Contacts of the helix formed by residues 1507 - 1521 (chain A) in PDB entry 4BHW
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 ASP1507 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1394A TYR* 2.4 44.7 + - + +
1436A TRP* 3.3 15.1 - - - +
1502A PRO 5.3 2.1 - - - +
1504A PHE* 3.2 28.4 + - + +
1505A GLU 3.1 4.2 + - - -
1506A GLY* 1.3 83.8 - - - +
1508A PHE* 1.3 71.2 + - - +
1509A TRP* 3.3 30.2 + - - +
1510A PRO* 3.5 14.8 - - + +
1511A ASN* 3.7 14.4 + - - -
1595A PHE* 4.3 3.3 - - - -
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Residues in contact with PHE1508 (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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1436A TRP* 3.4 37.1 - + + -
1507A ASP* 1.3 78.6 + - - +
1509A TRP* 1.3 79.1 + + - +
1511A ASN* 3.3 10.8 + - + +
1512A VAL* 3.3 49.0 + - + -
1591A HIS* 3.7 38.8 - + - -
1595A PHE* 3.3 32.5 - + + -
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Residues in contact with TRP1509 (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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1486A ILE* 3.4 39.1 - - + +
1501A LEU* 4.1 16.4 - - + -
1502A PRO 4.8 11.7 - - - +
1507A ASP* 3.3 22.4 + - - +
1508A PHE* 1.3 82.1 - + - +
1510A PRO* 1.3 72.9 - - + +
1511A ASN 3.1 0.2 + - - -
1512A VAL* 3.2 20.5 + - + +
1513A LEU* 2.9 40.2 + - + +
1584A LEU* 4.6 8.1 - - + -
1587A THR* 3.8 30.5 - - + -
1588A MET* 3.5 35.9 - - + -
1591A HIS* 5.0 0.7 - - + -
1595A PHE* 3.4 40.0 - + - -
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Residues in contact with PRO1510 (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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1333A VAL* 6.0 0.2 - - + -
1336A LYS* 4.0 16.0 - - - +
1339A MET* 5.4 0.5 - - - +
1503A TYR* 3.6 51.5 + - + +
1504A PHE 3.7 21.5 - - - +
1506A GLY 5.7 0.7 - - - +
1507A ASP* 3.5 23.6 - - + +
1509A TRP* 1.3 92.2 - - + +
1511A ASN* 1.3 61.1 + - - +
1513A LEU* 3.5 5.1 + - + +
1514A GLU* 3.3 26.3 + - - +
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Residues in contact with ASN1511 (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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700A 01K 6.2 1.6 - - - +
1336A LYS* 3.6 26.2 + - - +
1506A GLY* 5.4 3.2 + - - -
1507A ASP 3.7 18.2 + - - -
1508A PHE* 3.3 9.3 + - + +
1509A TRP 3.1 0.8 - - - -
1510A PRO* 1.3 75.5 - - - +
1512A VAL* 1.3 64.8 + - - +
1514A GLU* 3.1 17.8 + - - +
1515A GLU* 3.3 22.5 + - - +
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Residues in contact with VAL1512 (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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1508A PHE* 3.3 28.2 + - + +
1509A TRP* 3.2 43.9 + - + +
1511A ASN* 1.3 79.1 - - - +
1513A LEU* 1.3 66.3 + - + +
1515A GLU* 3.2 18.1 + - + +
1516A SER* 2.8 36.4 + - - +
1587A THR* 3.8 20.9 - - + -
1591A HIS* 5.9 0.4 - - - +
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Residues in contact with LEU1513 (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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1339A MET* 4.0 24.7 - - + -
1498A ALA* 3.6 40.8 - - + +
1501A LEU* 4.6 13.9 - - + +
1503A TYR* 5.5 4.7 - - + -
1509A TRP* 2.9 28.3 + - + +
1510A PRO* 3.8 7.6 - - + +
1512A VAL* 1.3 83.2 - - + +
1514A GLU* 1.3 58.6 + - - +
1516A SER* 3.5 16.2 - - - +
