Contacts of the helix formed by residues 501 - 518 (chain 3) in PDB entry 6FF7
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 LEU 501 (chain 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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851 GLU* 3.7 22.7 + - + +
861 ASP* 5.2 3.6 - - + +
5003 GLY* 1.3 78.4 - - - +
5023 ALA* 1.3 58.5 + - - +
5033 GLN 3.3 2.2 - - - -
5043 SER* 3.2 10.9 + - - -
5053 ARG* 2.9 28.8 + - - +
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Residues in contact with ALA 502 (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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851 GLU 4.2 12.1 + - - +
861 ASP* 4.7 13.1 - - + +
871 GLN* 5.3 2.5 - - + +
5003 GLY 4.3 1.5 - - - +
5013 LEU* 1.3 77.5 - - - +
5033 GLN* 1.3 57.4 + - - +
5053 ARG* 3.3 8.8 + - - +
5063 GLN* 2.9 25.6 + - - +
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Residues in contact with GLN 503 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5003 GLY* 5.3 7.1 - - - +
5013 LEU 3.3 1.2 - - - +
5023 ALA* 1.3 75.4 - - - +
5043 SER* 1.3 61.9 + - - +
5063 GLN* 3.3 10.1 + - - +
5073 GLN* 2.9 27.5 + - - +
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Residues in contact with SER 504 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5003 GLY 4.5 5.5 + - - -
5013 LEU* 3.2 19.7 + - - +
5033 GLN* 1.3 78.2 - - - +
5053 ARG* 1.3 57.9 + - - +
5073 GLN* 3.3 8.3 + - - +
5083 GLN* 2.9 28.6 + - - +
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Residues in contact with ARG 505 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5013 LEU 2.9 14.0 + - - +
5023 ALA* 3.5 12.6 - - - +
5043 SER* 1.3 76.8 - - - +
5063 GLN* 1.3 56.1 + - - +
5083 GLN* 3.4 6.9 + - - +
5093 GLN* 2.9 30.3 + - - +
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Residues in contact with GLN 506 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5023 ALA 2.9 14.4 + - - +
5033 GLN* 3.3 12.3 + - - +
5053 ARG* 1.3 73.4 - - - +
5073 GLN* 1.3 59.7 + - - +
5093 GLN* 3.8 4.7 - - - +
5103 ASN* 2.9 31.4 + - - +
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Residues in contact with GLN 507 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5033 GLN 2.9 14.2 + - - +
5043 SER* 3.3 11.2 + - - +
5063 GLN* 1.3 76.8 - - - +
5083 GLN* 1.3 57.0 + - - +
5103 ASN* 3.4 5.4 + - - +
5113 VAL* 2.9 30.8 + - - +
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Residues in contact with GLN 508 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5043 SER 2.9 17.3 + - - +
5053 ARG* 3.8 7.4 - - - +
5073 GLN* 1.3 76.8 - - - +
5093 GLN* 1.3 57.0 + - - +
5113 VAL* 3.4 3.8 + - - +
5123 GLU* 3.0 29.5 + - - +
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Residues in contact with GLN 509 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5053 ARG 2.9 17.4 + - - +
5063 GLN* 4.1 4.7 - - - +
5083 GLN* 1.3 76.5 - - - +
5103 ASN* 1.3 57.0 + - - +
5123 GLU* 3.8 6.0 - - - +
5133 ASP* 2.8 29.0 + - - +
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Residues in contact with ASN 510 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5063 GLN 2.9 18.5 + - - +
5073 GLN* 3.9 5.8 - - - +
5093 GLN* 1.3 75.5 - - - +
5113 VAL* 1.3 59.4 + - - +
5133 ASP* 3.3 8.4 + - - +
5143 ALA* 2.9 28.4 + - - +
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Residues in contact with VAL 511 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5073 GLN 2.9 17.9 + - - +
5083 GLN* 4.2 4.3 - - - +
5103 ASN* 1.3 74.1 - - - +
5123 GLU* 1.3 61.2 + - - +
5143 ALA* 3.3 7.1 + - - +
5153 MET* 3.0 29.5 + - - +
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Residues in contact with GLU 512 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5083 GLN 3.0 18.1 + - - +
5093 GLN* 3.9 6.3 - - - +
5113 VAL* 1.3 75.1 - - - +
5133 ASP* 1.3 58.6 + - - +
5153 MET* 3.4 4.2 + - - +
5163 LYS* 2.9 31.7 + - - +
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Residues in contact with ASP 513 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5093 GLN 2.8 20.7 + - - +
5103 ASN* 3.4 10.8 - - - +
5123 GLU* 1.3 76.3 - - - +
5143 ALA* 1.3 56.5 + - - +
5163 LYS* 3.4 5.4 + - - +
5173 GLU* 2.9 32.8 + - - +
1952A VAL* 5.2 9.7 - - + +
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Residues in contact with ALA 514 (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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5103 ASN 2.9 16.1 + - - +
5113 VAL* 3.7 7.9 - - - +
5123 GLU 3.3 0.2 - - - -
5133 ASP* 1.3 77.5 - - - +
5153 MET* 1.3 58.5 + - - +
5173 GLU* 4.7 2.9 - - - -
5183 MET* 2.9 37.1 + - + +
5193 GLN 4.4 0.2 + - - -
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Residues in contact with MET 515 (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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5113 VAL 3.0 16.2 + - - +
5123 GLU* 4.2 4.9 - - - +
5133 ASP 3.4 0.2 - - - -
5143 ALA* 1.3 77.0 - - - +
5163 LYS* 1.3 61.0 + - - +
5193 GLN* 4.1 11.7 - - - +
5203 LYS* 4.0 15.4 + - - +
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Residues in contact with LYS 516 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5123 GLU 2.9 18.8 + - - +
5133 ASP* 3.9 5.2 - - - +
5153 MET* 1.3 79.9 - - - +
5173 GLU* 1.3 56.6 + - - +
5203 LYS* 3.3 27.4 - - + +
5213 PRO 4.6 3.1 - - - +
1952A VAL* 5.3 13.2 - - + +
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Residues in contact with GLU 517 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5133 ASP 2.9 17.2 + - - +
5143 ALA* 4.2 2.9 - - - +
5163 LYS* 1.3 78.6 - - - +
5183 MET* 1.3 64.8 + - + +
5193 GLN 3.2 3.4 + - - -
5203 LYS 3.6 12.8 - - - +
1948A ASP* 4.8 22.2 - - + +
1951A LYS* 6.0 5.2 - - + -
1952A VAL* 5.2 7.0 - - + -
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Residues in contact with MET 518 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5143 ALA* 2.9 22.2 + - + +
5173 GLU* 1.3 74.8 - - + +
5193 GLN* 1.3 59.5 + - + +
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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
------------------------------------------------------------
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