Contacts of the helix formed by residues 1562 - 1572 (chain A) in PDB entry 5M5X
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 ILE1562 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1225A ILE* 4.6 16.1 - - + +
1544A ASN 4.9 4.5 - - - +
1546A VAL* 3.6 31.2 - - + -
1558A ALA 3.8 9.6 - - - +
1559A ARG 3.5 11.9 - - - +
1561A THR* 1.3 84.7 - - + +
1563A VAL* 1.3 63.0 + - - +
1564A ASN* 3.2 2.5 - - - -
1565A GLU* 3.0 10.4 + - + +
1566A ILE* 2.9 39.8 + - + +
1582A LEU 5.1 0.9 - - - +
1585A ILE* 5.3 4.3 - - + -
1586A ALA* 3.7 26.0 - - + +
1589A MET* 3.7 28.7 - - + -
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Residues in contact with VAL1563 (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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1559A ARG* 3.3 22.2 - - - +
1560A ASN* 4.2 17.0 - - + +
1561A THR 3.7 0.2 - - - -
1562A ILE* 1.3 77.0 - - - +
1564A ASN* 1.3 54.3 + - - +
1566A ILE* 3.3 9.4 - - - +
1567A ASN* 2.6 51.9 + - - +
1579A PHE* 4.7 11.0 - - + +
1582A LEU* 4.1 20.6 - - + +
1583A ASP* 5.0 5.6 - - + +
1586A ALA* 3.7 20.0 - - + -
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Residues in contact with ASN1564 (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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1542A THR* 4.6 14.5 + - - +
1560A ASN 4.0 14.6 + - - +
1561A THR* 2.8 28.2 + - - +
1563A VAL* 1.3 75.3 - - - +
1565A GLU* 1.3 71.7 + - - +
1567A ASN* 3.6 9.5 - - - +
1568A ASN* 2.8 38.8 + - - +
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Residues in contact with GLU1565 (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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1221A ARG* 2.6 38.3 + - - +
1225A ILE* 4.6 6.1 - - + -
1237A GLN* 4.7 5.6 - - - +
1542A THR* 5.7 1.9 + - - +
1543A SER 4.2 5.2 - - - +
1544A ASN* 3.2 33.0 - - - +
1561A THR 3.3 20.6 - - - +
1562A ILE* 3.0 11.3 + - + +
1564A ASN* 1.3 85.6 + - - +
1566A ILE* 1.3 61.5 + - - +
1567A ASN 3.1 1.1 - - - -
1568A ASN* 2.9 32.5 + - - +
1569A VAL* 3.1 14.4 + - - +
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Residues in contact with ILE1566 (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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1193A VAL* 3.9 23.1 - - + -
1221A ARG* 4.9 0.6 - - - +
1222A LEU* 3.7 24.9 - - + -
1225A ILE* 5.3 5.7 - - + +
1226A VAL* 5.8 3.4 - - + -
1562A ILE* 2.9 29.1 + - + +
1563A VAL* 3.3 16.8 - - - +
1565A GLU* 1.3 76.1 - - - +
1567A ASN* 1.3 58.5 + - - +
1569A VAL* 3.2 17.3 - - - +
1570A PHE* 3.4 23.1 - - + -
1582A LEU* 3.6 31.4 - - + +
1585A ILE* 4.5 15.9 - - + -
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Residues in contact with ASN1567 (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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1563A VAL* 2.6 38.1 + - - +
1564A ASN* 3.6 10.4 - - - +
1565A GLU 3.1 0.2 - - - -
1566A ILE* 1.3 76.5 - - - +
1568A ASN* 1.3 53.2 + - - +
1570A PHE* 3.4 3.2 + - - +
1571A SER* 2.6 45.5 + - - +
1577A VAL* 4.6 9.5 - - - +
1579A PHE* 3.3 41.6 - - - -
1582A LEU* 3.2 17.4 - - - +
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Residues in contact with ASN1568 (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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1217A LEU* 5.2 0.7 - - + -
1221A ARG* 5.8 1.1 - - - +
1564A ASN* 2.8 31.4 + - - +
1565A GLU* 2.9 24.9 + - - +
1567A ASN* 1.3 75.1 - - - +
1569A VAL* 1.3 66.5 + - - +
1571A SER* 3.7 5.7 - - - -
1572A ARG* 3.0 36.4 + - + +
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Residues in contact with VAL1569 (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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1217A LEU* 3.8 18.5 - - + +
1218A GLY* 3.9 29.4 - - - +
1221A ARG* 4.8 11.4 - - + +
1222A LEU* 4.4 16.8 - - + +
1565A GLU 3.1 12.6 + - - +
1566A ILE* 3.2 22.4 - - - +
1568A ASN* 1.3 77.0 - - - +
1570A PHE* 1.3 74.5 + - + +
1572A ARG* 3.7 3.8 + - - +
1573A TYR* 3.1 45.5 - - + -
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Residues in contact with PHE1570 (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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1192A SER 5.5 0.2 - - - -
1193A VAL* 3.8 44.9 - - + -
1196A PRO* 4.6 14.8 - - + -
1197A SER* 5.3 8.1 - - - -
1222A LEU* 4.6 12.8 - - + -
1566A ILE* 3.4 29.4 + - + +
1567A ASN* 3.4 4.4 + - - +
1568A ASN 3.2 0.4 - - - -
1569A VAL* 1.3 89.3 - - + +
1571A SER* 1.3 64.3 + - - +
1573A TYR* 3.3 15.1 + + - -
1575A ILE* 2.8 48.8 + - + +
1577A VAL* 3.6 31.9 - - + -
1582A LEU* 4.5 2.5 - - + -
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Residues in contact with SER1571 (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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1567A ASN* 2.6 36.1 + - - +
1568A ASN* 3.2 8.2 + - - -
1570A PHE* 1.3 69.2 - - - +
1572A ARG* 1.3 57.9 + - - +
1573A TYR 3.1 9.5 + - - -
1574A ALA* 3.5 10.9 + - - -
1575A ILE 4.4 4.5 - - - -
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Residues in contact with ARG1572 (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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1205A PHE* 3.3 42.6 + - + -
1214A ASN* 3.3 39.6 + - - +
1215A VAL* 4.5 8.1 - - - +
1217A LEU* 3.5 39.7 - - + +
1568A ASN* 3.0 26.1 + - + +
1569A VAL 4.1 5.4 - - - +
1570A PHE 3.3 0.8 - - - -
1571A SER* 1.3 77.0 - - - +
1573A TYR* 1.3 65.7 + - - +
1574A ALA 3.6 0.4 - - - -
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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