Contacts of the strand formed by residues 54 - 60 (chain D) 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 ARG 54 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50D ASP* 5.7 0.7 - - - -
51D LEU* 2.7 42.5 + - + +
52D GLY 5.1 0.2 - - - -
53D ASN* 1.3 86.4 - - - +
55D LYS* 1.3 76.4 + - - +
57D GLU* 5.6 2.0 + - - -
75D SER* 4.9 4.7 - - - +
76D GLY* 3.6 37.3 - - - +
77D ASP* 6.2 0.6 - - - -
163D ASN* 3.8 24.5 + - - +
203D ASN* 5.9 7.0 - - + +
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Residues in contact with LYS 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D ALA* 3.6 26.2 - - + -
49D VAL 3.7 6.5 - - - +
50D ASP* 3.5 24.2 - - - +
54D ARG* 1.3 87.4 - - - +
56D LEU* 1.3 61.1 + - - +
57D GLU* 2.6 36.4 + - - +
74D GLN 3.7 0.5 - - - +
75D SER* 2.9 26.2 + - - -
76D GLY 4.5 1.0 + - - -
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Residues in contact with LEU 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D VAL 3.9 0.3 - - - +
48D ALA* 3.5 2.9 - - - -
49D VAL* 3.0 53.9 + - + +
51D LEU* 4.3 13.0 - - + -
54D ARG 3.8 0.4 + - - -
55D LYS* 1.3 74.0 - - - +
57D GLU* 1.3 59.5 + - - +
58D ILE* 3.7 7.0 + - + -
73D VAL* 3.7 16.4 - - + -
74D GLN 3.6 1.6 - - - +
75D SER* 3.1 18.2 - - - +
167D VAL* 6.5 0.2 - - + -
168D LEU* 3.3 25.8 - - + -
171D ASN* 4.4 14.1 - - + +
203D ASN* 5.6 7.4 - - - +
255D ILE* 4.1 32.5 - - + -
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Residues in contact with GLU 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D ALA* 6.6 0.2 - - + -
47D VAL 3.6 6.3 - - - +
48D ALA* 4.5 5.8 - - + +
54D ARG* 5.6 2.3 + - - -
55D LYS* 2.6 42.1 + - - +
56D LEU* 1.3 70.2 - - - +
58D ILE* 1.3 62.7 + - - +
59D SER* 5.2 1.9 + - - -
72D VAL* 3.4 2.6 - - - +
73D VAL* 3.3 4.8 - - - -
74D GLN* 2.7 76.8 + - + +
76D GLY 4.6 8.0 + - - +
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Residues in contact with ILE 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D ALA* 3.3 2.4 - - - +
47D VAL* 2.7 46.6 + - + +
49D VAL* 5.0 9.6 - - + -
56D LEU* 4.5 11.4 - - + +
57D GLU* 1.3 76.6 - - - +
59D SER* 1.3 62.6 + - - +
72D VAL 3.5 7.0 - - - +
73D VAL* 4.6 14.4 - - + -
171D ASN* 5.8 1.6 - - + -
175D VAL* 3.5 40.8 - - + -
255D ILE* 4.8 11.4 - - + +
258D GLY* 5.1 3.8 - - - +
259D ILE* 3.7 34.5 - - + +
262D LEU* 3.6 13.3 - - + +
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Residues in contact with SER 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D SER 3.4 15.0 - - - -
46D ALA* 3.7 11.4 - - - +
57D GLU* 5.2 1.9 + - - -
58D ILE* 1.3 78.3 - - - +
60D SER* 1.3 64.9 + - - +
71D ALA* 3.4 5.9 - - - +
72D VAL* 2.9 53.7 + - - +
262D LEU* 4.8 3.8 - - - -
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Residues in contact with SER 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D MET 5.3 0.2 - - - -
44D ALA* 3.5 3.6 - - - +
45D SER* 3.0 34.1 + - - +
59D SER* 1.3 80.4 - - - +
61D GLY* 1.3 70.2 + - - +
62D LYS* 3.5 5.1 + - - +
70D SER* 2.6 30.6 + - - -
71D ALA* 4.6 2.9 - - - +
72D VAL* 4.7 5.2 - - - -
179D LEU* 3.6 22.6 - - - +
262D LEU* 5.2 0.2 - - - -
266D THR* 6.2 1.6 - - - -
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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