Contacts of the helix formed by residues 1442 - 1454 (chain D) in PDB entry 6M6A
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 ASN1442 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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615D ARG* 5.8 0.4 - - - +
1429D LEU* 5.2 13.2 - - + +
1441D GLN* 1.3 92.3 - - + +
1443D THR* 1.3 53.3 - - - +
1444D THR* 3.4 4.0 - - - -
1445D HIS* 2.9 60.2 + - - +
1446D VAL* 2.9 31.4 + - + +
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Residues in contact with THR1443 (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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103D TRP* 5.9 0.2 - - + -
607D LEU* 5.4 0.7 - - + -
608D SER* 4.3 23.1 - - - +
614D PHE* 3.6 31.5 - - + -
615D ARG* 3.6 16.5 + - - -
1438D ALA* 2.3 31.4 + - + +
1441D GLN 3.4 6.2 + - - -
1442D ASN* 1.3 74.7 - - - +
1444D THR* 1.3 59.9 + - - +
1446D VAL* 3.4 4.6 - - - +
1447D LEU* 2.9 46.3 + - + +
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Residues in contact with THR1444 (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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103D TRP* 3.4 44.5 + - - -
107D ASP* 4.6 4.7 + - - +
604D THR* 4.7 10.1 - - + -
608D SER* 5.4 1.2 - - - -
1442D ASN 4.9 1.3 - - - -
1443D THR* 1.3 79.4 - - - +
1445D HIS* 1.3 61.3 + - + +
1447D LEU* 3.5 1.9 + - - +
1448D THR* 2.9 32.3 + - - +
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Residues in contact with HIS1445 (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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107D ASP* 2.5 33.5 + - - +
108D VAL 3.2 19.3 - - - -
109D PRO* 5.2 1.3 - - + -
1442D ASN* 2.9 36.4 + - - +
1444D THR* 1.3 83.8 - - + +
1446D VAL* 1.3 60.3 + - + +
1448D THR* 2.3 25.6 + - - -
1449D GLU* 3.0 42.4 + - + +
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Residues in contact with VAL1446 (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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1429D LEU* 5.8 6.1 - - + +
1434D TRP* 4.6 7.1 - - + +
1437D ALA* 4.8 14.1 - - + +
1438D ALA* 3.7 32.8 - - + +
1441D GLN 4.0 1.3 - - - +
1442D ASN* 2.9 40.8 + - + +
1443D THR* 3.4 8.1 - - - +
1445D HIS* 1.3 76.2 - - + +
1447D LEU* 1.3 60.8 + - - +
1449D GLU* 4.0 7.4 - - + +
1450D ALA* 2.9 33.1 + - - +
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Residues in contact with LEU1447 (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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1095C LEU* 5.5 5.2 - - + -
1097C LEU* 6.3 2.5 - - + -
10D ILE* 4.4 8.6 - - + +
103D TRP* 3.6 31.2 - - + -
607D LEU* 5.7 7.6 - - + -
614D PHE* 4.9 9.6 - - + -
1434D TRP* 4.9 10.5 - - + +
1438D ALA* 3.7 24.5 - - + -
1443D THR* 2.9 38.2 + - + +
1444D THR 3.5 5.2 - - - +
1446D VAL* 1.3 76.4 - - - +
1448D THR* 1.3 64.7 + - - +
1450D ALA* 3.9 3.1 - - - +
1451D ALA* 3.0 25.3 + - - +
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Residues in contact with THR1448 (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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103D TRP* 3.5 48.0 - - + +
104D PHE* 5.1 10.7 - - + -
107D ASP* 2.4 24.2 + - + +
111D LYS* 5.8 2.9 - - - -
1444D THR* 2.9 15.0 + - - +
1445D HIS 2.3 28.4 + - - -
1447D LEU* 1.3 74.3 - - - +
1449D GLU* 1.3 59.1 + - - +
1451D ALA* 3.1 6.7 + - - +
1452D ILE* 2.9 37.5 + - - +
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Residues in contact with GLU1449 (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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107D ASP* 3.0 11.6 - - - +
108D VAL 5.3 0.2 - - - +
109D PRO* 5.5 2.9 - - - +
111D LYS* 3.7 12.3 + - - -
1445D HIS* 3.0 43.2 + - + +
1446D VAL* 4.0 6.7 - - + +
1447D LEU 3.3 0.2 - - - -
1448D THR* 1.3 96.4 + - - +
1450D ALA* 1.3 58.0 + - - +
1452D ILE* 3.3 22.5 + - - +
1453D ALA* 3.0 28.5 + - - +
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Residues in contact with ALA1450 (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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10D ILE* 3.7 17.9 - - + +
1434D TRP* 3.5 38.8 - - + +
1446D VAL 2.9 18.8 + - - +
1447D LEU* 4.1 0.7 - - + +
1449D GLU* 1.3 77.3 - - - +
1451D ALA* 1.3 57.9 + - - +
1453D ALA* 4.4 5.2 - - - -
1454D GLY* 2.7 24.2 + - - -
1455D LYS* 3.3 7.3 + - - +
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Residues in contact with ALA1451 (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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1097C LEU* 5.6 10.8 - - + -
10D ILE* 3.9 10.5 - - + +
11D ALA* 5.2 5.8 - - - +
12D LEU* 3.3 35.8 - - + +
104D PHE* 5.8 6.3 - - + -
507D ASN* 3.7 2.4 + - - -
1447D LEU 3.0 18.6 + - - +
1448D THR* 3.6 5.6 - - - +
1450D ALA* 1.3 77.4 - - - +
1452D ILE* 1.3 65.4 + - + +
1454D GLY* 3.0 12.7 + - - +
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Residues in contact with ILE1452 (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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12D LEU* 5.2 0.2 - - - -
104D PHE* 5.7 7.2 - - + -
111D LYS* 3.5 37.2 - - + +
498D VAL* 4.1 15.9 - - + -
501D ALA* 3.8 23.4 - - + +
502D PHE* 3.6 36.4 + - + -
505D SER* 4.3 0.2 + - - -
507D ASN* 4.0 7.8 + - - -
1448D THR* 2.9 27.4 + - - +
1449D GLU* 3.4 30.7 - - - +
1451D ALA* 1.3 78.8 - - + +
1453D ALA* 1.3 63.8 + - - +
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Residues in contact with ALA1453 (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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501D ALA* 4.0 15.1 - - + +
505D SER* 3.3 14.0 - - - -
1449D GLU 3.0 16.3 + - - +
1450D ALA* 3.9 6.5 - - - +
1452D ILE* 1.3 76.4 - - - +
1454D GLY* 1.3 64.5 + - - +
1455D LYS* 3.2 39.8 - - + +
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Residues in contact with GLY1454 (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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9D ARG* 3.2 24.4 + - - +
10D ILE 3.1 23.2 - - - +
11D ALA* 4.2 4.5 - - - -
505D SER* 4.8 1.2 - - - -
507D ASN* 4.2 10.1 - - - -
1450D ALA 2.7 16.4 + - - -
1451D ALA 3.0 13.8 + - - -
1453D ALA* 1.3 76.0 - - - +
1455D LYS* 1.3 58.5 + - - +
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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