Contacts of the helix formed by residues 141 - 151 (chain 3) in PDB entry 3KMB
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 ALA 141 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1403 ASN* 1.3 75.3 - - - +
1423 GLU* 1.3 61.8 + - - +
1443 ASN* 3.4 2.6 + - - +
1453 LYS* 3.0 23.4 + - - +
1783 TYR* 3.6 22.0 - - + +
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Residues in contact with GLU 142 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1093 LYS* 3.1 40.2 + - - +
1403 ASN* 3.0 17.4 + - - +
1413 ALA* 1.3 78.6 - - - +
1433 GLU* 1.3 65.0 + - + +
1453 LYS* 3.0 9.2 + - - +
1463 ALA* 2.9 27.5 + - + +
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Residues in contact with GLU 143 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1103 LYS* 2.7 41.1 + - + +
1123 PHE* 4.2 10.5 - - + -
1373 ILE 3.4 7.6 - - - +
1383 PRO* 4.0 5.4 - - + -
1393 ARG* 2.8 36.6 + - - +
1403 ASN* 2.9 29.8 + - - +
1423 GLU* 1.3 76.0 - - + +
1443 ASN* 1.3 65.5 + - - +
1463 ALA* 3.4 9.0 - - - +
1473 ILE* 2.9 30.0 + - - +
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Residues in contact with ASN 144 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1383 PRO* 3.5 18.5 - - + +
1403 ASN 2.9 18.2 + - - +
1413 ALA* 3.4 6.7 + - - +
1433 GLU* 1.3 78.2 - - - +
1453 LYS* 1.3 62.7 + - - +
1473 ILE* 3.8 0.6 - - - +
1483 GLN* 3.2 8.8 + - - +
1783 TYR* 3.7 15.0 + - - +
1803 ASN* 4.0 7.3 - - - +
1983 ILE* 3.1 31.0 - - - +
2023 GLY* 2.8 36.5 + - - -
2043 TRP* 2.8 25.7 + - - -
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Residues in contact with LYS 145 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1413 ALA 3.0 14.2 + - - +
1423 GLU* 3.0 10.1 + - - +
1443 ASN* 1.3 73.5 - - - +
1463 ALA* 1.3 65.9 + - - +
1483 GLN* 3.2 27.5 + - + +
1493 GLU* 3.0 35.9 + - + +
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Residues in contact with ALA 146 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1123 PHE* 3.8 19.7 - - + -
1423 GLU* 2.9 13.9 + - + +
1433 GLU* 3.2 10.7 + - - +
1453 LYS* 1.3 79.2 - - - +
1473 ILE* 1.3 61.4 + - - +
1493 GLU* 3.3 9.2 + - - +
1503 VAL* 3.1 29.3 + - + +
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Residues in contact with ILE 147 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1123 PHE* 3.5 33.2 - - + -
1363 ALA* 3.6 30.1 - - + +
1373 ILE 3.8 0.9 - - - +
1383 PRO* 3.5 39.0 - - + -
1433 GLU 2.9 19.0 + - - +
1443 ASN 3.8 4.3 - - - +
1463 ALA* 1.3 74.5 - - - +
1483 GLN* 1.3 64.6 + - - +
1503 VAL* 3.1 5.0 + - - +
1513 ALA* 2.9 23.8 + - + +
1553 ALA* 5.3 1.3 - - + -
1573 LEU* 4.2 15.3 - - + -
1983 ILE* 4.3 11.2 - - + -
2163 VAL* 4.4 12.3 - - + -
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Residues in contact with GLN 148 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1443 ASN* 3.2 9.0 + - - +
1453 LYS* 3.4 41.3 - - - +
1473 ILE* 1.3 80.4 - - - +
1493 GLU* 1.3 61.2 + - - +
1513 ALA* 4.2 2.3 - - - +
1523 LYS* 3.1 22.9 + - - -
1983 ILE* 3.7 15.7 - - + +
1993 VAL 4.3 7.9 - - - +
2003 ASP* 3.5 4.9 - - - -
2013 ASN* 2.9 18.1 + - - -
2023 GLY* 2.6 38.0 + - - +
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Residues in contact with GLU 149 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1453 LYS* 3.0 28.1 + - + +
1463 ALA* 3.5 11.5 - - - +
1483 GLN* 1.3 75.8 - - - +
1503 VAL* 1.3 63.2 + - + +
1523 LYS* 3.0 39.2 - - - +
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Residues in contact with VAL 150 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1123 PHE* 3.8 46.0 - - + +
1133 VAL* 4.3 1.1 - - - -
1143 THR* 3.6 24.6 - - + +
1163 HIS* 3.5 17.0 + - - -
1463 ALA 3.1 15.4 + - - +
1473 ILE 3.1 5.5 + - - +
1493 GLU* 1.3 79.2 - - + +
1513 ALA* 1.3 65.4 - - - +
1523 LYS* 3.6 3.5 + - - +
2163 VAL* 4.5 3.4 - - + -
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Residues in contact with ALA 151 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1143 THR* 4.5 3.8 - - - -
1163 HIS* 3.5 13.5 - - - -
1473 ILE* 2.9 17.1 + - + +
1483 GLN* 4.2 4.0 - - - +
1503 VAL* 1.3 76.6 - - - +
1523 LYS* 1.3 65.1 + - - +
1533 THR* 2.9 33.4 + - - +
1553 ALA* 3.7 10.1 - - + -
1983 ILE* 5.4 1.6 - - + -
2143 THR* 4.2 4.8 - - + +
2163 VAL* 3.6 26.5 - - + -
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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