Contacts of the strand formed by residues 1514 - 1521 (chain D) 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 LEU1514 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1439D VAL* 3.5 33.7 + - + +
1445D PRO* 5.2 13.5 - - + -
1497D GLY 5.9 2.0 - - - +
1500D PHE* 6.6 0.2 - - + -
1501D VAL* 4.4 22.9 - - + +
1512D THR 3.6 4.8 + - - +
1513D ASP* 1.3 75.3 - - - +
1515D VAL* 1.3 64.5 + - - +
1516D ILE* 5.6 2.8 - - + +
1532D ASN* 5.6 5.2 - - + -
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Residues in contact with VAL1515 (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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1436D SER* 5.8 3.4 - - - -
1437D VAL 3.5 19.7 - - - +
1438D ARG* 3.8 26.9 - - + +
1439D VAL 4.4 1.8 - - - +
1513D ASP* 5.5 3.4 - - + -
1514D LEU* 1.3 79.6 - - - +
1516D ILE* 1.3 66.8 + - - +
1531D ALA 5.2 0.2 - - - -
1532D ASN* 3.3 36.1 + - + +
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Residues in contact with ILE1516 (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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1434D TYR* 5.6 0.2 - - - -
1435D TYR 4.2 0.2 - - - +
1436D SER* 3.5 25.0 - - - -
1437D VAL* 3.7 17.2 + - + -
1448D VAL* 5.8 3.6 - - + -
1450D VAL* 3.8 36.1 - - + +
1495D VAL* 5.1 13.7 - - + +
1497D GLY* 5.8 7.2 - - - -
1500D PHE* 4.3 22.2 - - + -
1514D LEU* 5.6 3.1 - - + +
1515D VAL* 1.3 80.4 - - - +
1517D GLY* 1.3 62.8 + - - +
1529D PHE* 6.6 0.4 - - + -
1530D THR 3.3 13.0 - - - +
1531D ALA* 4.2 10.8 - - - -
1532D ASN 4.8 0.7 - - - +
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Residues in contact with GLY1517 (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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1434D TYR* 4.4 17.0 - - - -
1435D TYR 3.7 5.6 - - - -
1436D SER* 4.6 0.7 - - - -
1516D ILE* 1.3 77.6 - - - +
1518D CYS* 1.3 60.0 + - - +
1529D PHE* 3.6 5.9 - - - +
1530D THR* 2.5 49.4 + - - +
1531D ALA 4.1 3.2 + - - -
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Residues in contact with CYS1518 (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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1433D TYR 3.3 11.1 - - - +
1434D TYR* 3.6 10.2 - - - -
1435D TYR* 3.1 41.7 + - + +
1452D TRP* 5.0 2.7 - - - +
1517D GLY* 1.3 75.7 - - - +
1519D LEU* 1.3 60.0 + - - +
1520D VAL* 4.2 8.7 - - + -
1528D THR 3.8 6.1 - - - -
1529D PHE* 3.8 22.7 - - + +
1530D THR* 4.2 3.4 - - - +
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Residues in contact with LEU1519 (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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1432D THR* 6.1 4.0 - - - -
1433D TYR 3.5 7.2 - - - +
1518D CYS* 1.3 73.8 - - - +
1520D VAL* 1.3 62.3 + - - +
1526D LEU 3.7 3.6 - - - +
1527D MET* 3.7 1.9 - - - -
1528D THR* 2.8 50.4 + - - +
1529D PHE* 5.2 0.2 - - - -
1530D THR* 6.2 1.3 - - - -
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Residues in contact with VAL1520 (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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1295D VAL* 5.8 8.5 - - + -
1432D THR* 4.9 1.1 - - - -
1433D TYR* 3.1 45.8 + - + +
1435D TYR* 6.2 1.1 - - + -
1452D TRP* 3.6 40.2 - - + +
1518D CYS* 5.0 4.7 - - + -
1519D LEU* 1.3 79.9 - - - +
1521D ASP* 1.3 70.9 + - - +
1525D GLY 6.0 0.2 - - - +
1527D MET* 3.8 37.9 - - + +
1529D PHE* 5.7 1.1 - - + -
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Residues in contact with ASP1521 (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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1297D PHE* 4.8 3.6 - - - +
1431D THR* 3.3 19.7 - - - +
1432D THR* 5.1 2.9 - - - -
1433D TYR* 4.9 1.3 - - - -
1519D LEU 4.3 0.6 + - - -
1520D VAL* 1.3 84.2 - - - +
1522D LEU* 1.3 60.6 + - - +
1523D ALA* 3.5 2.9 - - + +
1525D GLY* 3.8 36.7 + - - +
1526D LEU 4.7 6.0 + - - +
1542D VAL* 5.9 0.3 - - - +
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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