Contacts of the strand formed by residues 84 - 98 (chain O) in PDB entry 1H2I
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 TRP 84 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26O PHE* 3.8 5.9 - - - -
72O ILE* 4.2 11.4 - - + -
75O ALA* 3.5 29.6 - - + -
76O ASN* 2.8 26.1 + - - +
79O PHE* 3.9 18.6 - + + -
80O GLY 3.4 16.4 - - - -
81O TYR 4.2 5.9 - - - +
82O ASN 3.6 0.7 - - - -
83O GLY* 1.3 77.5 + - - +
85O ALA* 1.3 81.8 + - - +
86O HIS* 3.7 17.3 - + - -
113O VAL* 4.1 9.9 - - + -
114O GLN 3.1 11.2 - - - +
115O LEU* 4.0 6.5 - - + -
151O LEU* 3.9 28.0 - - + -
155O LEU* 4.3 8.3 - - + -
119P SER* 4.7 3.1 - - - -
121P HIS* 3.4 38.5 + + - -
157P SER* 3.8 18.8 - - - -
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Residues in contact with ALA 85 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26O PHE* 3.7 14.6 - - + -
84O TRP* 1.3 81.3 - - - +
86O HIS* 1.3 61.6 + - - +
113O VAL* 3.1 8.3 - - - +
114O GLN 2.7 28.0 + - - +
120P TYR* 2.8 55.4 - - + +
121P HIS* 3.8 3.1 - - - -
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Residues in contact with HIS 86 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84O TRP* 3.7 5.4 - - + -
85O ALA* 1.3 79.5 - - - +
87O SER* 1.3 61.4 + - - +
88O ILE* 5.5 0.2 - - + -
111O VAL* 3.9 19.7 - - + -
112O ARG 3.1 12.6 - - - +
113O VAL* 4.0 4.3 - - + -
147O VAL* 5.1 7.0 - - + +
151O LEU* 3.8 36.6 - - + +
120P TYR* 3.2 13.0 + - - -
121P HIS* 2.9 46.2 - + + -
122P GLU 2.9 46.4 + - - -
123P ASP* 5.0 5.0 + - - -
157P SER* 3.6 18.6 - - - -
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Residues in contact with SER 87 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86O HIS* 1.3 75.4 - - - +
88O ILE* 1.3 64.0 + - - +
89O THR* 4.5 6.4 - - - +
111O VAL* 3.4 7.9 - - - +
112O ARG* 2.9 43.0 + - - +
112P ARG* 5.1 6.7 - - - -
120P TYR* 3.9 18.0 + - - -
122P GLU* 3.5 18.6 - - - -
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Residues in contact with ILE 88 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86O HIS* 5.5 0.2 - - + -
87O SER* 1.3 72.6 - - - +
89O THR* 1.3 64.5 + - - +
90O GLN* 3.6 28.3 - - - +
91O GLN* 4.2 4.3 - - + +
109O ALA* 5.0 2.5 - - + -
110O PHE 3.4 7.9 - - - +
111O VAL* 4.6 6.7 - - + -
147O VAL* 3.9 28.7 - - + -
110P PHE* 3.8 33.7 - - + -
122P GLU* 3.0 30.5 + - + +
123P ASP* 3.8 29.6 - - - -
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Residues in contact with THR 89 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87O SER* 3.7 6.5 + - - +
88O ILE* 1.3 75.7 - - - +
90O GLN* 1.3 64.9 + - - +
110O PHE* 2.7 23.8 + - - +
112O ARG* 4.0 26.5 - - + -
122O GLU* 2.6 31.5 + - - +
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Residues in contact with GLN 90 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88O ILE* 3.0 9.1 - - - +
89O THR* 1.3 87.9 + - - +
91O GLN* 1.3 65.7 + - - +
92O ASN* 3.7 32.1 - - - +
109O ALA* 3.4 1.6 - - - -
110O PHE* 2.8 50.0 + - + +
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Residues in contact with GLN 91 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88O ILE* 4.2 4.6 - - + +
