Contacts of the helix formed by residues 505 - 513 (chain E) in PDB entry 6C3P
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 GLY 505 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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501E GLU 3.9 3.2 + - - -
502E MET 3.6 6.6 + - - -
504E ARG* 1.3 78.2 - - - +
506E ILE* 1.3 63.0 + - - +
507E LYS* 3.1 3.6 - - - -
508E LEU* 3.0 24.6 + - - +
509E LEU* 3.3 10.0 - - - +
1429E VAL* 3.8 30.8 - - - +
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Residues in contact with ILE 506 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502E MET* 3.3 14.9 + - + +
503E LEU* 3.7 35.2 - - + +
504E ARG 3.3 5.2 + - - +
505E GLY* 1.3 75.6 - - - +
507E LYS* 1.3 59.4 + - + +
509E LEU* 3.2 16.7 + - + +
510E LYS* 2.9 30.3 + - + +
515E GLU* 3.8 17.5 - - - +
1105E ILE* 5.3 6.7 - - + -
1109E MET* 4.7 4.7 - - + -
1112E PHE* 3.7 54.1 - - + -
1117E LEU* 5.2 2.0 - - + -
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Residues in contact with LYS 507 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505E GLY 3.1 1.7 - - - -
506E ILE* 1.3 80.7 - - + +
508E LEU* 1.3 65.4 + - - +
510E LYS* 3.2 1.6 + - - +
511E LEU* 2.9 43.2 + - + +
1109E MET* 3.5 27.6 - - + -
1389E LEU* 5.2 12.7 - - + +
1394E MET* 4.1 16.8 - - + -
1425E LEU* 3.7 40.8 - - + +
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Residues in contact with LEU 508 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505E GLY* 3.0 15.6 + - - +
507E LYS* 1.3 78.5 - - - +
509E LEU* 1.3 60.5 + - + +
511E LEU* 3.1 5.5 + - - +
512E TYR* 2.9 64.3 + - + +
514E TRP* 4.2 12.8 - - + -
1425E LEU* 5.7 8.7 - - + +
1429E VAL* 3.6 31.9 - - + +
1431E PHE* 3.3 35.4 - - + -
1493E ARG* 3.2 24.2 - - - +
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Residues in contact with LEU 509 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501E GLU 5.5 0.2 - - - +
502E MET* 3.6 41.3 - - + +
505E GLY* 3.3 16.8 - - - +
506E ILE* 3.2 10.1 + - + +
508E LEU* 1.3 79.3 - - - +
510E LYS* 1.3 66.1 + - - +
513E ALA* 3.1 24.6 + - - -
514E TRP* 3.6 5.5 + - - +
515E GLU* 3.1 32.8 - - + +
518E PHE* 3.4 33.7 - - + -
1105E ILE* 6.2 0.2 - - + -
1431E PHE* 3.9 28.9 - - + -
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Residues in contact with LYS 510 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506E ILE* 2.9 19.8 + - + +
507E LYS 3.2 4.9 + - - +
509E LEU* 1.3 76.0 - - - +
511E LEU* 1.3 55.7 + - - +
513E ALA* 4.2 4.0 + - - +
515E GLU* 2.8 32.6 + - - +
1105E ILE 3.9 5.3 + - - +
1106E LEU 4.4 0.4 + - - -
1107E ALA 3.3 26.3 + - - +
1108E PRO* 4.4 9.2 - - - +
1109E MET* 3.5 28.3 - - + +
1112E PHE* 4.9 4.3 - - + -
1323E GLU* 5.1 0.8 - - - +
1325E TYR* 3.3 33.5 + - - -
1394E MET* 4.8 2.2 - - - -
1418E ARG* 2.6 40.3 + - - +
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Residues in contact with LEU 511 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507E LYS* 2.9 44.5 + - + +
508E LEU* 3.6 6.5 - - - +
510E LYS* 1.3 76.6 - - - +
512E TYR* 1.3 68.1 + - + +
513E ALA 3.3 0.4 - - - -
1389E LEU* 4.1 12.8 - - + -
1392E PHE* 3.4 31.3 - - + -
1394E MET* 3.7 31.0 - - + -
1418E ARG* 3.1 33.2 - - - +
1423E ILE* 4.2 23.6 - - + -
1425E LEU* 5.2 11.4 - - + -
1497E ARG* 5.1 0.2 + - - -
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Residues in contact with TYR 512 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508E LEU* 2.9 59.4 + - + +
511E LEU* 1.3 80.5 - - + +
513E ALA* 1.3 70.2 + - - +
514E TRP* 3.2 31.0 - + + +
1418E ARG 4.5 1.2 - - - +
1419E SER* 5.2 1.0 - - - -
1422E SER* 5.4 1.8 - - - -
1423E ILE* 2.5 39.9 + - + +
1424E ILE* 4.2 5.5 - - - -
1425E LEU* 4.6 7.0 + - + +
1490E CYS* 4.7 3.3 + - - +
1493E ARG* 3.9 22.7 + - + -
1494E ALA* 4.4 19.0 - - - +
1497E ARG* 2.8 50.1 + - - +
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Residues in contact with ALA 513 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509E LEU 3.1 9.7 + - - -
510E LYS 4.2 3.1 + - - +
511E LEU 3.3 3.0 - - - -
512E TYR* 1.3 79.1 - - - +
514E TRP* 1.3 67.0 + - - +
515E GLU* 3.5 4.9 - - - +
516E ASN* 5.4 1.5 + - - +
517E ILE* 4.4 4.7 - - - +
1415E HIS* 4.1 33.5 + - + +
1418E ARG* 4.5 6.7 - - + -
1419E SER* 3.9 28.5 - - - +
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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