Contacts of the helix formed by residues 63 - 71 (chain B) in PDB entry 3KDO
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 GLU 63 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62B TYR* 1.3 77.0 - - - +
64B GLN* 1.3 65.8 + - - +
65B GLU* 3.3 15.0 + - + +
66B ARG* 3.3 21.4 + - - +
67B TRP 3.3 16.8 + - - -
22F LYS* 2.6 37.3 + - - +
355F LYS* 3.1 24.4 + - - +
357F TYR* 3.0 23.9 + - - -
172G GLU* 3.0 19.7 + - - +
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Residues in contact with GLN 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B TYR* 6.0 0.6 - - - -
60B PRO* 5.9 2.4 - - - +
62B TYR* 3.2 24.4 + - - +
63B GLU* 1.3 73.5 - - - +
65B GLU* 1.3 63.3 + - - +
67B TRP* 3.4 28.6 + - - +
68B ALA* 3.0 27.8 + - + +
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Residues in contact with GLU 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLU* 3.3 13.0 - - + +
64B GLN* 1.3 80.4 - - - +
66B ARG* 1.3 61.8 + - - +
68B ALA* 4.0 5.0 - - - +
69B ASP* 3.1 27.5 + - - +
20F SER* 5.1 2.3 + - - -
21F LYS* 4.1 29.4 + - + +
22F LYS* 3.2 35.2 + - + +
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Residues in contact with ARG 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B GLU* 3.3 34.0 + - - +
64B GLN 3.3 0.4 - - - -
65B GLU* 1.3 74.9 - - - +
67B TRP* 1.3 67.2 + - - +
69B ASP* 3.1 14.4 + - + +
70B LEU* 3.1 30.2 + - + +
22F LYS* 4.0 12.1 - - - +
130F GLU* 2.8 41.4 + - - +
134F ARG* 4.4 0.4 - - - +
357F TYR* 3.9 5.9 - - - -
167G GLY 3.0 28.1 + - - +
168G TYR* 4.9 0.2 - - - +
169G SER* 3.6 15.2 + - - +
172G GLU* 3.1 36.1 + - - -
198G TRP* 4.3 7.2 - - + -
199G TYR* 3.9 24.0 - - - +
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Residues in contact with TRP 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B ILE* 6.4 1.3 - - + -
11B TYR* 3.5 44.2 - + + -
12B TYR* 3.3 21.5 - + - -
52B THR* 3.3 32.8 + - - +
62B TYR* 3.6 35.2 + + + -
63B GLU 3.3 2.4 + - - -
64B GLN* 3.6 30.5 - - - +
66B ARG* 1.3 78.2 - - - +
68B ALA* 1.3 83.0 + - + +
70B LEU* 3.0 13.7 + - - +
71B SER* 3.2 21.6 + - - -
164G PRO* 3.4 29.8 - - + +
166G VAL 4.2 3.1 - - - -
167G GLY* 4.0 12.9 + - - +
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Residues in contact with ALA 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B TYR* 3.4 22.9 + - - +
64B GLN* 3.0 19.8 + - + +
65B GLU* 4.1 5.2 - - - +
67B TRP* 1.3 93.0 - - + +
69B ASP* 1.3 59.8 + - - +
70B LEU 3.5 0.3 + - - -
71B SER* 3.6 15.4 + - - +
73B LYS* 5.2 1.2 + - - -
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Residues in contact with ASP 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B GLU* 3.1 22.5 + - - +
66B ARG* 3.1 7.2 + - - +
67B TRP 3.0 0.8 - - - -
68B ALA* 1.3 79.1 - - - +
70B LEU* 1.3 62.6 + - - +
71B SER 3.5 1.5 - - - +
92B PRO* 3.7 5.7 - - - +
94B HIS* 2.8 26.2 + - - -
20F SER* 4.4 2.9 + - - -
22F LYS* 3.6 26.8 - - + +
23F ARG* 2.7 49.1 + - - +
198G TRP* 5.2 1.9 - - - -
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Residues in contact with LEU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B SER* 4.6 4.5 - - - -
52B THR* 4.1 15.8 - - + +
66B ARG* 3.3 21.1 - - + +
67B TRP 3.0 5.6 + - - +
69B ASP* 1.3 80.0 - - - +
71B SER* 1.3 63.8 + - - +
72B ALA 3.7 1.6 + - - -
91B TYR* 6.0 0.3 - - - -
92B PRO* 3.8 13.5 - - - +
94B HIS* 3.7 46.9 - - + +
95B ALA* 3.8 21.5 - - + +
166G VAL* 5.3 1.6 - - + -
167G GLY* 3.7 27.4 - - - +
198G TRP* 4.3 4.7 - - + -
199G TYR* 3.7 28.5 - - + -
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Residues in contact with SER 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B TYR* 4.1 5.3 - - - -
12B TYR* 3.7 8.9 - - - -
52B THR* 2.4 28.3 + - - -
67B TRP* 3.2 25.1 + - - -
68B ALA 3.6 10.5 + - - +
69B ASP 3.5 3.2 - - - +
70B LEU* 1.3 79.3 - - - +
72B ALA* 1.3 62.4 + - - +
73B LYS* 3.6 24.3 + - - +
92B PRO* 4.1 7.9 - - - +
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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