Contacts of the helix formed by residues 134 - 142 (chain 7) in PDB entry 6CP3
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 THR 134 (chain 7).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1327 GLU 4.3 4.9 + - - -
1337 LEU* 1.3 83.8 - - - +
1357 VAL* 1.3 61.8 + - - +
1367 ASP* 3.5 24.7 - - + +
1377 ASP* 3.1 30.8 + - - +
1387 LEU* 3.3 3.6 + - - +
34U LEU* 5.7 6.4 - - - +
50X ASN* 3.4 28.2 + - - +
51X ASN* 3.3 14.4 - - + +
52X LYS* 4.7 0.2 - - - +
53X ILE* 4.7 0.7 - - - -
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Residues in contact with VAL 135 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1347 THR* 1.3 68.1 - - - +
1367 ASP* 1.3 66.8 + - - +
1377 ASP 3.2 0.2 - - - -
1387 LEU* 3.1 10.3 + - - +
1397 THR* 2.9 29.9 + - - -
1457 ILE* 5.7 0.3 - - - +
378 ARG* 4.5 17.7 - - + +
388 LEU* 3.8 29.8 - - + -
418 SER* 3.9 18.6 - - - +
51X ASN* 2.8 37.3 + - + +
53X ILE* 3.7 23.3 - - + +
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Residues in contact with ASP 136 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1347 THR* 3.1 14.2 - - + +
1357 VAL* 1.3 79.8 - - - +
1377 ASP* 1.3 56.6 + - - +
1397 THR* 3.3 4.2 + - - -
1407 LYS* 2.8 29.9 + - - +
378 ARG* 3.5 25.0 + - - +
51X ASN* 2.9 31.0 + - - -
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Residues in contact with ASP 137 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1337 LEU* 3.5 21.3 - - + +
1347 THR* 3.1 18.7 + - - +
1367 ASP* 1.3 79.1 - - - +
1387 LEU* 1.3 59.8 + - - +
1407 LYS* 2.8 35.1 + - - +
1417 ILE* 2.8 26.6 + - - +
32U LYS* 3.6 22.8 - - - +
33U SER* 4.1 1.9 - - - -
34U LEU* 4.0 18.9 + - + +
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Residues in contact with LEU 138 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1337 LEU* 3.7 20.4 - - + -
1347 THR 3.3 7.7 + - - +
1357 VAL* 3.1 12.8 + - + +
1377 ASP* 1.3 77.3 - - - +
1397 THR* 1.3 60.2 + - - +
1417 ILE* 3.3 17.5 - - + +
1427 LYS* 2.9 30.5 + - + +
1457 ILE* 3.7 14.0 - - + +
418 SER* 4.0 21.8 - - - +
448 PHE* 6.5 0.9 - - + -
458 ILE* 3.8 15.9 - - + -
29U HIS* 4.3 18.8 - - + +
53X ILE* 3.7 28.9 - - + -
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Residues in contact with THR 139 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1357 VAL 2.9 6.5 + - - -
1367 ASP* 3.6 7.6 - - - -
1387 LEU* 1.3 76.2 - - - +
1407 LYS* 1.3 62.0 + - - +
1427 LYS 2.9 24.1 - - - +
1437 PRO* 3.7 6.1 - - + +
1457 ILE* 4.1 10.5 - - - +
1467 ASP* 4.2 29.2 - - + +
378 ARG* 2.5 36.9 + - - +
3J LYS* 5.1 7.9 - - + -
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Residues in contact with LYS 140 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1367 ASP 2.8 15.5 + - - +
1377 ASP* 2.8 34.9 + - - +
1397 THR* 1.3 79.1 - - - +
1417 ILE* 1.3 56.8 + - - +
1437 PRO* 5.2 2.9 - - - +
32U LYS* 3.3 42.7 + - + +
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Residues in contact with ILE 141 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1377 ASP* 2.8 16.4 + - - +
1387 LEU* 3.3 28.3 - - + +
1407 LYS* 1.3 78.5 - - - +
1427 LYS* 1.3 82.7 + - + +
1437 PRO* 4.3 3.6 - - - +
28U VAL* 3.3 32.1 - - - +
29U HIS* 3.4 23.8 - - - +
31U TYR* 4.6 8.7 + - + -
32U LYS* 3.7 40.2 - - + +
33U SER* 4.2 5.6 - - - +
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Residues in contact with LYS 142 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1387 LEU* 2.9 15.1 + - + +
1397 THR* 2.9 13.5 - - - +
1407 LYS 3.4 0.4 - - - -
1417 ILE* 1.3 96.7 + - + +
1437 PRO* 1.3 64.8 - - + +
1447 GLU* 3.1 13.7 - - + +
1457 ILE* 3.4 26.0 + - + +
1467 ASP 4.3 0.2 + - - -
448 PHE* 4.0 33.2 - - + -
25U ALA* 4.6 7.4 - - - +
28U VAL* 3.4 32.0 + - + +
29U HIS* 3.5 31.3 + - - +
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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