Contacts of the strand formed by residues 34 - 39 (chain K) in PDB entry 1I9R
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 MET 34 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4K LEU* 3.5 26.0 - - + -
22K CYS* 4.0 11.0 - - - -
24K ALA* 4.0 6.5 - - + -
27K TYR* 3.4 25.6 - - - +
29K PHE* 4.4 10.1 - - + -
32K TYR 3.3 5.6 + - - +
33K TYR* 1.3 71.4 - - - +
35K TYR* 1.3 67.1 + - - +
36K TRP* 4.2 12.0 - - - +
50K GLU* 3.5 1.6 - - - -
51K ILE* 3.1 46.3 + - + +
53K PRO* 5.2 5.2 - - + -
79K ALA* 4.3 12.8 - - + -
96K CYS* 4.5 4.3 - - + -
97K THR 3.1 29.2 - - - +
98K ARG* 3.6 4.3 - - + -
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Residues in contact with TYR 35 (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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33K TYR* 4.1 4.5 - - + -
34K MET* 1.3 77.7 - - - +
36K TRP* 1.3 79.1 + - - +
47K TRP* 2.9 37.7 - + + +
49K GLY 3.4 4.9 - - - -
50K GLU* 3.9 25.7 + - + -
96K CYS* 3.6 1.6 - - - -
97K THR* 2.7 40.5 + - + +
99K SER* 3.1 28.9 - - - -
102K ARG* 2.8 38.9 + - + +
103K ASN* 4.4 4.3 + - - -
105K MET* 3.7 28.9 - - + -
100M PRO* 4.4 9.0 - - + -
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Residues in contact with TRP 36 (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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6K GLN* 4.2 10.3 - - - -
20K LEU* 4.0 17.3 - - + -
21K SER 4.2 3.4 - - - -
22K CYS* 3.8 22.2 - - + -
34K MET* 4.2 12.4 + - - +
35K TYR* 1.3 96.9 + - - +
37K VAL* 1.3 59.7 + - - +
47K TRP* 3.6 2.8 - - - -
48K ILE* 2.7 42.2 + - + +
49K GLY 3.2 6.3 + - - +
51K ILE* 4.8 3.6 - - - +
70K LEU* 3.8 31.8 - - + +
79K ALA* 3.9 21.9 - - + +
80K TYR 3.9 15.5 + - - -
81K MET* 3.3 58.1 - - + -
94K TYR* 5.0 0.2 - - + -
95K TYR 3.2 17.3 - - - -
96K CYS* 3.9 10.3 - - + -
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Residues in contact with VAL 37 (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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35K TYR* 4.8 1.6 - - + -
36K TRP* 1.3 82.8 - - - +
38K LYS* 1.3 68.8 + - - +
45K LEU* 4.2 8.5 - - + -
46K GLU 2.9 27.4 - - - +
47K TRP* 4.8 3.6 - - + -
48K ILE* 4.1 3.1 - - - -
93K VAL 3.7 0.7 - - - +
94K TYR* 3.5 2.6 - - - +
95K TYR* 2.8 35.3 + - + +
97K THR* 3.7 12.1 - - + -
105K MET* 3.3 33.2 - - + -
108K TRP* 3.8 17.7 - - + -
102M PHE* 3.9 15.7 - - + -
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Residues in contact with LYS 38 (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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37K VAL* 1.3 76.1 - - - +
39K GLN* 1.3 60.7 + - - +
40K ALA* 4.5 7.2 - - + +
43K GLN* 6.4 0.9 - - + -
44K GLY 3.4 0.3 - - - +
45K LEU* 3.5 2.1 - - - -
46K GLU* 2.6 55.2 + - + +
48K ILE* 3.9 10.2 - - + +
63K LYS* 6.4 0.2 - - - +
64K PHE* 3.6 27.9 - - - -
67K LYS* 5.8 2.4 - - - +
83K LEU* 5.8 1.2 - - - +
89K GLU 4.4 8.3 + - - -
90K ASP* 3.7 23.8 + - - +
92K ALA* 3.6 20.2 - - + -
93K VAL 3.4 4.5 - - - -
94K TYR* 2.4 51.1 + - + +
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Residues in contact with GLN 39 (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 LYS* 1.3 73.5 - - - +
40K ALA* 1.3 63.3 + - - +
41K PRO* 4.0 1.0 - - - +
43K GLN 3.7 15.1 + - - +
44K GLY* 3.1 12.8 - - - +
45K LEU* 3.1 29.7 - - + +
92K ALA* 3.5 2.8 - - - -
93K VAL* 2.9 38.6 + - + +
95K TYR* 4.2 14.3 + - + -
42M GLN* 3.0 29.4 + - - +
91M TYR* 3.3 21.8 + - - -
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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