Contacts of the helix formed by residues 1571 - 1578 (chain A) in PDB entry 3CLY
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 ASN1571 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1488A GLY* 5.3 0.6 - - - -
1570A GLY* 1.3 75.6 - - - -
1572A LEU* 1.3 63.3 + - - +
1573A ARG* 2.9 12.0 + - - +
1574A GLU* 2.8 52.7 + - - +
1575A TYR* 3.0 20.9 + - - +
1629A ALA 3.9 1.8 - - - +
1630A ARG* 3.6 26.7 - - - +
1632A VAL 3.0 13.5 - - - +
1633A LEU* 4.1 3.3 - - + +
1803A ACP 3.0 36.8 + - - +
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Residues in contact with LEU1572 (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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1570A GLY 4.0 0.4 + - - -
1571A ASN* 1.3 72.6 - - - +
1573A ARG* 1.3 56.9 + - - +
1575A TYR* 3.4 15.8 + - + +
1576A LEU* 2.9 60.4 + - + +
1606A CYS* 4.8 4.9 - - + -
1610A LEU* 4.0 13.0 - - + -
1629A ALA* 3.4 16.3 + - + +
1632A VAL* 2.7 31.4 + - + -
1634A VAL* 4.1 3.1 - - + +
1640A MET* 3.9 21.8 - - + -
1692A LEU* 4.0 13.7 - - + -
1696A ILE* 3.8 25.6 - - + -
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Residues in contact with ARG1573 (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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1571A ASN* 2.9 10.3 + - - +
1572A LEU* 1.3 77.4 - - - +
1574A GLU* 1.3 69.1 + - + +
1576A LEU* 3.9 1.3 - - - +
1577A ARG* 3.0 46.6 + - + +
1629A ALA* 3.8 18.3 + - + +
1630A ARG* 4.8 11.1 - - - +
1669A TRP* 4.0 18.6 - - - -
1695A GLU* 3.2 24.4 + - - -
1700A GLY* 3.8 29.4 + - - +
1701A GLY 3.7 13.3 + - - -
1702A SER* 4.1 15.7 + - - +
1703A PRO* 4.2 0.4 - - - +
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Residues in contact with GLU1574 (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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1488A GLY* 4.1 2.3 - - - -
1489A GLU* 3.2 54.1 + - - +
1490A GLY 4.8 0.9 + - - -
1569A LYS 5.2 2.5 - - - +
1570A GLY* 4.3 6.9 - - - -
1571A ASN* 2.8 45.0 + - - +
1573A ARG* 1.3 74.0 - - + +
1575A TYR* 1.3 63.6 + - - +
1577A ARG* 3.4 6.9 + - - +
1578A ALA* 3.1 25.8 + - - +
1803A ACP 4.6 2.3 + - - -
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Residues in contact with TYR1575 (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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1569A LYS* 3.8 19.2 + - + +
1571A ASN 3.0 17.6 + - - +
1572A LEU* 3.5 8.3 - - + +
1574A GLU* 1.3 79.3 - - - +
1576A LEU* 1.3 67.6 + - + +
1578A ALA 3.5 0.2 + - - -
1579A ARG* 2.8 77.4 + - - +
1598A MET* 4.1 32.1 - - + +
1606A CYS* 4.8 2.1 - - - -
1634A VAL* 3.8 37.0 - - + -
1638A ASN* 3.0 32.9 + - + +
1640A MET* 4.4 8.4 - - + +
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Residues in contact with LEU1576 (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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1572A LEU* 2.9 47.2 + - + +
1573A ARG* 4.0 1.8 - - - +
1575A TYR* 1.3 79.1 - - + +
1577A ARG* 1.3 66.4 + - - +
1579A ARG* 3.0 23.0 + - - +
1580A ARG* 3.6 5.5 + - - +
1598A MET* 3.5 37.5 - - + -
1603A LEU* 4.2 3.6 - - + -
1606A CYS* 5.0 1.8 - - - -
1629A ALA* 5.8 0.7 - - + -
1695A GLU 4.1 0.9 - - - +
1696A ILE* 3.7 32.8 - - + +
1699A LEU* 3.7 27.5 - - + +
1700A GLY* 3.8 13.0 - - - +
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Residues in contact with ARG1577 (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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1573A ARG* 3.0 38.4 + - - +
1574A GLU* 3.4 6.7 + - - +
1576A LEU* 1.3 76.0 - - - +
1578A ALA* 1.3 61.5 + - - +
1579A ARG 3.1 0.7 + - - -
1580A ARG* 3.6 39.9 + - - +
1699A LEU 3.7 15.3 - - - +
1700A GLY 3.1 24.1 + - - +
1701A GLY* 4.8 3.8 - - - -
1702A SER* 5.0 7.7 - - - +
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Residues in contact with ALA1578 (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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1574A GLU 3.1 17.1 + - - +
1575A TYR* 4.8 0.2 - - - -
1576A LEU 3.2 0.4 - - - -
1577A ARG* 1.3 77.0 - - - +
1579A ARG* 1.3 83.0 + - - +
1580A ARG 3.6 1.2 + - - -
1595A GLU* 3.8 18.5 - - - +
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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