Contacts of the helix formed by residues 297 - 308 (chain A) in PDB entry 2J51
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 ASN 297 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A VAL* 4.0 10.5 - - + -
166A ASP* 3.0 25.9 + - - +
167A GLY 3.4 15.3 - - - +
168A ASP* 3.0 29.9 + - - +
296A SER* 1.3 69.6 + - - +
298A LYS* 1.3 66.9 + - - +
299A PRO* 3.3 3.8 - - - -
300A ILE* 2.8 15.6 + - - -
301A ARG* 3.0 27.2 + - - +
1310A EDO 3.5 11.5 + - - +
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Residues in contact with LYS 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A SER* 3.2 14.7 + - - +
297A ASN* 1.3 77.1 + - - +
299A PRO* 1.4 70.1 - - + +
301A ARG* 3.0 37.5 + - - +
302A GLU* 2.9 43.1 + - + +
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Residues in contact with PRO 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A SER* 3.7 42.0 - - - +
131A GLN* 3.5 29.3 + - + +
134A VAL* 4.1 5.2 - - + -
296A SER* 3.8 12.8 - - - +
297A ASN 3.3 4.9 - - - -
298A LYS* 1.4 92.9 - - + +
300A ILE* 1.3 55.6 + - - +
302A GLU* 3.5 15.3 + - - +
303A LEU 3.2 19.6 + - - -
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Residues in contact with ILE 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A LEU* 4.7 0.2 - - + -
131A GLN* 3.6 36.1 - - + +
134A VAL* 3.8 28.9 - - + -
135A VAL* 3.9 16.2 - - + -
163A PHE* 3.6 34.8 - - + -
167A GLY* 3.1 30.3 - - - +
169A ILE* 5.4 0.7 - - + -
297A ASN 2.8 10.6 + - - +
299A PRO* 1.3 71.1 - - - +
301A ARG* 1.3 58.8 + - - +
302A GLU 3.2 0.2 - - - -
303A LEU* 3.1 6.2 + - + -
304A ILE* 2.9 33.2 + - + +
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Residues in contact with ARG 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A LEU 5.8 0.4 - - - +
166A ASP* 3.4 28.5 - - - +
167A GLY* 4.1 2.2 - - - -
296A SER* 4.8 2.6 + - - -
297A ASN* 3.0 26.0 + - - +
298A LYS* 3.0 44.7 + - + +
300A ILE* 1.3 75.2 - - - +
302A GLU* 1.3 62.9 + - + +
304A ILE* 3.5 9.7 - - + +
305A ALA* 3.1 26.3 + - - +
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Residues in contact with GLU 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A GLN* 5.4 3.1 + - - +
298A LYS* 2.9 35.4 + - + +
299A PRO* 3.6 16.7 - - - +
301A ARG* 1.3 74.6 - - + +
303A LEU* 1.3 65.7 + - - +
305A ALA* 3.6 4.9 - - - +
306A GLU* 3.2 22.7 + - - +
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Residues in contact with LEU 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A VAL* 4.0 17.0 - - + -
123A LEU* 3.5 28.4 - - + +
125A ARG* 3.7 19.5 - - - +
126A PRO 5.8 1.6 - - - +
127A LEU* 3.9 30.3 - - + -
131A GLN* 3.9 23.3 - - - +
163A PHE* 4.1 18.4 - - + -
299A PRO 3.2 10.9 + - - +
300A ILE* 3.1 13.5 + - + +
302A GLU* 1.3 78.9 - - - +
304A ILE* 1.3 63.5 - - + +
306A GLU* 3.2 8.6 + - - +
307A ALA* 3.1 19.6 + - - +
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Residues in contact with ILE 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A GLY* 5.3 7.2 - - - -
119A VAL* 5.3 3.6 - - + -
163A PHE* 3.9 41.3 - - + -
164A THR 4.9 4.7 - - - +
165A LEU 4.7 11.0 - - - +
167A GLY* 4.6 9.6 - - - -
300A ILE* 2.9 32.9 + - + +
301A ARG* 3.5 13.2 - - + +
303A LEU* 1.3 76.2 - - + +
305A ALA* 1.3 60.2 + - - +
307A ALA* 3.4 8.8 + - - +
308A LYS* 3.0 27.5 + - - +
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Residues in contact with ALA 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A ARG 3.1 21.6 + - - +
302A GLU* 3.6 7.0 - - - +
304A ILE* 1.3 77.7 - - - +
306A GLU* 1.3 62.9 + - - +
308A LYS* 3.2 25.2 + - - +
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Residues in contact with GLU 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A LEU* 4.1 16.1 - - + +
125A ARG* 3.0 42.6 + - - +
302A GLU 3.2 10.3 + - - +
303A LEU* 3.2 9.6 + - - +
305A ALA* 1.3 80.9 - - - +
307A ALA* 1.3 61.0 + - - +
308A LYS 3.4 6.4 + - - +
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Residues in contact with ALA 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A VAL* 4.6 27.1 - - + -
122A GLU* 5.8 4.9 - - + -
123A LEU* 4.5 13.8 - - + +
303A LEU 3.1 12.7 + - - +
304A ILE* 3.7 13.0 - - + +
305A ALA 3.3 0.4 - - - -
306A GLU* 1.3 75.2 - - - +
308A LYS* 1.3 59.3 + - - +
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Residues in contact with LYS 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A ILE 3.0 13.1 + - - +
305A ALA* 3.2 21.2 + - - +
306A GLU 3.6 7.2 - - - +
307A ALA* 1.3 79.5 - - - +
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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