Contacts of the helix formed by residues 127 - 137 (chain B) in PDB entry 2O25
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 127 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B TRP* 5.6 0.2 - - - -
82B PRO 3.3 4.8 + - - +
84B ILE 3.6 16.8 - - - +
85B SER* 4.2 4.9 + - - -
86B SER* 2.7 34.8 + - - -
87B VAL* 4.7 4.0 + - - +
125B PRO* 4.6 0.7 - - - -
126B GLN* 1.3 77.2 - - - +
128B ALA* 1.3 66.3 + - - +
129B VAL* 3.6 12.5 + - - +
130B VAL* 3.2 30.6 + - + +
131B ALA* 3.0 24.3 + - - +
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Residues in contact with ALA 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B PRO* 4.8 8.6 - - + +
126B GLN 3.9 3.4 + - - -
127B ASP* 1.3 72.6 + - - +
129B VAL* 1.3 58.9 + - + +
131B ALA* 3.4 6.4 + - - +
132B ASN* 2.8 36.6 + - - +
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Residues in contact with VAL 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B TRP* 4.8 7.6 - - + -
127B ASP* 3.3 10.0 + - - +
128B ALA* 1.3 79.6 - - + +
130B VAL* 1.3 61.5 - - + +
132B ASN* 3.5 6.0 + - - +
133B GLN* 3.1 22.1 + - + +
184B SER 5.1 0.9 - - - +
185B SER* 4.1 39.5 - - - +
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Residues in contact with VAL 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B TRP* 3.6 48.7 - - + +
81B HIS 3.6 29.6 - - - +
82B PRO* 3.7 3.1 - - + -
86B SER* 4.3 3.1 - - - +
127B ASP* 3.2 31.7 + - + +
129B VAL* 1.3 71.9 - - - +
131B ALA* 1.3 55.7 + - - +
133B GLN* 2.8 8.1 + - - +
134B TYR* 2.8 32.6 + - - +
141B PHE* 3.7 20.9 - - + -
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Residues in contact with ALA 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B PRO* 4.1 16.5 - - + +
122B PRO* 4.1 14.4 - - - +
125B PRO* 3.8 25.1 - - + -
127B ASP 3.0 10.5 + - - +
128B ALA* 3.5 9.0 - - - +
130B VAL* 1.3 77.7 - - - +
132B ASN* 1.3 63.0 + - - +
134B TYR* 3.2 14.4 + - - +
135B LYS* 3.2 21.0 + - + +
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Residues in contact with ASN 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B ALA 2.8 21.4 + - - +
129B VAL* 3.7 7.0 - - - +
131B ALA* 1.3 74.1 - - - +
133B GLN* 1.3 57.4 + - - +
135B LYS* 3.4 10.5 + - - +
136B GLN* 2.9 55.2 + - - +
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Residues in contact with GLN 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B TRP* 2.8 31.6 + - + -
129B VAL* 3.1 13.2 + - + +
130B VAL* 2.8 16.9 + - - +
132B ASN* 1.3 69.4 - - - +
134B TYR* 1.3 64.9 + - - +
136B GLN* 4.6 3.6 - - - +
137B ASN* 2.9 31.1 + - + +
140B MET* 3.6 32.1 - - + +
141B PHE* 3.4 26.7 - - - +
144B THR* 3.6 7.9 + - - -
184B SER 3.4 22.2 + - - +
187B SER* 5.0 3.2 + - - +
188B TRP* 4.8 1.0 - - - +
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Residues in contact with TYR 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B PRO* 3.5 20.4 - - + -
120B ALA* 3.6 33.7 + - + +
122B PRO* 3.6 29.7 - - + +
130B VAL 2.8 14.8 + - - +
131B ALA* 3.4 9.2 - - - +
133B GLN* 1.3 74.5 - - - +
135B LYS* 1.3 62.5 + - + +
138B PRO* 3.5 24.9 - - - +
141B PHE* 3.3 49.3 - + + +
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Residues in contact with LYS 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B PRO* 4.3 32.1 - - + +
123B ASP* 5.2 6.7 + - - +
131B ALA* 3.2 17.0 + - + +
132B ASN* 3.6 11.7 - - - +
133B GLN 3.1 0.4 - - - -
134B TYR* 1.3 78.4 - - + +
136B GLN* 1.3 67.0 + - + +
137B ASN 3.2 1.9 + - - -
138B PRO* 3.5 12.4 - - - +
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Residues in contact with GLN 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B ASN* 2.9 43.5 + - - +
133B GLN* 4.4 2.7 - - - +
135B LYS* 1.3 76.2 - - + +
137B ASN* 1.3 64.0 + - + +
138B PRO* 3.8 2.6 - - - +
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Residues in contact with ASN 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A GLU* 3.5 23.0 + - - -
133B GLN* 2.9 19.6 + - + +
136B GLN* 1.3 82.6 - - + +
138B PRO* 1.3 68.0 - - - +
139B GLU* 3.8 8.8 + - - +
140B MET* 3.1 38.2 + - + +
141B PHE 2.9 17.2 + - - -
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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