90O GLN* 1.3 81.5 + - - +
92O ASN* 1.3 63.4 + - - +
93O VAL 4.3 0.2 + - - -
107O VAL* 3.7 18.8 - - + +
108O CYS 3.3 13.0 - - - +
109O ALA* 3.9 1.7 - - + +
143O ARG* 2.8 69.1 + - - +
146O ALA* 3.7 5.5 - - - +
147O VAL* 3.5 15.3 - - - +
110P PHE* 3.2 36.9 - - + -
124P VAL* 3.8 1.2 - - - +
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Residues in contact with ASN 92 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143N ARG* 4.9 4.5 + - - +
90O GLN* 3.7 22.8 - - - +
91O GLN* 1.3 77.1 + - - +
93O VAL* 1.3 75.5 + - - +
94O ASP* 3.4 14.7 + - - +
107O VAL* 3.6 2.7 - - - +
108O CYS* 2.8 50.7 + - - -
110O PHE* 5.6 0.4 - - + -
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Residues in contact with VAL 93 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91O GLN 4.3 0.4 + - - -
92O ASN* 1.3 81.3 + - - +
94O ASP* 1.3 63.9 + - - +
95O PHE* 3.8 14.1 - - - +
96O VAL* 3.9 24.9 - - + -
107O VAL* 3.8 24.5 - - + -
139O LEU* 4.5 7.2 - - + -
143O ARG* 3.5 38.5 - - - +
94P ASP* 5.8 0.4 - - - -
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Residues in contact with ASP 94 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93N VAL* 5.3 1.2 - - - +
139N LEU* 3.5 14.4 - - + +
143N ARG* 2.5 34.1 + - - -
92O ASN* 3.4 17.4 + - - +
93O VAL* 1.3 73.5 - - - +
95O PHE* 1.3 73.7 + - + +
106O GLY 2.9 14.4 + - - +
126O TYR* 2.6 33.5 + - - +
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Residues in contact with PHE 95 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135N LYS* 3.7 35.9 - - + +
136N ALA* 3.4 35.4 - - + -
139N LEU* 4.0 13.0 - - + -
93O VAL* 3.4 4.6 - - - +
94O ASP* 1.3 91.3 - - + +
96O VAL* 1.3 69.9 + - - +
97O ASP* 3.6 22.0 - - - +
104O TYR* 3.3 36.3 - - + -
105O VAL* 3.4 5.2 - - - +
106O GLY* 3.3 37.6 + - - +
126O TYR* 4.0 1.1 - - - -
130O GLU* 5.7 0.2 - - - -
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Residues in contact with VAL 96 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93O VAL* 3.9 17.7 - - + -
95O PHE* 1.3 78.4 - - - +
97O ASP* 1.3 64.3 + - - +
98O LEU 4.2 0.5 + - - -
103O PHE* 4.2 21.8 - - + -
104O TYR 3.5 3.6 - - - -
105O VAL* 4.2 9.4 - - + -
135O LYS* 4.3 24.0 - - + -
139O LEU* 4.0 23.3 - - + -
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Residues in contact with ASP 97 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103N PHE* 6.0 0.2 - - - -
135N LYS* 2.7 39.2 + - - +
95O PHE* 3.6 10.2 - - - +
96O VAL* 1.3 79.4 + - - +
98O LEU* 1.3 59.5 + - - +
99O ASN* 4.0 18.9 - - - +
102O LYS 3.7 0.5 - - - +
103O PHE* 3.2 9.3 - - - -
104O TYR* 2.7 51.9 + - + +
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Residues in contact with LEU 98 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96O VAL 4.2 1.0 + - - -
97O ASP* 1.3 73.1 - - - +
99O ASN* 1.3 65.0 + - - +
100O ASN 3.9 20.4 - - - +
101O GLY* 4.1 19.5 - - - +
102O LYS 3.4 3.8 - - - +
103O PHE* 3.8 34.5 - - + -
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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