Contacts of the helix formed by residues 63 - 68 (chain L) in PDB entry 6D6Q
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 SER 63 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69G PRO* 4.6 5.9 - - - +
112G VAL* 4.3 12.1 - - - -
113G LYS 4.4 5.5 + - - -
115G ASP* 4.0 6.1 + - - -
61L GLU* 3.7 12.7 - - - +
62L GLN* 1.3 80.8 - - - +
64L PHE* 1.3 61.9 + - - +
65L LEU* 3.1 33.6 + - - +
66L LEU* 4.2 13.7 + - - +
67L CYS* 3.6 16.1 + - - +
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Residues in contact with PHE 64 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G PRO* 3.6 35.0 - - + -
101G TRP* 5.4 2.0 - + - -
102G VAL 4.3 15.0 - - - -
103G ASP* 5.5 0.2 - - - -
104G SER* 5.0 8.5 - - - -
106G GLN* 6.3 0.9 - - - -
112G VAL* 6.3 1.6 - - + -
115G ASP* 5.3 4.2 + - - -
204G LEU* 6.3 0.9 - - + -
208G ARG* 3.1 57.2 - - + +
233G MET* 5.0 14.8 - - + -
62L GLN 4.6 6.7 - - - -
63L SER* 1.3 72.8 + - - +
65L LEU* 1.3 62.0 + - + +
67L CYS* 3.8 19.3 - - - -
68L GLU* 2.9 26.0 + - + +
70L LEU* 4.4 6.2 - - + +
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Residues in contact with LEU 65 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114G GLY 3.0 29.2 - - - +
115G ASP* 3.6 10.8 - - - +
116G HIS* 6.2 3.1 - - + -
233G MET* 5.5 3.6 - - + -
63L SER* 3.1 12.7 - - - +
64L PHE* 1.3 76.7 - - + +
66L LEU* 1.3 69.8 + - + +
67L CYS 3.2 0.4 - - - -
68L GLU 2.5 24.0 + - - +
69L ASP* 4.4 2.3 - - - -
70L LEU* 3.8 34.5 - - + +
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Residues in contact with LEU 66 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66G VAL* 5.6 5.6 - - + -
89G LYS* 3.4 19.1 + - - -
99G VAL* 5.0 5.5 - - + +
61L GLU* 3.8 37.2 - - + +
63L SER* 4.2 12.0 + - - +
65L LEU* 1.3 79.6 - - + +
67L CYS* 1.3 65.8 + - - +
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Residues in contact with CYS 67 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68G GLY* 6.1 0.4 - - - -
69G PRO* 5.0 3.4 - - + -
89G LYS* 3.0 21.1 - - - +
99G VAL* 4.4 16.1 - - + +
101G TRP* 3.2 65.9 - - + -
208G ARG* 6.1 0.2 - - - -
63L SER 3.6 18.4 + - - +
64L PHE* 3.8 19.3 - - + -
66L LEU* 1.3 76.7 - - - +
68L GLU* 1.3 67.6 + - - +
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Residues in contact with GLU 68 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87G ARG* 6.2 0.3 - - - -
89G LYS* 4.8 3.6 - - - +
101G TRP* 5.1 9.8 + - + -
208G ARG* 3.6 39.6 - - - +
212G ALA* 4.9 9.0 - - - +
64L PHE 2.9 19.8 + - - +
65L LEU* 2.5 29.5 + - - +
66L LEU 4.2 0.4 - - - -
67L CYS* 1.3 86.7 - - - +
69L ASP* 1.3 80.2 + - - +
70L LEU* 3.8 7.2 + - + +
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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
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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