1517A ILE* 3.0 39.1 + - + +
1524A GLY 6.3 0.2 - - - -
1584A LEU* 4.0 18.4 - - + -
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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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1336A LYS* 3.4 30.3 - - + +
1337A PRO* 3.6 10.7 - - - +
1338A GLY* 2.8 24.4 + - - -
1339A MET* 2.9 33.6 + - - +
1503A TYR* 4.8 0.2 + - - -
1510A PRO 3.3 16.0 + - - +
1511A ASN* 3.1 9.5 + - - +
1513A LEU* 1.3 76.2 - - - +
1515A GLU* 1.3 64.6 + - + +
1517A ILE* 4.1 4.1 - - - +
1518A LYS* 3.1 26.8 + - - +
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Residues in contact with GLU1515 (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 ASN* 3.5 22.8 - - - +
1512A VAL* 3.2 18.7 + - + +
1514A GLU* 1.3 75.2 - - + +
1516A SER* 1.3 56.1 - - - +
1518A LYS* 3.3 6.1 + - - +
1519A GLU* 2.7 47.7 + - + +
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Residues in contact with SER1516 (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 VAL* 2.8 34.3 + - - +
1513A LEU* 3.5 20.2 - - - +
1515A GLU* 1.3 71.6 - - - +
1517A ILE* 1.3 58.6 + - - +
1519A GLU* 4.1 4.8 + - - +
1520A SER* 2.9 35.5 + - - -
1523A SER 4.6 2.0 - - - -
1524A GLY* 6.2 2.5 - - - -
1583A LYS* 5.2 16.0 + - - +
1584A LEU* 6.0 0.7 - - - +
1587A THR* 4.6 9.7 + - - -
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Residues in contact with ILE1517 (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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1338A GLY* 3.8 13.0 - - - +
1339A MET* 3.6 54.3 - - + +
1342A ARG* 4.3 13.0 - - + -
1343A PHE* 4.9 0.2 - - + -
1513A LEU* 3.0 19.6 + - + +
1514A GLU* 4.1 2.9 - - - +
1516A SER* 1.3 71.9 - - - +
1518A LYS* 1.3 65.7 + - - +
1521A GLY 3.2 2.4 + - - -
1522A GLY* 2.9 44.6 + - - +
1523A SER 3.4 23.3 - - - +
1524A GLY* 4.6 5.4 - - - -
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Residues in contact with LYS1518 (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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1514A GLU 3.1 18.6 + - - +
1515A GLU* 3.6 5.8 - - - +
1517A ILE* 1.3 75.7 - - - +
1519A GLU* 1.3 63.7 + - - +
1521A GLY* 3.0 16.6 + - - -
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Residues in contact with GLU1519 (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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1515A GLU* 2.7 29.2 + - + +
1516A SER* 4.1 4.0 + - - +
1518A LYS* 1.3 72.7 - - - +
1520A SER* 1.3 58.7 + - - +
1521A GLY 3.7 0.2 + - - -
1583A LYS* 6.3 3.4 - - + -
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Residues in contact with SER1520 (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 SER 2.9 22.5 + - - -
1517A ILE 3.7 0.7 + - - -
1519A GLU* 1.3 76.8 - - - +
1521A GLY* 1.3 59.1 + - - +
1522A GLY 3.7 0.2 + - - -
1523A SER* 3.3 32.5 + - - -
1582A GLN* 4.1 27.5 - - - +
1583A LYS* 5.3 6.3 - - - -
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Residues in contact with GLY1521 (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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1517A ILE 3.2 1.1 + - - -
1518A LYS 3.0 13.0 + - - -
1519A GLU 3.4 1.0 + - - -
1520A SER* 1.3 79.8 - - - +
1522A GLY* 1.3 56.8 + - - +
1523A SER 3.8 0.2 - - - -
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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