Contacts of the strand formed by residues 97 - 103 (chain D) 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 TYR 97 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40D PHE 3.4 0.5 - - - +
41D ARG* 3.4 3.5 - - - +
42D VAL* 2.7 45.8 + - + +
44D PRO* 4.3 7.9 - - + -
50D PRO* 3.9 35.0 - - + +
87D ILE* 4.0 25.1 - - + -
88D GLU 3.4 6.3 - - - +
89D PRO* 3.8 28.0 - - + -
90D VAL* 3.9 3.8 - - - -
95D ASN* 3.3 33.0 + - - -
96D GLN* 1.3 88.8 - - - +
98D ILE* 1.3 64.5 + - - +
99D CYS* 3.8 7.7 + - - -
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Residues in contact with ILE 98 (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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39D ALA* 4.3 10.1 - - + -
40D PHE 3.2 5.6 - - - +
41D ARG* 3.9 31.6 - - + +
86D HIS 3.8 0.9 - - - +
87D ILE* 3.4 4.2 - - - +
88D GLU* 2.8 49.3 + - + +
89D PRO 5.3 0.4 - - - +
90D VAL* 3.9 21.1 - - + -
97D TYR* 1.3 73.2 - - - +
99D CYS* 1.3 61.3 + - - +
100D TYR* 3.6 31.5 - - + +
136D GLU* 4.9 1.8 - - + -
358D ARG* 4.5 10.3 - - - +
363D TYR* 4.1 26.5 - - + +
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Residues in contact with CYS 99 (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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38D ALA 3.6 1.4 - - - +
39D ALA* 3.7 0.2 - - - -
40D PHE* 2.9 36.8 + - + +
42D VAL* 3.7 31.0 - - + -
50D PRO* 4.4 4.9 - - - -
54D GLY* 3.9 21.1 - - - -
57D VAL* 6.4 0.7 - - + -
84D CYS* 4.1 12.6 - - - -
86D HIS 3.5 3.8 - - - -
87D ILE* 4.0 23.1 - - - -
97D TYR* 4.4 4.9 - - - -
98D ILE* 1.3 77.2 - - - +
100D TYR* 1.3 64.9 + - - +
101D VAL* 3.9 4.4 + - + -
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Residues in contact with TYR 100 (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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38D ALA 3.3 4.0 - - - +
39D ALA* 4.2 10.1 - - + -
84D CYS* 3.2 7.4 - - - -
85D TYR* 3.0 53.6 + + + -
86D HIS* 2.8 47.2 + + + +
88D GLU* 2.9 25.2 + - - -
98D ILE* 3.6 22.9 - - + -
99D CYS* 1.3 74.8 - - - +
101D VAL* 1.3 60.4 + - - +
358D ARG* 3.5 13.0 + - - -
363D TYR* 3.8 16.9 + + + +
364D PHE* 3.7 35.7 - + - -
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Residues in contact with VAL 101 (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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36D ILE 3.8 0.5 - - - +
37D LEU* 3.4 3.6 - - - -
38D ALA* 2.8 39.0 + - - +
40D PHE* 4.0 23.3 - - + -
54D GLY 4.6 4.7 - - - +
57D VAL* 4.8 1.6 - - + -
58D ALA* 3.8 31.4 - - + +
83D ARG 3.3 14.1 - - - +
84D CYS* 4.3 7.6 - - + -
85D TYR* 3.7 3.4 - - - -
99D CYS* 4.3 5.8 - - + +
100D TYR* 1.3 80.4 - - - +
102D ALA* 1.3 63.3 + - - +
103D TYR* 3.6 35.0 - - + +
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Residues in contact with ALA 102 (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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29D TYR* 3.8 28.9 - - + -
31D THR* 4.4 0.2 - - + -
35D ASP* 4.0 5.8 - - - +
36D ILE 3.5 4.3 - - - -
37D LEU* 3.8 19.5 - - + -
81D LYS 4.2 0.5 - - - +
82D GLY* 3.2 5.0 - - - -
83D ARG* 2.9 35.5 + - + +
85D TYR* 3.8 10.5 - - + -
101D VAL* 1.3 74.4 - - - +
103D TYR* 1.3 62.5 + - - +
104D PRO* 4.1 2.6 - - - +
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Residues in contact with TYR 103 (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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35D ASP* 3.4 5.3 - - - -
36D ILE* 2.8 49.8 + - + +
38D ALA* 3.9 20.2 - - + -
40D PHE* 3.7 21.5 - - - -
57D VAL 4.5 0.5 + - - -
58D ALA 4.5 0.9 - - - -
61D SER* 2.7 48.6 + - - -
62D SER* 4.2 15.3 - - - -
82D GLY* 4.3 4.0 - - - -
101D VAL* 3.6 23.9 - - + +
102D ALA* 1.3 73.6 - - - +
104D PRO* 1.3 68.8 - - + +
107D LEU* 4.3 5.8 - - + -
108D PHE* 3.6 25.6 - + + -
119D SER* 5.9 0.2 - - - -
120D ILE* 4.0 25.8 - - + +
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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