Contacts of the strand formed by residues 1527 - 1531 (chain H) in PDB entry 6X34
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 MET1527 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1295H VAL* 5.7 3.6 - - + -
1452H TRP* 3.5 48.5 - - + -
1493H TYR* 5.1 15.7 - - + -
1519H LEU 3.7 4.7 - - - -
1520H VAL* 3.8 36.8 - - + +
1525H GLY 4.1 0.9 + - - +
1526H LEU* 1.3 70.0 - - - +
1528H THR* 1.3 59.7 + - - +
1529H PHE* 4.1 11.3 + - + -
1539H PHE* 3.3 22.9 - - - -
1540H PHE* 3.6 14.9 + - + +
1542H VAL* 4.1 23.6 - - + +
1546H THR* 5.5 9.6 - - + -
1548H LEU* 4.5 11.7 - - + -
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Residues in contact with THR1528 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1519H LEU* 2.8 47.7 + - - +
1520H VAL* 5.5 0.2 - - - +
1526H LEU* 3.3 20.6 - - + +
1527H MET* 1.3 73.4 - - - +
1529H PHE* 1.3 67.5 + - - +
1530H THR* 5.1 0.3 - - - -
1538H THR 4.0 5.4 - - - -
1539H PHE* 4.1 15.7 - - + -
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Residues in contact with PHE1529 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1450H VAL* 3.8 14.4 - - + -
1451H GLY* 3.7 23.3 - - - -
1452H TRP* 4.0 26.7 - + - -
1493H TYR* 4.8 7.4 - - + -
1494H MET* 4.1 12.6 - - - -
1495H VAL* 3.7 24.7 - - + -
1516H ILE* 6.5 0.4 - - + -
1517H GLY 3.7 5.2 - - - +
1518H CYS* 3.8 19.5 - - + +
1519H LEU 5.2 0.2 - - - -
1520H VAL* 5.7 0.9 - - + -
1527H MET* 4.1 11.4 - - + -
1528H THR* 1.3 82.0 + - - +
1530H THR* 1.3 62.2 + - - +
1535H GLU* 4.7 2.1 - - - +
1536H SER* 3.4 30.2 + - - -
1537H ASN 4.7 1.2 + - - -
1538H THR* 3.6 20.8 + - + +
1540H PHE* 5.7 8.7 - + - -
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Residues in contact with THR1530 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1434H TYR* 6.2 0.7 - - - -
1516H ILE* 3.3 8.4 - - - +
1517H GLY* 2.5 52.1 + - - +
1518H CYS* 4.2 3.1 - - - -
1519H LEU* 6.2 0.9 - - - -
1528H THR 5.1 0.9 - - - -
1529H PHE* 1.3 74.9 - - - +
1531H ALA* 1.3 61.3 + - - +
1534H LYS 3.7 10.8 - - - -
1535H GLU* 4.5 2.0 - - - +
1536H SER* 3.9 7.4 - - - +
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Residues in contact with ALA1531 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1500H PHE* 4.0 23.6 - - + +
1515H VAL 3.9 4.5 - - - -
1516H ILE* 4.2 10.0 - - + -
1517H GLY* 4.1 4.9 + - - -
1530H THR* 1.3 78.4 - - - +
1532H ASN* 1.3 62.8 + - - +
1533H GLY 3.0 8.7 + - - -
1534H LYS* 2.9 30.5 + - + +
1535H GLU 4.5 8.3 - - - +
1536H SER* 3.9 8.5 - - - +
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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