Contacts of the helix formed by residues 289 - 297 (chain A) in PDB entry 1GM5
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 PRO 289 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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287A THR 3.8 4.7 - - - +
288A LEU* 1.3 86.6 - - + +
290A GLU* 1.3 61.3 + - - +
291A ARG* 3.1 7.6 - - + +
292A ILE* 2.9 48.6 + - + +
293A LEU* 3.5 3.1 - - - +
330A PHE* 5.1 5.6 - - + -
755A TRP* 6.5 1.1 - - + -
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Residues in contact with GLU 290 (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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286A GLU* 6.0 2.9 - - + -
288A LEU 3.7 0.4 + - - -
289A PRO* 1.3 71.9 - - - +
291A ARG* 1.3 52.8 + - - +
292A ILE 3.1 1.3 + - - -
293A LEU* 3.0 27.8 - - + +
294A GLU* 2.7 49.7 + - - +
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Residues in contact with ARG 291 (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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289A PRO* 3.1 7.2 + - + +
290A GLU* 1.3 77.8 - - - +
292A ILE* 1.3 67.1 + - + +
294A GLU* 3.9 9.8 - - - +
295A LYS* 3.6 33.6 + - - +
752A LEU* 6.0 4.2 - - - +
755A TRP 5.7 3.0 + - - -
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Residues in contact with ILE 292 (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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288A LEU* 3.3 26.0 - - + -
289A PRO* 2.9 50.7 + - + +
291A ARG* 1.3 77.9 - - + +
293A LEU* 1.3 59.9 - - - +
294A GLU 2.8 0.9 - - - -
295A LYS* 2.1 46.6 + - + +
296A ARG* 3.4 5.1 + - + -
326A TYR* 3.5 26.9 - - + +
330A PHE* 4.6 11.2 - - + -
752A LEU* 4.9 11.0 - - + -
755A TRP 5.9 3.1 - - - +
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Residues in contact with LEU 293 (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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286A GLU* 4.7 9.2 - - + +
288A LEU* 3.1 34.5 - - + +
289A PRO 3.5 7.0 - - - +
290A GLU* 3.0 44.4 - - + +
292A ILE* 1.3 85.3 - - - +
294A GLU* 1.3 64.5 + - + +
295A LYS 2.6 0.5 + - - -
296A ARG* 2.8 12.5 + - - +
297A LYS* 2.8 15.0 + - - +
298A LEU 4.6 13.9 + - - +
299A LEU 5.1 0.2 - - - +
300A GLY* 4.6 24.2 - - - +
323A ARG* 5.2 1.3 - - - +
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Residues in contact with GLU 294 (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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290A GLU* 2.7 41.8 - - - +
291A ARG* 3.9 10.2 + - - +
292A ILE 2.5 4.4 + - - -
293A LEU* 1.3 73.9 - - + +
295A LYS* 1.3 66.3 + - - +
297A LYS* 4.0 6.6 + - - +
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Residues in contact with LYS 295 (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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291A ARG* 3.6 29.9 + - - +
292A ILE* 2.1 37.6 + - + +
294A GLU* 1.3 74.2 - - - +
296A ARG* 1.3 97.4 + - + +
297A LYS* 5.2 0.2 - - - +
751A LYS* 4.4 9.7 + - - +
752A LEU* 3.6 32.7 - - + +
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Residues in contact with ARG 296 (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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292A ILE* 3.4 4.7 + - + +
293A LEU* 2.8 5.1 + - - +
295A LYS* 1.3 130.5 + - + +
297A LYS* 1.3 68.4 + - - +
298A LEU* 3.7 15.0 + - + +
319A LYS* 5.0 1.6 + - - -
322A GLU* 4.6 2.0 - - - +
326A TYR* 5.0 6.1 - - + -
748A ARG* 1.5 79.4 - - - +
751A LYS* 5.1 4.6 - - - +
752A LEU* 3.0 14.0 - - + +
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Residues in contact with LYS 297 (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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90A GLU 5.6 0.8 + - - -
93A GLU* 3.8 33.8 + - + +
94A LYS* 5.4 0.6 - - - +
97A SER* 5.4 13.2 - - - +
293A LEU 2.8 19.3 + - - -
294A GLU* 4.0 4.4 + - - +
295A LYS 3.7 1.0 - - - -
296A ARG* 1.3 77.6 - - - +
298A LEU* 1.3 61.9 + - - +
299A LEU* 3.8 6.8 + - - +
315A TYR* 4.8 7.0 - - - +
319A LYS* 3.8 21.5 - - - +
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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