Contacts of the strand formed by residues 39 - 45 (chain T) in PDB entry 1IR1
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 VAL 39 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33T LEU* 4.2 0.2 - - - -
37T LYS 4.8 4.3 - - - +
38T TRP* 1.3 73.0 - - - +
40T PRO* 1.3 73.3 - - - +
73T PRO* 3.9 10.8 - - + -
74T MET 3.8 16.8 - - - +
75T PHE* 3.8 37.0 - - + -
76T GLY 5.5 2.0 - - - +
103T GLY* 3.3 3.6 - - - -
104T PHE* 2.8 52.6 + - + +
106T SER* 5.4 10.8 - - - +
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Residues in contact with PRO 40 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33T LEU* 4.0 18.1 - - + -
34T LEU* 4.1 11.7 - - + -
38T TRP 3.4 10.1 - - - +
39T VAL* 1.3 87.2 - - + +
41T CYS* 1.3 63.0 + - - +
73T PRO* 3.6 1.0 - - - +
74T MET* 2.9 54.6 + - + +
77T CYS* 4.1 8.5 - - + +
83T VAL* 3.9 33.7 - - + -
101T ILE* 5.5 1.1 - - + -
102T ILE 3.4 7.9 - - - +
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Residues in contact with CYS 41 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40T PRO* 1.3 77.7 - - - +
42T LEU* 1.3 78.9 + - - +
43T GLU* 5.0 2.0 - - - -
69T MET* 4.0 25.1 - - - -
70T TRP 5.0 0.9 - - - -
72T LEU 4.5 3.4 - - - -
73T PRO* 3.9 24.7 - - + -
74T MET* 4.9 1.8 - - - +
100T ARG 3.8 0.2 - - - +
101T ILE* 3.6 3.5 - - - +
102T ILE* 2.9 44.8 + - + +
104T PHE* 3.8 24.0 - - + -
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Residues in contact with LEU 42 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41T CYS* 1.3 88.1 - - - +
43T GLU* 1.3 66.1 + - - +
69T MET* 3.8 1.7 - - - -
70T TRP* 2.9 47.8 + - + +
72T LEU 5.7 0.2 + - - -
74T MET* 5.0 6.5 - - - -
83T VAL* 4.3 26.9 - - + +
86T GLU* 3.7 17.0 - - + +
87T LEU* 3.6 39.9 - - + +
90T CYS* 4.2 8.3 - - + -
99T ILE* 4.6 6.7 - - + -
100T ARG 3.4 8.1 - - - +
101T ILE* 4.5 14.1 - - + -
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Residues in contact with GLU 43 (chain T).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187C ARG* 2.9 32.1 + - - -
41T CYS* 5.0 3.7 - - - -
42T LEU* 1.3 80.3 - - - +
44T PHE* 1.3 62.5 + - - +
66T TYR* 6.1 0.5 - - - -
67T TRP* 4.0 20.9 + - + +
68T THR 3.1 11.8 - - - +
69T MET* 4.8 7.3 - - + +
70T TRP 4.5 0.2 - - - +
98T PHE 3.9 0.2 - - - +
99T ILE* 3.4 5.0 - - - +
100T ARG* 2.8 78.3 + - - +
102T ILE* 3.8 27.4 - - + +
111T GLN* 5.3 1.2 + - - -
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Residues in contact with PHE 44 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43T GLU* 1.3 75.5 - - - +
45T GLU* 1.3 64.3 + - - +
46T THR* 4.8 2.5 - - + -
67T TRP* 4.1 2.9 - - - -
68T THR* 2.8 64.9 + - + -
69T MET 3.7 16.6 - - - -
70T TRP* 4.0 23.8 - + + -
90T CYS* 4.2 19.5 - - - -
94T TYR* 3.5 49.1 - + - -
97T ALA* 4.3 10.3 - - + -
98T PHE 3.2 11.4 - - - +
99T ILE* 4.3 2.0 - - + -
3U VAL* 4.1 10.5 - - + -
6U THR* 4.0 16.4 - - + -
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Residues in contact with GLU 45 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227C LYS* 2.9 31.1 + - - -
44T PHE* 1.3 78.7 - - - +
46T THR* 1.3 62.6 + - - +
47T ASP* 3.1 16.9 + - - +
48T HIS* 3.0 51.7 + - - +
49T GLY* 4.2 2.0 - - - +
64T GLY* 6.5 0.2 - - - -
67T TRP* 3.4 38.1 - - + +
68T THR* 4.5 3.6 + - - -
97T ALA* 3.2 1.6 - - - +
98T PHE* 2.9 36.3 + - + -
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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