Contacts of the helix formed by residues 52 - 56 (chain C) in PDB entry 1KQN
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 52 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C VAL* 1.3 85.2 - - - +
53C ASP* 1.3 66.4 + - - -
54C ALA* 3.1 3.6 - - - -
55C TYR* 3.1 20.5 + - - +
60C LEU* 4.0 0.5 - - - +
63C ALA* 4.7 0.7 - - - -
66C ARG* 4.0 0.2 - - - -
86C GLU* 3.6 24.1 + - - +
87C SER* 3.9 12.1 - - - -
89C GLN 4.9 4.9 - - - -
92C TRP* 5.4 3.5 - - - -
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Residues in contact with ASP 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C GLY* 1.3 71.6 - - - -
54C ALA* 1.3 60.8 + - - +
55C TYR 3.0 1.1 - - - -
56C LYS* 3.1 26.3 + - - +
60C LEU* 4.1 9.7 - - + +
61C ILE 3.2 9.7 - - - +
62C PRO* 3.6 7.2 - - - +
63C ALA* 3.0 32.6 + - - +
66C ARG* 2.9 21.2 + - - +
87C SER 4.9 1.9 + - - +
89C GLN 5.4 1.2 + - - -
261C ARG* 4.8 8.1 + - - +
262C ASN* 5.0 1.7 + - - -
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Residues in contact with ALA 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C GLY* 3.1 1.9 - - - -
53C ASP* 1.3 73.5 - - - +
55C TYR* 1.3 65.5 + - - +
56C LYS* 3.0 23.0 + - - +
89C GLN 4.7 4.4 + - - +
90C LYS 3.5 20.9 - - - +
91C GLU* 4.1 2.0 - - - -
92C TRP* 3.4 29.3 - - - +
268C ALA* 3.4 11.8 - - - +
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Residues in contact with TYR 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C SER* 4.0 8.3 - - - -
51C VAL* 3.9 19.3 - - + -
52C GLY 3.1 15.7 + - - +
53C ASP 3.0 0.4 - - - -
54C ALA* 1.3 77.6 - - - +
56C LYS* 1.3 61.4 - - - +
57C LYS* 3.4 41.0 + - + +
60C LEU* 4.5 2.0 - - + -
92C TRP* 3.2 37.1 - + + +
267C LEU* 3.6 20.4 - - + +
268C ALA* 3.0 26.4 + - - -
269C PRO* 3.7 28.5 - - + -
779C NAD 3.4 43.5 + + - -
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Residues in contact with LYS 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C ASP* 3.1 17.0 + - - +
54C ALA* 3.0 21.0 - - - +
55C TYR* 1.3 77.6 - - - +
57C LYS* 1.3 64.6 + - - +
58C LYS 3.5 0.9 + - - -
60C LEU* 4.7 1.2 - - - +
262C ASN* 3.2 43.6 + - - +
265C VAL* 4.1 29.5 - - + +
266C ILE 4.3 8.1 - - - +
267C LEU* 4.4 3.7 - - - +
268C ALA* 4.6 1.3 - - + +
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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