Contacts of the strand formed by residues 83 - 89 (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 ARG 83 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24D TYR 3.7 9.4 - - - +
26D THR* 3.3 32.0 - - + +
29D TYR* 3.7 52.0 + - + -
58D ALA* 4.1 1.3 - - - -
78D ASP* 2.9 30.7 + - - +
79D ARG 4.0 1.6 + - - -
81D LYS* 3.0 47.2 + - + +
82D GLY* 1.3 74.2 - - - +
84D CYS* 1.3 62.1 + - - +
85D TYR* 3.3 3.1 + - - -
101D VAL* 3.3 7.2 - - - +
102D ALA* 2.9 39.9 + - + +
104D PRO* 3.9 16.4 - - - +
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Residues in contact with CYS 84 (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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24D TYR 3.0 15.4 + - - +
25D TYR* 3.4 15.0 - - + -
26D THR* 3.0 21.8 + - - -
54D GLY* 3.8 26.7 - - - +
55D ALA 4.3 1.3 - - - +
58D ALA* 3.8 4.0 - - + +
83D ARG* 1.3 71.5 - - - +
85D TYR* 1.3 55.6 + - - +
86D HIS 4.1 4.0 - - - -
87D ILE* 3.8 35.0 - - - -
99D CYS* 4.1 13.7 - - - -
100D TYR 3.2 15.3 - - - -
101D VAL* 4.3 4.3 - - + +
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Residues in contact with TYR 85 (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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25D TYR* 5.1 0.9 - - - -
26D THR* 3.5 18.6 - - - +
27D PRO* 3.4 25.1 - - - +
29D TYR* 4.1 25.4 - + + +
31D THR* 3.7 21.5 - - + +
37D LEU* 3.9 21.5 - - + +
83D ARG 3.7 9.9 - - - +
84D CYS* 1.3 73.5 - - - +
86D HIS* 1.3 70.9 + - + +
100D TYR* 3.0 49.1 + + + +
101D VAL 3.7 13.0 - - - -
102D ALA* 3.8 16.2 - - + -
364D PHE* 3.9 5.0 - - - -
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Residues in contact with HIS 86 (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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25D TYR* 5.1 2.4 - - - -
27D PRO* 5.9 0.4 - - - -
84D CYS* 3.6 3.1 - - - -
85D TYR* 1.3 97.0 + - + +
87D ILE* 1.3 84.7 + - - +
88D GLU* 4.3 12.5 + - + +
99D CYS* 3.5 0.5 - - - -
100D TYR* 2.8 60.4 + + + +
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Residues in contact with ILE 87 (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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25D TYR* 3.7 22.7 + - + +
50D PRO* 3.7 15.7 - - + +
51D GLU* 3.7 37.7 - - + +
84D CYS* 3.8 17.0 - - - -
86D HIS* 1.3 95.2 + - - +
88D GLU* 1.3 65.4 + - - +
89D PRO* 4.6 1.7 - - + +
97D TYR* 4.0 33.0 - - + -
98D ILE 3.4 5.2 - - - +
99D CYS* 4.0 7.6 - - - -
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Residues in contact with GLU 88 (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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86D HIS* 4.3 13.1 + - + +
87D ILE* 1.3 75.6 - - - +
89D PRO* 1.3 77.4 - - + +
97D TYR* 3.4 5.0 - - - -
98D ILE* 2.8 48.1 + - + +
100D TYR* 2.9 31.1 + - + -
358D ARG* 3.0 27.0 + - - -
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Residues in contact with PRO 89 (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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87D ILE* 4.6 1.8 - - + +
88D GLU* 1.3 99.1 - - + +
90D VAL* 1.3 64.4 + - - +
91D ALA 4.0 1.0 + - - -
96D GLN 3.9 1.1 - - - +
97D TYR* 3.8 26.7 - - + -
98D ILE* 5.3 0.3 - - - +
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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