Contacts of the strand formed by residues 88 - 100 (chain I) in PDB entry 2OR9
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 ALA 88 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38I ARG* 4.2 11.4 - - + -
39I GLN 3.1 16.8 - - - +
40I THR* 3.7 18.2 - - + +
41I PRO* 5.4 2.2 - - - -
86I ASP 3.2 9.1 + - - +
87I THR* 1.3 77.6 - - - +
89I MET* 1.3 61.7 + - - +
90I TYR* 3.4 14.5 - - + -
108I SER* 4.0 2.1 - - - -
109I VAL 3.1 29.5 + - - +
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Residues in contact with MET 89 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37I VAL 4.0 0.2 - - - +
38I ARG* 3.0 3.1 - - - -
39I GLN* 2.7 46.4 + - + +
88I ALA* 1.3 70.6 - - - +
90I TYR* 1.3 61.5 + - - +
91I TYR* 3.5 39.7 + - + +
105I GLN 4.9 3.1 - - - +
106I GLY* 3.9 6.3 - - - -
107I ALA 3.6 22.4 - - - -
108I SER* 3.6 23.6 - - - +
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Residues in contact with TYR 90 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6I GLU* 2.3 26.2 - - - +
20I LEU* 3.3 31.9 - - + -
36I TRP* 4.6 6.5 - + + -
37I VAL 3.9 2.7 - - - -
38I ARG* 2.8 44.9 + - + +
48I VAL* 4.9 3.6 - - + -
67I PHE* 4.0 12.9 - + - -
80I LEU* 4.0 12.3 - - + -
82I MET* 3.7 19.3 - - - -
86I ASP* 2.6 37.1 + - - +
88I ALA* 3.4 19.5 - - + -
89I MET* 1.3 73.9 - - - +
91I TYR* 1.3 54.5 + - - +
106I GLY* 4.2 0.2 - - - -
107I ALA 2.8 27.2 + - - +
109I VAL* 3.9 18.4 - - + -
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Residues in contact with TYR 91 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6I GLU* 3.2 5.2 - - - +
36I TRP* 3.2 10.2 - - - -
37I VAL 2.8 42.0 + - - +
39I GLN* 3.7 27.7 + - + -
45I LEU* 4.8 2.7 - - + -
89I MET* 3.5 28.1 - - + +
90I TYR* 1.3 73.7 - - - +
92I CYS* 1.3 62.5 + - - +
103I TRP* 3.7 28.7 - + + -
104I GLY 3.4 18.2 - - - +
105I GLN 3.3 19.5 - - - -
106I GLY* 3.5 11.7 - - - -
38M GLN* 3.4 22.7 + - - -
41M GLY 5.5 0.9 - - - -
42M GLN 3.4 7.7 + - - -
43M PRO* 3.6 17.3 - - + -
44M PRO* 4.4 2.9 - - + -
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Residues in contact with CYS 92 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I LEU* 4.3 4.0 - - - -
6I GLU* 3.3 20.3 + - - -
22I CYS* 2.0 49.8 - - + -
35I SER 3.3 8.7 - - - +
36I TRP* 3.6 17.5 - - + -
78I LEU* 3.9 7.2 - - + -
91I TYR* 1.3 75.6 - - - +
93I ALA* 1.3 65.6 + - - +
103I TRP* 3.4 3.5 - - - +
104I GLY* 3.0 31.3 + - - -
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Residues in contact with ALA 93 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I LEU* 4.3 2.7 - - - -
34I MET* 3.4 10.9 - - - +
35I SER* 2.9 35.5 + - - +
37I VAL* 5.5 2.2 - - + -
78I LEU* 5.0 0.2 - - - +
92I CYS* 1.3 78.2 - - - +
94I ARG* 1.3 68.2 + - - +
100I MET* 4.3 13.2 - - + +
102I TYR 3.2 11.4 - - - +
103I TRP* 3.7 31.9 - - + +
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Residues in contact with ARG 94 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2I VAL* 4.3 3.8 - - - +
4I LEU* 4.1 4.8 - - + +
27I PHE* 3.6 37.3 - - + +
32I TYR* 3.0 49.1 + - + -
34I MET* 3.2 26.0 - - + -
93I ALA* 1.3 71.8 - - - +
95I ARG* 1.3 57.8 + - - +
96I SER 3.7 0.4 - - - -
100I MET* 2.9 46.2 + - - +
101I ASP* 2.6 45.5 + - - +
102I TYR* 2.9 46.2 + - + +
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Residues in contact with ARG 95 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99H TYR* 3.1 25.9 + - - -
100H GLY* 5.1 5.1 + - - -
32I TYR* 4.7 0.9 - - - -
33I GLY* 2.4 60.3 + - - +
34I MET* 3.8 0.4 - - - +
35I SER* 3.7 22.7 - - - +
50I THR* 3.7 33.4 + - - +
51I ILE 5.2 0.9 - - - -
52I GLY* 6.4 0.4 - - - -
56I TYR* 5.8 3.2 - - - -
93I ALA 3.5 0.4 + - - -
94I ARG* 1.3 69.4 - - - +
96I SER* 1.3 59.9 + - - +
97I GLU* 3.2 8.1 + - - +
100I ALA* 4.1 10.6 - - + -
94M VAL* 3.6 18.0 - - - +
95M PRO* 5.6 0.2 - - - +
96M TRP* 3.1 61.1 - - + +
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Residues in contact with SER 96 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32I TYR* 3.5 15.5 - - - -
94I ARG* 3.6 0.3 + - - -
95I ARG* 1.3 70.5 - - - +
97I GLU* 1.3 53.9 + - - +
98I PHE* 3.4 24.2 - - - -
100I ALA* 2.7 63.2 + - - -
101I ASP* 2.6 36.1 + - - -
96M TRP* 3.2 3.9 - - - -
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Residues in contact with GLU 97 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99H TYR* 2.3 30.5 + - - -
100H TYR* 3.1 46.2 - - - +
95I ARG* 3.2 15.1 + - - +
96I SER* 1.3 73.9 - - - +
98I PHE* 1.3 72.8 + - - +
100I TYR* 3.2 23.8 - - + -
91M THR 6.0 0.2 - - - -
94M VAL* 4.6 0.2 - - - +
96M TRP* 3.7 10.5 - - + -
1P GLU* 2.6 41.8 + - - +
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Residues in contact with PHE 98 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100H TYR* 3.4 12.9 + - - -
31I HIS* 3.5 29.2 - - + -
32I TYR* 3.9 17.5 - + - -
96I SER* 3.4 28.3 - - - -
97I GLU* 1.3 86.6 - - - +
99I TYR* 1.3 59.5 + - - +
100I TYR* 2.7 99.7 - + + +
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Residues in contact with TYR 99 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100H TYR* 3.5 48.5 - - + +
98I PHE* 1.3 75.2 - - - +
100I TYR* 1.3 149.9 + - + +
2P GLN* 5.5 2.2 - - - -
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Residues in contact with TYR 100 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32I TYR* 2.6 32.1 + - - -
94I ARG* 3.5 16.7 + - - -
98I PHE* 3.3 47.6 - - + +
99I TYR* 1.3 95.0 - - + +
100I THR* 1.3 162.7 + + - +
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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