Contacts of the helix formed by residues 1607 - 1615 (chain D) 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 SER1607 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1603D THR* 3.4 26.8 + - - -
1604D ASP* 3.0 18.6 + - - -
1606D GLY* 1.3 75.6 - - - +
1608D VAL* 1.3 59.5 + - - +
1609D PRO 3.4 1.3 - - - -
1610D HIS* 2.9 11.3 + - - +
1611D VAL* 2.8 29.7 + - - +
1620D TYR* 3.7 22.5 - - - -
1621D ALA* 5.0 8.8 - - - +
1622D GLY* 5.0 1.0 + - - -
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Residues in contact with VAL1608 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1609B PRO* 3.9 19.7 - - + -
1603D THR* 4.6 0.7 - - + -
1604D ASP 4.0 8.7 - - - +
1605D ALA* 3.1 20.2 + - - +
1607D SER* 1.3 76.3 - - - +
1609D PRO* 1.3 62.4 - - + +
1612D ASN* 2.8 53.8 + - - +
1656D HIS* 4.4 17.3 - - + -
1658D TYR* 3.4 24.0 - - + +
1715D LEU* 3.8 24.0 - - + -
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Residues in contact with PRO1609 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1566B LYS* 5.3 7.7 + - - +
1605B ALA* 3.8 19.7 - - + +
1608B VAL* 4.0 23.1 - - + -
1609B PRO* 4.1 8.3 - - + -
1656B HIS* 6.2 4.0 - - + +
1715B LEU* 6.2 1.1 - - + -
1D CL 4.2 13.0 - - + -
1536D PHE* 4.7 5.5 - - + -
1605D ALA 3.6 6.1 - - - +
1606D GLY 3.6 12.3 - - - +
1607D SER 3.6 2.7 - - - -
1608D VAL* 1.3 94.3 - - + +
1610D HIS* 1.3 61.8 + - - +
1612D ASN* 4.2 2.4 - - + +
1613D ARG* 3.5 19.6 + - - +
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Residues in contact with HIS1610 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1652B ASN* 4.9 6.7 + - - -
1654B ARG* 5.3 9.2 + - - -
1606D GLY 4.8 2.4 + - - +
1607D SER* 2.9 16.6 + - - +
1609D PRO* 1.3 79.7 - - - +
1611D VAL* 1.3 59.7 + - - +
1613D ARG 3.1 2.6 + - - -
1614D ASN* 2.8 58.8 + - - +
1615D GLY 3.8 12.8 - - - -
1617D ASN* 2.8 23.4 + - - -
1619D SER* 3.1 30.2 + - - -
1620D TYR* 3.6 25.5 + + + -
1621D ALA 5.8 0.2 - - - -
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Residues in contact with VAL1611 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1575D LEU* 4.3 0.5 - - - +
1603D THR* 5.4 0.4 - - + -
1607D SER* 2.8 17.8 + - - +
1610D HIS* 1.3 75.3 - - - +
1612D ASN* 1.3 64.4 + - - +
1615D GLY* 2.9 31.4 + - - +
1616D PHE* 3.7 31.9 - - + -
1620D TYR* 3.9 25.8 - - + -
1658D TYR* 3.5 33.2 - - + +
1712D PRO* 3.6 26.6 - - + +
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Residues in contact with ASN1612 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D CL 3.7 15.4 - - - +
1536D PHE* 3.7 35.9 - - + +
1538D VAL* 4.3 8.1 - - - +
1570D ILE* 3.6 28.8 - - + +
1572D ASN* 3.0 21.1 + - - +
1575D LEU* 4.5 2.1 - - - +
1608D VAL* 2.8 39.3 + - - +
1609D PRO 4.2 0.9 - - - +
1611D VAL* 1.3 76.6 - - - +
1613D ARG* 1.3 57.0 + - - +
1658D TYR* 2.6 32.2 + - - -
1712D PRO* 5.0 0.7 - - - -
1715D LEU* 5.2 1.4 - - - +
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Residues in contact with ARG1613 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1538B VAL* 3.4 23.0 + - - +
1540B GLU* 3.9 20.9 + - - +
1566B LYS* 3.7 14.3 - - - +
1568B GLU* 3.0 29.7 + - - -
1533D GLN 2.7 32.1 + - - +
1534D GLN* 2.9 38.3 + - + +
1535D ASN* 3.3 19.9 + - - +
1536D PHE* 4.1 10.3 - - + -
1572D ASN* 2.9 20.7 + - - +
1575D LEU* 4.1 1.6 - - - +
1609D PRO 3.5 10.0 + - - +
1610D HIS 3.1 6.6 + - - +
1611D VAL 3.1 0.4 - - - -
1612D ASN* 1.3 79.8 - - - +
1614D ASN* 1.3 79.0 + - - +
1615D GLY 3.7 0.7 - - - -
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Residues in contact with ASN1614 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1566B LYS* 6.0 0.2 - - - +
1654B ARG* 5.6 4.2 - - - +
1534D GLN* 3.7 12.0 + - - +
1575D LEU* 3.9 13.6 - - - +
1610D HIS* 2.8 51.3 + - - +
1613D ARG* 1.3 99.0 - - - +
1615D GLY* 1.3 62.2 + - - +
1617D ASN* 3.4 37.7 + - - +
1707D ASP 4.4 3.1 - - - +
1708D TYR* 5.1 2.6 - - - -
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Residues in contact with GLY1615 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1575D LEU* 3.6 16.6 - - - +
1610D HIS* 3.8 11.4 - - - -
1611D VAL* 2.9 35.1 + - - +
1614D ASN* 1.3 80.5 - - - +
1616D PHE* 1.3 65.0 + - - -
1617D ASN 3.2 6.2 + - - -
1707D ASP 5.3 0.9 - - - -
1710D ALA 4.6 3.6 - - - -
1712D PRO* 4.5 4.3 - - - -
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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