Contacts of the helix formed by residues 142 - 156 (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 LYS 142 (chain 7).
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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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Residues in contact with PRO 143 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1397 THR* 3.7 7.8 - - + +
1407 LYS 5.2 2.5 - - - +
1417 ILE 4.3 4.5 - - - +
1427 LYS* 1.3 82.8 - - + +
1447 GLU* 1.3 59.8 + - + +
1457 ILE 3.2 2.0 - - - -
1467 ASP* 3.5 9.1 + - + +
1477 ALA* 2.9 29.0 + - - +
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Residues in contact with GLU 144 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1427 LYS* 4.5 10.7 - - + +
1437 PRO* 1.3 79.9 - - + +
1457 ILE* 1.3 68.2 + - - +
1477 ALA* 4.1 5.8 - - - -
1487 LYS* 2.9 73.2 + - - +
408 VAL* 5.9 1.5 - - - +
448 PHE* 3.2 42.8 - - + -
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Residues in contact with ILE 145 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1357 VAL 5.7 0.4 - - - +
1387 LEU* 3.7 16.2 - - + +
1397 THR* 4.1 17.7 - - - +
1427 LYS* 3.4 27.1 - - + +
1437 PRO 3.2 0.2 - - - -
1447 GLU* 1.3 91.3 - - - +
1467 ASP* 1.3 59.9 + - - +
1487 LYS* 3.8 1.9 - - - +
1497 VAL* 2.9 41.1 + - + +
378 ARG* 5.1 14.8 - - + +
408 VAL* 4.6 11.5 - - + +
418 SER* 4.8 15.7 - - - -
448 PHE* 3.7 32.1 - - + -
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Residues in contact with ASP 146 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1397 THR* 4.2 18.3 - - + +
1427 LYS 4.3 0.6 + - - -
1437 PRO* 3.5 9.8 + - + +
1447 GLU 3.5 0.2 - - - -
1457 ILE* 1.3 79.7 - - - +
1477 ALA* 1.3 58.5 + - - +
1497 VAL* 4.3 4.4 - - - +
1507 GLU* 2.9 32.9 + - - +
378 ARG* 5.8 3.6 - - - +
3J LYS* 2.8 33.0 + - - -
5J PHE* 3.5 25.9 - - - -
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Residues in contact with ALA 147 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1437 PRO 2.9 19.3 + - - +
1447 GLU* 3.7 9.0 - - - +
1457 ILE 3.2 0.2 - - - -
1467 ASP* 1.3 77.5 - - - +
1487 LYS* 1.3 63.1 + - + +
1507 GLU* 3.9 3.1 - - - +
1517 GLU* 2.9 31.6 + - - +
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Residues in contact with LYS 148 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1447 GLU* 2.9 51.0 + - - +
1457 ILE 3.9 2.2 - - - +
1477 ALA* 1.3 76.6 - - + +
1497 VAL* 1.3 60.7 + - - +
1517 GLU* 3.8 13.4 - - + +
1527 MET* 2.8 39.6 + - + +
408 VAL* 4.8 12.1 - - + -
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Residues in contact with VAL 149 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1457 ILE* 2.9 24.8 + - + +
1467 ASP* 3.9 6.1 - - - +
1487 LYS* 1.3 76.3 - - - +
1507 GLU* 1.3 57.5 + - - +
1527 MET* 3.2 6.7 + - - +
1537 VAL* 2.9 32.8 + - + +
338 PRO* 4.6 2.2 - - + +
368 LEU* 3.8 14.4 - - + -
378 ARG* 3.8 23.1 - - + -
408 VAL* 3.8 32.8 - - + -
5J PHE* 3.7 32.1 - - + -
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Residues in contact with GLU 150 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1467 ASP* 2.9 22.9 + - - +
1477 ALA* 4.0 4.0 - - - +
1497 VAL* 1.3 76.9 - - - +
1517 GLU* 1.3 57.8 + - - +
1537 VAL* 3.3 8.1 + - - +
1547 LYS* 2.9 67.4 + - + +
5J PHE* 3.5 35.0 - - - +
6J PRO* 3.4 24.7 - - - +
7J THR* 5.7 0.3 - - - +
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Residues in contact with GLU 151 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1477 ALA 2.9 19.4 + - - +
1487 LYS* 4.0 13.9 - - + +
1507 GLU* 1.3 76.5 - - - +
1527 MET* 1.3 60.7 + - - +
1547 LYS* 3.9 7.1 - - + +
1557 LYS* 2.9 56.3 + - - +
1577 LYS* 3.8 13.3 + - - -
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Residues in contact with MET 152 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1487 LYS* 2.8 27.7 + - + +
1497 VAL 3.4 6.1 - - - +
1507 GLU 3.2 0.2 - - - -
1517 GLU* 1.3 80.5 + - - +
1537 VAL* 1.3 59.8 + - - +
1567 GLY* 2.8 23.3 + - - +
1577 LYS* 3.1 56.3 + - + +
1587 TRP* 5.4 0.5 - - - -
1597 ASP 4.6 4.9 - - - +
1607 VAL* 4.5 11.2 - - + -
1617 PRO* 5.1 9.6 - - + -
368 LEU* 3.7 31.4 - - + -
408 VAL* 4.2 17.3 - - + -
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Residues in contact with VAL 153 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1497 VAL* 2.9 19.1 + - + +
1507 GLU* 3.3 10.1 + - - +
1527 MET* 1.3 77.3 - - - +
1547 LYS* 1.3 65.6 + - + +
1567 GLY* 3.2 12.5 + - - -
1587 TRP* 4.3 27.7 + - + -
338 PRO* 4.2 24.0 - - + -
368 LEU* 4.7 11.0 - - + -
5J PHE* 5.3 2.5 - - + -
6J PRO 5.7 0.2 - - - +
7J THR* 3.7 35.0 - - + -
8J PRO* 4.4 13.6 - - + +
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Residues in contact with LYS 154 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1507 GLU* 2.9 42.6 + - + +
1517 GLU* 3.9 7.6 - - + +
1537 VAL* 1.3 79.1 - - + +
1557 LYS* 1.3 59.2 + - - +
6J PRO* 3.2 34.7 - - - +
8J PRO* 4.7 17.0 - - + +
11J LYS* 5.1 14.5 - - - +
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Residues in contact with LYS 155 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1517 GLU* 2.9 37.0 + - - +
1527 MET 4.4 0.7 - - - +
1547 LYS* 1.3 78.7 - - - +
1567 GLY* 1.3 59.3 + - - +
1577 LYS* 3.4 37.9 - - + +
84X LEU* 3.5 19.3 - - - +
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Residues in contact with GLY 156 (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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1527 MET 2.8 14.1 + - - -
1537 VAL 3.2 11.2 + - - -
1557 LYS* 1.3 80.3 - - - +
1577 LYS* 1.3 57.8 + - - +
1587 TRP* 2.9 31.4 + - - -
81X ASN* 6.1 0.2 - - - -
82X TRP* 5.6 0.5 + - - -
83X GLY* 3.4 16.0 + - - -
84X LEU* 4.2 11.2 + - - +
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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
------------------------------------------------------------
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