Contacts of the strand formed by residues 41 - 48 (chain K) in PDB entry 1OZT
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 41 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39K THR 3.3 0.4 + - - -
40K GLU* 1.3 79.2 - - - +
42K LEU* 1.3 68.9 + - - -
43K HIS* 3.4 9.4 - - - -
88K THR* 3.4 6.6 - - - -
89K ALA 2.8 40.3 + - - -
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Residues in contact with LEU 42 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41K GLY* 1.3 73.2 - - - -
43K HIS* 1.3 67.5 + - - +
86K ASN* 3.9 23.1 - - + +
87K VAL 3.5 2.5 - - - +
88K THR* 3.2 33.2 - - + +
121K GLU 4.4 0.7 - - - +
122K LYS* 4.5 0.2 - - - -
123K ALA* 3.4 36.9 + - + +
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Residues in contact with HIS 43 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38K LEU* 3.5 20.4 - - + +
39K THR* 2.8 47.1 + - + -
40K GLU 4.8 0.2 + - - -
41K GLY 3.4 23.4 + - - -
42K LEU* 1.3 76.4 + - - +
44K GLY* 1.3 65.9 + - - +
86K ASN* 3.1 6.4 + - - -
87K VAL* 2.9 37.4 + - + +
89K ALA* 4.3 2.5 - - + -
119K VAL* 3.9 13.9 - - + -
120K HIS 2.8 23.6 + - - +
121K GLU* 2.9 20.5 + - + -
122K LYS 3.8 1.8 - - - -
144K LEU* 4.2 12.9 - - + +
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Residues in contact with GLY 44 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43K HIS* 1.3 72.7 - - - +
45K PHE* 1.3 59.5 + - - -
46K ARG* 4.8 5.6 - - - -
85K GLY 3.6 3.1 - - - -
86K ASN* 3.2 13.1 + - - -
119K VAL* 3.3 4.0 - - - +
120K HIS* 2.5 44.1 + - - -
122K LYS 2.9 20.5 + - - -
124K ASP* 4.2 7.9 - - - -
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Residues in contact with PHE 45 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8K LEU* 5.5 1.1 - - + -
18K ILE* 4.1 19.5 - - + -
31K VAL* 4.1 9.0 - - + -
35K ILE* 4.1 18.6 - - + -
43K HIS 4.1 2.5 - - - +
44K GLY* 1.3 72.1 - - - -
46K ARG* 1.3 62.6 + - - +
84K LEU* 3.2 56.4 + - + +
85K GLY 3.0 16.2 + - - +
86K ASN 4.2 3.1 - - - -
87K VAL* 3.5 31.4 - - + -
97K VAL* 4.3 2.5 - - + -
99K ILE* 3.9 18.2 - - + -
117K LEU* 3.9 34.1 - - + -
118K VAL 3.6 10.1 - - - -
119K VAL* 4.6 10.3 - - + -
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Residues in contact with ARG 46 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44K GLY* 4.9 4.6 - - - -
45K PHE* 1.3 84.4 - - - +
47K VAL* 1.3 64.5 + - - +
48K HIS* 3.6 16.5 - - + +
63K HIS* 2.9 45.8 + - + -
82K GLY 3.3 10.5 - - - +
83K ASP* 3.2 16.4 + - - +
84K LEU* 4.7 1.1 - - - +
117K LEU* 3.4 4.9 - - - +
118K VAL 2.7 40.6 + - - +
120K HIS* 3.3 34.7 + - - +
122K LYS 5.8 0.2 + - - -
123K ALA 5.2 1.4 + - - -
124K ASP* 3.4 36.4 + - - +
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Residues in contact with VAL 47 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20K PHE* 5.3 0.4 - - + -
46K ARG* 1.3 75.7 - - - +
48K HIS* 1.3 69.8 + - - +
63K HIS* 3.8 3.1 - - - -
64K PHE* 2.9 27.6 + - + +
82K GLY* 2.9 23.6 + - - +
84K LEU* 4.2 16.6 - - + -
104K ILE* 4.8 2.2 - - + -
112K ILE* 3.9 42.8 - - + -
115K ARG* 4.0 12.3 - - + -
116K THR 3.2 9.9 - - - +
117K LEU* 4.1 15.0 - - + -
149K ILE* 4.3 6.1 - - + -
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Residues in contact with HIS 48 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46K ARG* 3.6 16.0 - - + +
47K VAL* 1.3 79.6 - - - +
49K GLU* 1.3 67.3 + - - +
50K PHE 3.4 0.7 - - - -
60K ALA* 3.6 23.8 - - + +
61K GLY 3.0 17.4 + - - -
62K PRO 3.3 12.4 + - - +
63K HIS* 3.8 17.0 - + - -
64K PHE* 3.7 2.5 - - - +
115K ARG* 3.4 7.4 - - - +
116K THR 2.6 29.7 + - - +
118K VAL* 3.3 21.4 - - + +
120K HIS* 3.0 36.1 + + - -
143K ARG* 3.5 22.2 + - - -
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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