Contacts of the strand formed by residues 1710 - 1719 (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 ALA1710 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1575D LEU* 5.1 5.4 - - - +
1579D TYR* 3.9 4.7 - - - +
1615D GLY* 4.6 6.6 - - - -
1616D PHE* 3.9 16.7 + - + +
1634D PHE* 3.9 22.0 - - + -
1660D VAL* 3.7 20.0 - - + -
1661D ARG 3.2 6.3 - - - +
1662D VAL* 4.0 5.6 - - + -
1704D ALA* 5.5 1.1 - - + -
1706D TYR 4.8 0.6 + - - -
1707D ASP 4.8 3.2 + - - +
1708D TYR 3.4 3.6 - - - -
1709D GLN* 1.3 81.3 + - + +
1711D TYR* 1.3 62.1 + - - +
1712D PRO* 3.9 6.3 - - - +
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Residues in contact with TYR1711 (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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4D GOL 2.7 23.8 + - - -
1570D ILE* 2.6 30.6 + - + -
1572D ASN* 2.8 21.5 + - + +
1575D LEU* 3.9 24.0 - - + -
1576D TRP* 3.5 52.9 - + + -
1579D TYR* 3.8 23.9 - - + -
1660D VAL* 3.3 3.2 - - - +
1661D ARG* 2.9 35.1 + - + +
1710D ALA* 1.3 73.6 - - - +
1712D PRO* 1.4 65.0 - - + +
1713D GLU* 2.9 31.1 + - + -
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Residues in contact with PRO1712 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1570D ILE* 3.5 27.3 - - + +
1575D LEU* 3.9 18.2 - - + -
1611D VAL* 3.6 43.7 - - + +
1615D GLY* 4.5 3.4 - - - -
1616D PHE* 3.9 7.6 - - + -
1658D TYR* 3.6 19.1 - - + -
1659D TYR 4.5 0.2 - - - -
1660D VAL* 4.1 10.5 - - + -
1710D ALA 3.9 4.7 - - - +
1711D TYR* 1.4 86.3 - - + +
1713D GLU* 1.3 65.3 + - - +
1714D TYR 3.5 2.0 + - - -
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Residues in contact with GLU1713 (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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4D GOL 4.2 15.8 + - - +
1547D GLU* 4.7 2.3 - - - +
1569D ARG* 3.4 12.7 - - + +
1570D ILE 2.7 29.3 + - - -
1576D TRP* 5.2 6.7 - - - -
1598D GLN* 3.9 4.2 + - - -
1659D TYR 3.8 7.7 + - - +
1661D ARG* 2.9 42.6 + - + +
1711D TYR* 2.9 27.9 + - + +
1712D PRO* 1.3 72.6 - - - +
1714D TYR* 1.3 93.1 + - + +
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Residues in contact with TYR1714 (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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1541D LEU* 3.8 24.2 - - + -
1547D GLU* 2.3 44.4 + - + +
1551D VAL* 3.6 30.3 - - + -
1567D ILE* 4.3 10.5 - - + -
1568D GLU 3.2 13.5 - - - +
1569D ARG* 4.2 10.3 - - + -
1570D ILE* 3.9 3.8 - - - -
1598D GLN* 4.5 8.3 - - - -
1658D TYR* 3.3 9.7 - - - -
1659D TYR* 3.0 46.7 + + + +
1713D GLU* 1.3 111.7 + - + +
1715D LEU* 1.3 60.3 + - - +
1716D ILE* 5.3 0.2 - - + -
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Residues in contact with LEU1715 (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* 6.0 2.2 - - + -
1566D LYS 3.7 1.2 - - - +
1567D ILE* 3.2 5.5 - - - -
1568D GLU* 2.8 60.6 + - - +
1570D ILE* 3.7 17.6 - - + +
1608D VAL* 3.8 29.8 - - + -
1612D ASN* 5.2 1.6 - - - +
1656D HIS* 4.3 14.4 - - + -
1657D VAL 3.9 15.7 - - - +
1658D TYR* 3.7 34.3 - - + +
1714D TYR* 1.3 73.4 - - - +
1716D ILE* 1.3 65.1 + - - +
1717D THR* 3.8 12.9 + - - +
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Residues in contact with ILE1716 (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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1551D VAL* 3.7 31.9 - - + -
1555D PHE* 3.6 29.6 - - + -
1564D ILE* 4.2 31.9 - - + -
1566D LYS 3.6 2.9 - - - +
1567D ILE* 4.3 7.2 - - + -
1600D PHE* 3.8 18.6 - - + -
1656D HIS* 3.7 2.8 - - - -
1657D VAL* 2.7 43.8 + - + +
1659D TYR* 4.6 6.7 - - + -
1715D LEU* 1.3 75.9 - - - +
1717D THR* 1.3 60.9 - - - +
1718D PHE* 3.6 21.1 - - + -
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Residues in contact with THR1717 (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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1564D ILE* 3.7 1.0 - - - -
1565D GLU* 2.7 35.0 + - + +
1566D LYS* 2.8 50.1 + - + +
1568D GLU* 4.3 1.9 + - - -
1654D ARG* 4.2 24.5 - - + -
1655D LYS 3.5 9.6 - - - +
1656D HIS* 3.7 27.6 - - - +
1715D LEU* 3.8 9.4 + - - +
1716D ILE* 1.3 71.8 - - - +
1718D PHE* 1.3 59.0 + - - +
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Residues in contact with PHE1718 (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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1555D PHE* 3.8 17.5 - + + -
1562D PHE* 3.7 30.7 - + + -
1563D ARG 3.3 15.9 - - - +
1564D ILE* 3.7 14.6 - - + -
1565D GLU* 3.9 5.4 - - - +
1642D ALA* 4.3 6.3 - - + -
1647D SER* 4.2 0.7 - - - -
1654D ARG* 3.7 3.3 - - - +
1655D LYS* 2.9 75.6 + - + +
1657D VAL* 3.4 41.5 - - + -
1716D ILE* 3.6 17.9 - - + -
1717D THR* 1.3 76.6 - - - +
1719D ARG* 1.3 64.9 + - - +
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Residues in contact with ARG1719 (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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1562D PHE* 3.6 9.4 - - - -
1563D ARG* 2.8 69.6 + - + +
1565D GLU* 2.9 40.0 + - + -
1652D ASN* 3.1 27.9 + - - +
1653D GLY* 3.6 17.4 + - - +
1654D ARG* 3.6 18.7 - - - +
1655D LYS* 5.0 2.2 - - - -
1718D PHE* 1.3 77.9 - - - +
1720D LYS* 1.3 65.0 + - - +
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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