Contacts of the helix formed by residues 1273 - 1278 (chain L) in PDB entry 3F5P
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 GLY1273 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1271L GLU* 3.2 3.6 + - - +
1272L PRO* 1.3 78.9 - - - +
1274L PHE* 1.3 63.7 + - - +
1276L GLU* 2.9 33.4 + - - +
1277L VAL* 3.6 10.8 + - - +
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Residues in contact with PHE1274 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061L HIS* 3.6 24.5 - + - -
1114L GLN* 5.2 2.8 - - - +
1117L GLY 4.0 18.4 - - - -
1118L GLU* 4.7 2.2 - - + -
1121L ASP* 4.1 5.8 - - + -
1263L ILE* 3.8 30.3 - - + -
1267L LYS* 5.1 4.3 - - + -
1270L MET* 4.0 40.6 - - + -
1271L GLU 3.3 15.8 + - - +
1272L PRO 3.0 0.4 + - - -
1273L GLY* 1.3 74.7 - - - +
1275L ARG* 1.3 63.8 + - - +
1276L GLU 3.0 0.2 + - - -
1277L VAL* 4.1 5.8 - - + -
1278L SER* 2.9 57.9 + - - -
1280L TYR* 4.6 3.4 - + + -
1281L TYR* 4.3 16.6 - + + -
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Residues in contact with ARG1275 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1268L GLU* 5.2 5.9 + - - -
1272L PRO 3.5 9.4 + - - +
1273L GLY 3.0 1.2 + - - -
1274L PHE* 1.3 79.2 - - - +
1276L GLU* 1.3 58.9 + - + +
1277L VAL 3.7 0.2 + - - -
1278L SER 4.4 1.0 + - - +
1281L TYR* 3.1 86.7 + - + +
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Residues in contact with GLU1276 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1272L PRO 4.9 0.2 + - - -
1273L GLY* 2.9 20.7 + - - +
1275L ARG* 1.3 80.0 - - + +
1277L VAL* 1.3 73.8 + - + +
1278L SER 5.1 0.7 - - - -
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Residues in contact with VAL1277 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1060L HIS* 3.1 65.3 + - + +
1061L HIS* 4.4 5.2 - - + +
1273L GLY* 3.8 14.4 - - - +
1274L PHE* 3.9 10.1 - - - +
1276L GLU* 1.3 99.4 - - + +
1278L SER* 1.3 72.1 + - - +
1279L PHE 3.9 0.2 + - - -
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Residues in contact with SER1278 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061L HIS* 4.0 3.6 - - - -
1121L ASP* 3.4 8.3 - - - -
1274L PHE* 2.9 52.4 + - - -
1275L ARG 4.4 0.7 + - - +
1276L GLU 3.8 1.1 - - - -
1277L VAL* 1.3 82.9 - - - +
1279L PHE* 1.3 61.5 + - - +
1280L TYR* 3.2 7.1 + - - +
1281L TYR* 2.9 27.7 + - - +
1282L SER* 3.5 16.8 + - - -
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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