Contacts of the helix formed by residues 1570 - 1577 (chain A) in PDB entry 4CRU
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 ALA1570 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1566A PRO 4.1 1.4 + - - -
1567A LYS 3.3 16.6 + - - +
1568A GLN 3.1 2.2 - - - -
1569A LEU* 1.3 77.4 - - - +
1571A VAL* 1.3 63.3 + - - +
1573A GLU* 3.3 15.2 + - - +
1574A GLU* 3.0 23.0 + - - +
30B SER* 3.7 8.5 - - - +
31B SER* 3.7 27.8 - - - +
32B PRO* 4.6 4.0 - - + +
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Residues in contact with VAL1571 (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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1568A GLN 4.0 4.0 - - - +
1570A ALA* 1.3 76.6 - - - +
1572A TYR* 1.3 81.7 + - + +
1574A GLU* 3.2 6.1 + - - -
1575A PHE* 3.3 3.6 + - + -
30B SER* 3.0 32.5 + - - +
35B ARG* 3.9 5.2 - - - +
61B GLY* 3.8 24.0 - - - +
64B ALA* 3.8 9.0 - - + -
65B ALA* 3.5 34.3 - - + +
68B GLN* 2.9 37.0 + - - +
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Residues in contact with TYR1572 (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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1423A ILE* 3.7 14.6 - - - +
1424A VAL* 4.0 10.1 - - + +
1427A ASP* 2.6 34.0 + - - +
1428A PHE* 4.1 7.6 - + - -
1440A ALA* 3.5 44.0 - - + -
1443A HIS* 4.1 9.5 - - - +
1444A MET* 3.9 21.5 - - + -
1569A LEU* 2.9 16.3 + - + +
1571A VAL* 1.3 88.2 - - + +
1573A GLU* 1.3 66.4 + - - +
1575A PHE* 3.2 31.7 + + - +
1576A ALA* 3.5 4.3 + - - +
60B PHE* 3.7 30.1 - + - -
61B GLY* 4.6 0.2 - - - -
64B ALA* 3.9 6.0 - - + +
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Residues in contact with GLU1573 (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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1443A HIS* 6.3 0.2 - - - -
1566A PRO* 4.2 7.5 - - - +
1569A LEU* 3.0 34.7 + - + +
1570A ALA* 3.6 13.5 - - - +
1572A TYR* 1.3 78.8 - - + +
1574A GLU* 1.3 61.1 + - - +
1576A ALA* 3.1 11.0 + - - +
1577A ARG* 3.1 20.3 + - - +
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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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1570A ALA 3.0 11.7 + - - +
1571A VAL 3.2 9.4 + - - +
1573A GLU* 1.3 73.6 - - - +
1575A PHE* 1.3 65.6 + - - +
1577A ARG* 2.8 48.4 + - - +
1578A ASN* 3.0 41.5 + - + +
32B PRO* 3.8 28.7 - - + +
35B ARG* 5.3 0.2 - - - +
68B GLN* 3.2 26.7 - - + +
72B ASN* 4.7 2.9 + - - +
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Residues in contact with PHE1575 (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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1443A HIS 3.6 18.7 - - - +
1444A MET* 3.6 38.4 - - + -
1447A ASN* 3.0 44.2 + - + +
1448A LEU* 3.7 21.3 - - + -
1571A VAL* 3.3 15.5 + - + -
1572A TYR* 3.2 18.7 + + - +
1574A GLU* 1.3 80.0 - - - +
1576A ALA* 1.3 59.8 + - - +
1578A ASN 3.9 0.3 - - - +
1579A VAL* 3.7 9.7 - - - +
64B ALA* 3.5 37.7 - - + -
67B LEU 5.1 0.2 - - - -
68B GLN* 3.3 32.7 - - + +
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Residues in contact with ALA1576 (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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1443A HIS* 3.6 42.5 - - + +
1572A TYR 3.5 2.3 + - - +
1573A GLU* 3.1 14.0 + - - +
1574A GLU 3.1 0.4 - - - -
1575A PHE* 1.3 82.1 - - - +
1577A ARG* 1.3 60.4 + - - +
1579A VAL* 4.1 10.4 - - - +
1585A THR* 4.3 8.4 + - - +
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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 GLU 3.1 11.9 + - - +
1574A GLU* 2.8 45.7 + - - +
1576A ALA* 1.3 77.3 - - - +
1578A ASN* 1.3 75.2 + - - +
1579A VAL* 3.9 1.9 + - - +
1584A PRO* 3.4 27.7 - - - +
1585A THR* 3.2 53.9 + - - +
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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