Contacts of the strand formed by residues 45 - 50 (chain A) in PDB entry 3U1K
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 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A MET* 3.1 19.1 + - - +
44A ALA* 1.3 73.4 + - - +
46A ALA* 1.3 62.4 + - - +
59A SER* 3.1 6.9 - - - -
60A SER* 2.9 34.1 + - - +
179A LEU* 6.2 0.4 - - - -
262A LEU* 3.8 20.6 - - - -
265A GLU* 4.4 2.9 - - - +
266A THR* 4.1 9.5 + - - -
375B ASP* 3.8 8.5 - - - -
597B ARG* 3.0 23.7 + - - +
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Residues in contact with ALA 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A SER* 1.3 79.1 - - - +
47A VAL* 1.3 62.7 + - - +
57A GLU* 6.0 1.3 - - - +
58A ILE 3.1 10.3 - - - +
59A SER* 3.8 9.9 - - - -
262A LEU* 3.7 7.0 - - - +
265A GLU* 5.1 6.2 + - - +
375B ASP* 4.0 14.5 + - - +
378B LYS* 6.0 1.6 - - - +
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Residues in contact with VAL 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ALA* 1.3 77.1 - - - +
48A ALA* 1.3 74.7 + - - +
49A VAL* 4.9 1.6 - - + -
56A LEU 3.7 0.5 - - - +
57A GLU* 3.6 4.8 - - - +
58A ILE* 2.8 44.0 + - + -
258A GLY* 3.7 39.9 - - - +
261A GLN* 4.9 6.3 - - + -
262A LEU* 4.0 22.9 - - + -
378B LYS* 5.8 2.5 - - - +
602B GLU* 3.7 24.9 - - - +
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Residues in contact with ALA 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A VAL* 1.3 85.1 - - - +
49A VAL* 1.3 62.3 + - - +
50A ASP 4.1 1.3 + - - -
55A LYS* 3.6 25.6 - - + -
56A LEU 3.3 4.0 - - - -
57A GLU* 3.4 20.0 - - - +
378B LYS* 4.0 26.8 + - - +
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Residues in contact with VAL 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A VAL* 4.9 2.5 - - + -
48A ALA* 1.3 77.0 - - - +
50A ASP* 1.3 74.9 + - - +
51A LEU 3.7 0.5 + - - -
54A ARG 4.0 0.3 - - - +
55A LYS* 3.4 3.3 - - - -
56A LEU* 2.7 52.0 + - + +
58A ILE* 4.5 15.3 - - + -
254A GLN* 4.0 30.7 - - + +
255A ILE* 4.2 18.2 - - + +
258A GLY* 4.2 25.1 - - - -
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Residues in contact with ASP 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ALA 4.1 2.0 + - - -
49A VAL* 1.3 79.0 - - - +
51A LEU* 1.3 58.4 + - - +
52A GLY* 2.9 35.4 + - - +
54A ARG 4.4 3.7 - - - +
55A LYS* 4.3 18.5 - - - +
254A GLN* 3.2 24.3 + - - -
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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