Contacts of the strand formed by residues 127 - 133 (chain G) in PDB entry 3PHW
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 127 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21G PRO* 3.7 15.4 - - + +
22G ARG* 4.4 9.0 - - - +
23G PHE* 3.1 48.1 + - + +
25G ILE* 3.4 32.8 - - + -
119G TRP* 3.8 26.5 - - + -
120G THR 3.7 7.4 - - - +
121G VAL* 4.0 3.4 - - + -
126G GLU* 1.3 73.7 - - - +
128G GLU* 1.3 64.8 + - - +
129G ALA 3.6 15.7 - - - +
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Residues in contact with GLU 128 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G ASN* 3.4 20.4 - - - +
21G PRO 4.1 4.0 - - - +
120G THR* 3.0 23.7 + - + +
121G VAL 3.8 8.1 - - - +
122G ALA* 3.2 29.5 - - + +
126G GLU 4.0 7.9 - - - +
127G VAL* 1.3 78.6 - - - +
129G ALA* 1.3 62.9 + - - +
149G GLN* 5.2 6.9 + - - -
9H THR* 3.4 34.0 - - + +
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Residues in contact with ALA 129 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G SER 3.3 8.3 - - - +
20G ASN* 3.7 2.0 - - - +
118G ILE 4.0 0.3 - - - +
119G TRP* 3.7 9.4 - - - -
120G THR* 3.1 37.0 + - + +
127G VAL* 3.6 3.0 - - - +
128G GLU* 1.3 81.2 - - + +
130G GLY* 1.3 58.5 + - - +
131G ILE* 5.5 0.7 - - + -
8H LEU* 3.3 49.4 - - + +
9H THR* 4.4 0.9 - - + +
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Residues in contact with GLY 130 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G TRP* 3.5 7.6 - - - -
18G VAL* 3.3 7.3 - - - +
19G SER* 2.9 35.7 + - - +
117G ILE* 4.8 0.2 - - - -
118G ILE 3.5 6.5 - - - -
119G TRP* 3.6 22.9 - - - -
129G ALA* 1.3 74.9 - - - +
131G ILE* 1.3 64.7 + - - +
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Residues in contact with ILE 131 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G TRP* 4.3 1.1 - - - -
16G GLN* 5.5 3.8 - - + +
17G TYR 3.4 8.7 - - - +
18G VAL* 4.4 2.7 - - + -
102G THR* 4.9 2.0 - - + -
116G ILE 3.8 1.4 - - - +
117G ILE* 3.4 2.4 - - - +
118G ILE* 2.9 41.7 + - + +
129G ALA* 5.5 0.7 - - + -
130G GLY* 1.3 72.6 - - - +
132G LYS* 1.3 63.4 + - - +
133G PHE* 3.4 36.3 - - + -
8H LEU* 3.4 45.5 - - + -
70H VAL* 3.5 23.8 - - + -
71H LEU 3.9 11.7 - - - +
73H LEU* 4.2 13.0 - - + -
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Residues in contact with LYS 132 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G TRP* 3.4 49.3 - - + +
15G GLY 3.6 1.2 - - - +
16G GLN* 3.3 7.6 - - - +
17G TYR* 2.8 55.3 + - + +
115G THR* 3.7 6.3 - - + -
116G ILE 3.6 2.0 - - - -
117G ILE* 3.6 30.1 - - + +
131G ILE* 1.3 71.4 - - - +
133G PHE* 1.3 64.7 + - - +
134G GLY 2.8 26.4 + - - +
135G ASP* 3.5 10.5 + - - +
136G GLY 2.7 28.7 + - - +
137G ASP* 5.0 2.0 - - - +
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Residues in contact with PHE 133 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G GLY 3.6 3.6 - - - +
16G GLN* 3.8 32.3 - - + -
78G GLU* 5.0 0.9 - - - -
102G THR* 3.6 32.3 - - + -
105G ALA* 4.0 14.4 - - + +
106G SER* 3.7 24.7 - - - +
109G ALA* 3.7 22.6 - - + +
115G THR* 3.3 4.1 - - - +
116G ILE* 2.7 47.7 + - + +
118G ILE* 3.7 24.7 - - + -
131G ILE* 3.4 32.3 - - + -
132G LYS* 1.3 73.6 - - - +
134G GLY* 1.3 58.4 + - - +
42H ARG* 5.0 4.7 - - - -
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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