H SER* 3.3 7.4 - - - -
132H PHE* 2.9 29.9 + - + +
134H VAL* 5.8 0.4 - - + -
139H PHE* 1.3 78.3 - - - +
141H LYS* 1.3 65.0 + - - +
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Residues in contact with LYS 141 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72H ILE 4.1 0.4 - - - +
73H ASN* 3.4 27.3 + - - +
74H ALA 4.7 0.7 - - - +
75H LEU* 5.7 1.6 - - - +
129H GLU* 3.2 31.1 + - - +
130H VAL 3.7 4.3 - - - +
131H SER* 3.8 23.3 - - - +
140H ALA* 1.3 81.7 - - - +
142H VAL* 1.3 67.7 + - - +
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Residues in contact with VAL 142 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72H ILE* 3.2 22.4 - - + +
74H ALA 3.7 16.2 - - - +
75H LEU* 4.7 2.2 - - - +
76H GLU* 3.0 31.2 - - + +
78H VAL* 3.9 16.8 - - + -
103H VAL* 5.5 4.0 - - + -
129H GLU* 3.5 10.1 - - - +
130H VAL* 3.0 31.8 + - + +
132H PHE* 3.4 33.0 - - + -
141H LYS* 1.3 73.5 - - - +
143H ILE* 1.3 63.4 + - - +
144H VAL* 5.6 0.7 - - + -
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Residues in contact with ILE 143 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75H LEU 5.4 3.7 + - - +
76H GLU 4.2 1.1 + - - +
77H THR* 3.6 17.4 - - - +
78H VAL* 2.8 29.0 + - - +
127H GLU* 4.1 23.3 - - + +
128H HIS 3.4 7.2 - - - +
129H GLU* 4.2 19.1 - - + +
142H VAL* 1.3 80.6 - - - +
144H VAL* 1.3 62.1 + - - +
145H ASN* 3.5 19.5 - - - +
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Residues in contact with VAL 144 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78H VAL* 3.5 15.0 - - + -
80H ILE* 3.7 21.8 - - + -
94H ILE* 5.0 0.2 - - + -
99H ILE* 3.6 21.8 - - + -
122H LEU* 3.6 25.4 - - + -
126H GLY 3.3 6.4 - - - +
127H GLU* 3.3 0.7 - - - -
128H HIS* 2.9 40.3 + - - +
130H VAL* 3.5 30.1 - - + -
142H VAL* 5.3 0.9 - - + -
143H ILE* 1.3 74.7 - - - +
145H ASN* 1.3 61.3 + - - +
146H VAL* 3.7 9.6 + - + -
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Residues in contact with ASN 145 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77H THR* 3.4 29.5 - - + +
78H VAL 2.6 13.1 + - - +
79H THR* 3.4 6.9 - - - -
80H ILE* 2.9 28.4 + - - +
126H GLY 3.6 4.0 - - - -
127H GLU* 3.2 33.8 + - - +
143H ILE* 3.5 7.3 - - - +
144H VAL* 1.3 72.6 - - - +
146H VAL* 1.3 62.2 + - - +
147H VAL* 3.6 11.1 + - + +
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Residues in contact with VAL 146 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80H ILE* 3.7 3.6 - - + +
82H SER* 3.7 10.8 - - - -
90H LEU* 3.7 31.0 - - + -
94H ILE* 3.6 32.1 - - + -
122H LEU* 4.4 3.6 - - + -
124H THR 4.1 3.1 - - - +
125H THR* 3.2 21.9 - - - +
126H GLY* 3.0 18.6 + - - +
128H HIS* 3.5 32.8 - - + +
144H VAL* 4.2 10.1 - - + -
145H ASN* 1.3 73.7 - - - +
147H VAL* 1.3 58.2 + - - +
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Residues in contact with VAL 147 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79H THR* 3.3 28.0 - - - +
80H ILE 2.8 15.6 + - - +
81H ALA* 3.7 6.5 - - + -
82H SER 2.9 30.6 + - - +
125H THR* 5.0 0.4 - - - -
145H ASN* 4.2 12.6 - - + +
146H VAL* 1.3 73.4 - - - +
148H ALA* 1.3 72.6 + - - +
149H GLU* 3.5 0.6 + - + +
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Residues in contact with ALA 148 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82H SER 3.4 6.7 - - - -
84H ALA* 3.5 28.5 - - + +
125H THR* 4.4 8.1 - - + +
146H VAL 3.9 3.6 + - - -
147H VAL* 1.3 81.8 - - - +
149H GLU* 1.3 63.3 + - - +
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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