Contacts of the helix formed by residues 1705 - 1716 (chain A) in PDB entry 2FR1
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 GLY1705 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1703A ALA 3.5 0.6 + - - -
1704A ASP* 1.3 79.2 + - - +
1706A ALA* 1.3 63.4 + - - +
1707A GLY 3.1 4.6 - - - +
1708A GLU* 3.4 20.3 + - - +
1709A LEU* 3.0 24.9 + - - +
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Residues in contact with ALA1706 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1674A THR* 4.4 8.9 - - + -
1700A GLY 4.0 16.2 - - - +
1701A PRO* 4.2 11.9 - - + +
1703A ALA* 3.3 24.6 + - + +
1704A ASP 3.2 3.6 + - - -
1705A GLY* 1.3 79.1 - - - +
1707A GLY* 1.3 64.7 + - - +
1709A LEU* 3.1 21.0 + - - +
1710A VAL* 3.2 19.8 + - - +
1722A VAL* 4.9 6.3 - - + -
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Residues in contact with GLY1707 (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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1701A PRO 5.6 0.6 + - - -
1703A ALA 4.8 0.8 + - - -
1705A GLY* 3.1 2.2 - - - +
1706A ALA* 1.3 82.8 - - - +
1708A GLU* 1.3 59.3 + - - +
1709A LEU 3.3 0.2 + - - -
1710A VAL* 3.6 5.1 + - - +
1711A ALA* 3.6 16.1 + - - +
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Residues in contact with GLU1708 (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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1705A GLY* 3.5 18.2 - - - +
1707A GLY* 1.3 72.5 - - - +
1709A LEU* 1.3 62.6 + - - +
1711A ALA* 3.8 10.5 - - + +
1712A GLU* 2.9 43.3 + - - +
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Residues in contact with LEU1709 (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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1673A GLY 3.7 23.6 - - - +
1674A THR* 4.0 22.4 - - + +
1675A GLY 5.7 0.2 - - - +
1679A GLY* 4.9 8.3 - - - +
1682A ALA* 5.1 0.2 - - + -
1683A ARG* 4.7 23.3 - - - +
1695A LEU* 4.2 11.0 - - + -
1705A GLY 3.0 14.5 + - - +
1706A ALA* 3.2 14.6 - - - +
1707A GLY 3.1 0.4 - - - -
1708A GLU* 1.3 76.4 - - - +
1710A VAL* 1.3 62.3 + - + +
1712A GLU* 3.1 8.1 + - + +
1713A LEU* 2.9 51.8 + - + +
1722A VAL* 5.9 0.7 - - + -
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Residues in contact with VAL1710 (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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1695A LEU* 5.7 0.2 - - + -
1706A ALA 3.2 14.1 + - - +
1707A GLY* 4.0 6.1 - - - +
1709A LEU* 1.3 75.4 - - - +
1711A ALA* 1.3 54.3 + - - +
1713A LEU* 3.0 6.2 + - - +
1714A GLU* 2.7 66.4 + - + +
1720A THR* 4.1 23.6 - - + +
1722A VAL* 3.6 28.7 - - + +
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Residues in contact with ALA1711 (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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1707A GLY 3.6 10.5 + - - +
1708A GLU* 3.8 11.9 - - + +
1709A LEU 3.3 0.4 - - - -
1710A VAL* 1.3 80.1 - - - +
1712A GLU* 1.3 58.3 + - - +
1714A GLU* 4.0 8.5 - - - +
1715A ALA* 3.1 28.1 + - - +
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Residues in contact with GLU1712 (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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1683A ARG* 2.8 47.6 + - + +
1708A GLU* 2.9 31.9 + - - +
1709A LEU* 3.5 7.8 - - + +
1710A VAL 3.1 0.2 - - - -
1711A ALA* 1.3 77.2 - - - +
1713A LEU* 1.3 64.1 + - + +
1715A ALA* 3.4 8.3 + - + +
1716A LEU* 3.4 28.7 + - + +
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Residues in contact with LEU1713 (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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1682A ALA* 3.6 39.3 - - + +
1683A ARG* 3.6 20.4 - - + +
1686A ALA* 4.1 6.7 - - + +
1693A LEU* 4.1 7.9 - - + -
1695A LEU* 3.7 11.0 - - + -
1709A LEU* 2.9 36.1 + - + +
1710A VAL 3.6 1.3 - - - +
1712A GLU* 1.3 74.5 - - + +
1714A GLU* 1.3 63.2 + - - +
1715A ALA 3.1 2.0 - - - -
1716A LEU* 3.1 19.2 + - + +
1718A ALA* 3.3 18.4 + - - +
1720A THR* 3.2 38.6 - - + +
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Residues in contact with GLU1714 (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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1710A VAL* 2.7 46.6 + - + +
1711A ALA* 4.2 6.2 - - - +
1713A LEU* 1.3 70.9 - - - +
1715A ALA* 1.3 65.0 + - - +
1717A GLY* 3.1 14.0 + - - -
1718A ALA 3.4 17.9 + - - +
1719A ARG* 4.3 9.9 - - - +
1720A THR* 3.9 17.0 + - - +
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Residues in contact with ALA1715 (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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1711A ALA 3.1 21.5 + - - +
1712A GLU* 3.5 10.3 - - + +
1713A LEU 3.1 0.4 - - - -
1714A GLU* 1.3 76.4 - - - +
1716A LEU* 1.3 62.3 - - + +
1717A GLY* 3.1 1.3 + - - -
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Residues in contact with LEU1716 (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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1683A ARG* 3.8 25.8 - - + +
1686A ALA* 3.6 37.7 - - + +
1687A ARG* 4.1 21.9 - - + +
1712A GLU* 3.5 19.3 - - + +
1713A LEU* 3.1 13.5 + - + +
1715A ALA* 1.3 79.0 - - + +
1717A GLY* 1.3 59.2 + - - +
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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