Contacts of the helix formed by residues 302 - 308 (chain D) in PDB entry 5MG3
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 SER 302 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337C SER* 5.8 1.3 + - - -
246D PRO* 6.2 2.2 - - - -
301D ASP* 1.4 77.0 - - - +
303D GLU* 1.3 56.7 + - - +
304D VAL 3.6 3.1 + - - -
305D LYS* 3.1 17.5 + - - +
306D GLN* 2.7 35.8 + - - +
63F GLU* 3.9 13.9 + - - -
65F PRO* 5.2 8.3 - - - +
154Y PHE* 5.4 11.3 - - - +
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Residues in contact with GLU 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239D ASN* 3.3 29.2 + - + +
240D GLN 2.8 33.4 + - - +
242D GLY* 3.2 7.4 + - - -
243D VAL* 3.0 43.1 + - - +
246D PRO* 5.8 2.4 - - + +
302D SER* 1.3 72.5 + - - +
304D VAL* 1.3 51.8 + - - +
306D GLN* 3.5 6.3 - - - +
307D THR* 2.6 42.9 + - - -
63F GLU* 3.6 20.1 + - + +
125F ASN* 3.1 22.9 + - - +
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Residues in contact with VAL 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302D SER* 3.6 1.6 + - - -
303D GLU* 1.3 74.0 - - - +
305D LYS* 1.4 57.8 + - - +
307D THR* 3.6 1.1 - - - -
308D ARG* 2.9 45.4 + - + +
63F GLU* 4.2 8.6 + - + -
65F PRO* 4.0 36.8 - - + +
66F ALA* 3.8 20.2 - - + +
123F ASN* 4.5 9.2 - - + +
125F ASN* 3.7 32.1 - - + +
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Residues in contact with LYS 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296D GLY 5.8 2.0 - - - +
302D SER* 3.1 23.5 + - - +
304D VAL* 1.4 74.2 - - - +
306D GLN* 1.4 56.1 + - - +
308D ARG* 3.4 7.3 - - + +
309D GLU* 2.9 54.4 + - - +
65F PRO* 5.5 1.8 - - - +
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Residues in contact with GLN 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239D ASN* 6.0 4.0 - - + +
293D ALA* 2.9 35.9 + - - +
296D GLY 3.3 24.5 - - - +
297D ARG* 3.8 2.9 + - - +
301D ASP* 3.8 31.9 - - + +
302D SER 2.7 23.1 + - - +
303D GLU* 3.7 8.5 - - + +
305D LYS* 1.4 72.3 - - - +
307D THR* 1.3 62.0 + - - +
308D ARG 3.4 0.2 - - - -
309D GLU* 3.3 28.8 + - - +
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Residues in contact with THR 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239D ASN* 5.8 0.9 - - - +
240D GLN* 3.8 29.7 + - - +
303D GLU* 2.6 27.4 + - - +
304D VAL* 3.2 4.7 + - - -
306D GLN* 1.3 70.9 - - - +
308D ARG* 1.4 66.3 + - - +
309D GLU 3.5 7.3 + - - +
122F THR* 3.4 31.6 - - - +
125F ASN* 3.1 23.0 + - - +
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Residues in contact with ARG 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304D VAL* 2.9 26.5 + - + +
305D LYS* 3.4 7.9 - - + +
307D THR* 1.4 82.1 + - - +
309D GLU* 1.3 61.9 + - - +
310D GLY 3.8 5.7 + - - +
122F THR* 2.8 50.0 + - - +
123F ASN* 4.1 20.5 - - - +
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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