Contacts of the helix formed by residues 110 - 116 (chain B) in PDB entry 3K3B
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 110 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108B GLY 3.4 0.8 - - - -
109B THR* 1.3 79.5 - - - +
111B LYS* 1.3 60.4 + - - +
112B THR 3.3 1.6 - - - -
113B PHE* 3.7 1.6 - - - +
114B THR* 2.9 35.7 + - - -
335B THR* 4.1 4.0 - - - -
371B ADP 2.8 41.7 + - - -
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Residues in contact with LYS 111 (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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103B ALA* 3.6 32.6 - - + +
104B TYR* 3.9 3.1 - - - -
105B GLY 2.9 39.9 + - - +
106B GLN 3.2 9.9 + - - -
107B THR* 3.6 7.1 + - - +
109B THR 3.9 0.2 - - - -
110B GLY* 1.3 75.7 - - - +
112B THR* 1.3 57.6 + - - +
114B THR* 3.4 0.7 + - - -
115B MET* 2.9 29.5 + - - +
233B SER* 6.5 0.7 - - - +
265B ASP* 3.2 14.1 - - - +
266B LEU 3.1 25.8 - - - +
267B ALA 3.9 8.7 - - - +
268B GLY* 4.0 2.7 - - - +
335B THR* 3.5 19.9 + - - +
371B ADP 2.8 32.7 + - - +
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Residues in contact with THR 112 (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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111B LYS* 1.3 70.9 - - - +
113B PHE* 1.3 59.8 + - - +
115B MET 4.4 0.2 - - - +
116B GLU* 2.8 55.1 + - + +
117B GLY 3.1 7.8 + - - +
118B GLU* 6.3 1.3 - - + -
265B ASP* 2.4 25.3 + - - -
370B MG 2.4 27.8 - - - -
371B ADP 2.8 19.2 + - - +
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Residues in contact with PHE 113 (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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24B ARG* 3.7 16.4 - - - -
78B GLN* 2.7 54.9 + - + -
110B GLY 3.4 6.7 + - - +
112B THR* 1.3 74.4 - - - +
114B THR* 1.3 55.9 + - - +
117B GLY* 3.0 15.5 + - - +
118B GLU* 3.3 39.7 - - + +
132B LEU* 4.2 26.0 - - + -
371B ADP 2.8 83.8 + + + +
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Residues in contact with THR 114 (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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24B ARG* 2.9 37.8 + - - +
78B GLN* 4.1 2.1 - - - +
81B VAL* 4.1 8.2 - - + +
103B ALA* 5.1 2.5 - - + -
110B GLY 2.9 20.7 + - - -
111B LYS* 3.7 4.9 - - - -
113B PHE* 1.3 77.4 - - - +
115B MET* 1.3 59.9 + - + +
134B GLY* 3.5 2.9 - - - -
135B ILE* 2.9 46.8 + - + +
333B ILE* 3.7 24.2 - - + -
335B THR* 4.1 6.4 - - - +
371B ADP 5.6 0.3 + - - -
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Residues in contact with MET 115 (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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101B ILE* 3.0 54.1 - - + +
102B PHE 3.4 15.5 - - - +
103B ALA* 3.5 20.2 - - + +
111B LYS 2.9 12.5 + - - +
112B THR 4.4 0.4 - - - +
114B THR* 1.3 78.5 - - - +
116B GLU* 1.3 62.3 + - + +
135B ILE* 3.8 17.9 - - + +
136B ILE* 2.9 39.7 + - + +
263B LEU* 4.0 21.8 - - - +
264B VAL 3.5 13.2 - - - +
265B ASP* 4.4 13.5 - - + -
333B ILE* 5.1 0.9 - - + -
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Residues in contact with GLU 116 (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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112B THR* 2.8 37.2 + - + +
115B MET* 1.3 78.8 - - + +
117B GLY* 1.3 65.1 + - - +
134B GLY* 2.9 17.5 + - - -
136B ILE* 4.4 3.5 - - + +
137B PRO* 3.2 9.0 - - - +
218B ALA* 5.8 0.5 - - - +
221B ARG* 2.6 42.1 + - - -
237B SER* 4.8 1.4 + - - -
265B ASP* 4.5 8.1 - - + +
372B L31 3.1 58.2 + - + +
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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