Contacts of the strand formed by residues 1536 - 1541 (chain B) in PDB entry 3SE2
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 PHE1536 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1534B GLN 4.0 1.8 - - - -
1535B ASN* 1.3 79.5 - - - +
1537B CYS* 1.3 67.4 + - - +
1538B VAL* 3.9 18.2 - - + -
1570B ILE* 4.6 4.0 - - + -
1571B GLN 3.2 13.9 - - - +
1572B ASN* 3.8 13.5 - - + +
1573B PRO* 5.2 0.7 - - - -
1609B PRO* 4.1 8.1 - - + -
1612B ASN* 3.4 50.3 - - + +
1613B ARG* 3.9 30.5 - - + -
1D CL 4.1 11.0 - - + -
1537D CYS* 3.2 2.6 - - - +
1538D VAL* 2.8 63.4 + - + +
1568D GLU* 5.1 0.9 - - - -
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Residues in contact with CYS1537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1536B PHE* 1.3 76.3 - - - +
1538B VAL* 1.3 64.4 + - - +
1539B VAL* 4.0 6.3 - - + -
1569B ARG 3.7 1.0 - - - +
1570B ILE* 3.8 2.1 - - - -
1571B GLN* 2.8 53.9 + - + +
1536D PHE 3.2 6.3 - - - +
1537D CYS* 2.1 46.4 - - - -
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Residues in contact with VAL1538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1536B PHE* 3.9 17.9 - - + -
1537B CYS* 1.3 78.3 - - - +
1539B VAL* 1.3 60.4 + - - +
1568B GLU* 3.5 42.2 - - + +
1569B ARG 3.6 2.7 - - - -
1570B ILE* 4.1 10.5 - - + -
1612B ASN* 4.0 12.3 - - - +
1715B LEU* 6.2 0.7 - - + -
1535D ASN* 3.4 19.5 - - - +
1536D PHE* 2.8 46.7 + - + -
1613D ARG* 3.4 10.4 + - - +
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Residues in contact with VAL1539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1537B CYS* 4.9 4.7 - - + -
1538B VAL* 1.3 77.0 - - - +
1540B GLU* 1.3 73.4 + - - +
1541B LEU* 3.6 3.7 + - + +
1568B GLU* 3.3 2.6 - - - -
1569B ARG* 2.8 53.4 + - + +
1571B GLN* 3.0 38.6 - - + +
1533D GLN* 5.2 0.4 - - - +
1535D ASN* 3.7 19.7 - - + +
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Residues in contact with GLU1540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1539B VAL* 1.3 80.8 - - - +
1541B LEU* 1.3 73.8 + - - +
1542B LEU* 3.9 3.9 + - + +
1543B PRO* 5.7 1.4 - - - +
1565B GLU 4.4 3.5 - - - +
1566B LYS* 3.5 30.9 - - + +
1567B ILE 3.7 9.0 - - - +
1568B GLU* 3.8 6.3 - - + -
1618C ARG* 4.5 8.1 + - - -
1533D GLN* 3.3 38.2 + - - +
1535D ASN* 2.9 19.1 + - - +
1613D ARG* 3.9 25.7 + - - +
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Residues in contact with LEU1541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1539B VAL* 3.6 3.8 + - + +
1540B GLU* 1.3 83.2 - - - +
1542B LEU* 1.3 63.8 + - - +
1543B PRO* 3.7 3.1 - - - +
1545B ASP* 4.0 12.6 - - - +
1547B GLU* 3.8 11.9 - - - +
1548B TYR* 3.5 43.1 - - + +
1567B ILE* 2.8 41.7 + - + +
1569B ARG* 3.1 41.3 - - + +
1714B TYR* 3.8 22.9 - - + -
1618C ARG* 5.0 0.5 + - - -
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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