Contacts of the helix formed by residues 1511 - 1520 (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 GLY1511 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1509A ARG* 3.3 3.6 - - - +
1510A CYS* 1.3 94.9 - - - +
1512A ARG* 1.3 64.2 + - - -
1513A ASP* 3.4 2.5 - - - -
1514A GLU 3.9 1.6 + - - -
1515A LEU* 3.6 14.2 + - - +
1554A SER* 3.6 16.8 + - - -
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Residues in contact with ARG1512 (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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1511A GLY* 1.3 70.8 - - - -
1513A ASP* 1.3 77.0 + - - +
1515A LEU 3.3 0.5 + - - -
1516A ALA* 2.9 32.1 + - - +
1554A SER* 3.6 21.8 + - - +
1557A GLN* 3.4 57.5 + - + +
1558A ALA* 3.7 6.4 - - - +
1561A SER* 4.4 10.1 + - - -
1762A ASP* 2.8 36.0 + - - +
1765A THR* 6.4 0.9 - - - +
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Residues in contact with ASP1513 (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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1511A GLY* 3.4 0.9 - - - -
1512A ARG* 1.3 90.8 + - - +
1514A GLU* 1.3 62.7 + - - +
1516A ALA* 3.2 7.7 + - - +
1517A GLU* 3.2 22.0 + - - +
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Residues in contact with GLU1514 (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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1507A ASP* 4.0 15.9 - - - +
1510A CYS* 3.6 36.9 + - + +
1511A GLY 3.9 8.3 + - - +
1512A ARG 3.3 0.4 - - - -
1513A ASP* 1.3 79.8 - - - +
1515A LEU* 1.3 63.3 + - - +
1517A GLU* 3.3 6.7 + - - +
1518A ARG* 3.3 48.6 + - - +
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Residues in contact with LEU1515 (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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1504A LEU* 5.0 10.8 - - + -
1506A VAL* 4.0 31.6 - - + -
1510A CYS* 3.7 13.7 - - - -
1511A GLY 3.6 7.5 + - - +
1512A ARG 3.3 3.7 + - - +
1513A ASP 3.3 0.6 - - - -
1514A GLU* 1.3 77.1 - - + +
1516A ALA* 1.3 57.4 + - - +
1518A ARG* 3.4 22.2 + - + +
1519A LEU* 2.9 37.6 + - + +
1551A ASP* 4.5 2.2 - - - +
1554A SER* 3.8 14.8 - - - -
1555A LEU* 3.7 37.7 - - + +
1558A ALA* 3.5 15.3 - - + -
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Residues in contact with ALA1516 (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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1512A ARG 2.9 17.9 + - - +
1513A ASP* 3.5 9.0 - - - +
1515A LEU* 1.3 77.1 - - - +
1517A GLU* 1.3 62.4 + - - +
1519A LEU* 3.5 2.8 + - - +
1520A ARG* 3.3 45.3 + - - +
1558A ALA* 3.5 22.1 - - + +
1561A SER* 4.4 12.6 - - - -
1562A ALA* 4.0 1.4 - - - +
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Residues in contact with GLU1517 (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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1513A ASP 3.2 9.4 + - - +
1514A GLU* 3.7 9.0 - - - +
1516A ALA* 1.3 79.8 - - - +
1518A ARG* 1.3 65.2 + - + +
1520A ARG* 3.1 28.9 + - - +
1521A SER* 3.3 22.3 + - - +
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Residues in contact with ARG1518 (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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1504A LEU* 3.9 28.0 - - + +
1505A VAL* 2.7 44.2 + - - +
1506A VAL* 4.3 3.6 - - - +
1507A ASP* 4.8 3.2 + - - +
1514A GLU* 3.3 40.0 + - + +
1515A LEU* 3.4 23.1 + - - +
1517A GLU* 1.3 80.1 - - + +
1519A LEU* 1.3 63.0 + - + +
1521A SER* 3.2 19.8 + - - -
1522A VAL* 3.6 8.1 + - - +
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Residues in contact with LEU1519 (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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1475A LEU* 3.8 26.7 - - + -
1504A LEU* 4.3 15.9 - - + -
1515A LEU* 2.9 21.5 + - + +
1516A ALA 4.0 0.2 - - - +
1517A GLU 3.3 0.2 - - - -
1518A ARG* 1.3 76.5 - - + +
1520A ARG* 1.3 57.3 + - - +
1521A SER 3.1 3.1 - - - -
1522A VAL* 3.3 19.9 - - + +
1523A GLY 4.5 1.6 + - - +
1528A VAL* 5.6 1.6 - - + -
1555A LEU* 4.0 9.0 - - + -
1558A ALA* 3.9 8.7 - - + -
1559A MET* 3.7 43.5 - - + +
1562A ALA* 3.7 16.4 - - + -
1564A LEU* 3.5 32.4 - - + +
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Residues in contact with ARG1520 (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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1516A ALA* 3.3 32.3 + - - +
1517A GLU* 3.1 24.1 + - - +
1519A LEU* 1.3 77.8 - - - +
1521A SER* 1.3 61.0 + - - +
1523A GLY* 4.7 3.6 + - - -
1561A SER* 3.2 35.3 + - - -
1562A ALA* 3.8 21.1 - - + +
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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