Contacts of the strand formed by residues 84 - 98 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26D PHE* 3.8 6.0 - - - -
72D ILE* 4.1 13.2 - - + -
75D ALA* 3.5 30.1 - - + -
76D ASN* 2.9 26.3 + - - +
79D PHE* 3.9 18.4 - + + -
80D GLY 3.5 15.7 - - - -
81D TYR 4.2 5.7 - - - +
82D ASN 3.7 0.4 - - - -
83D GLY* 1.3 78.8 + - - +
85D ALA* 1.3 76.5 + - - +
86D HIS* 3.7 16.8 - + - -
113D VAL* 4.1 10.5 - - + -
114D GLN 3.1 9.6 - - - +
115D LEU* 4.0 7.0 - - + -
151D LEU* 3.8 27.4 - - + -
155D LEU* 4.2 9.2 - - + -
119E SER* 4.6 3.3 - - - -
121E HIS* 3.4 41.8 + + - -
157E SER* 3.8 19.5 - - - -
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Residues in contact with ALA 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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26D PHE* 3.6 16.2 - - + -
84D TRP* 1.3 80.6 - - - +
86D HIS* 1.3 61.5 + - - +
113D VAL* 3.1 8.3 - - - +
114D GLN 2.7 28.5 + - - +
120E TYR* 2.9 52.7 - - + +
121E HIS* 3.9 4.0 - - - -
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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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84D TRP* 3.7 4.4 - + + -
85D ALA* 1.3 79.3 - - - +
87D SER* 1.3 61.8 + - - +
88D ILE* 5.4 0.4 - - + -
111D VAL* 3.9 16.4 - - + -
112D ARG 3.1 12.1 - - - +
113D VAL* 4.0 4.5 - - + -
147D VAL* 5.1 6.0 - - + +
151D LEU* 3.7 42.5 - - + +
120E TYR* 3.2 12.4 + - - -
121E HIS* 2.8 46.3 - + + -
122E GLU 3.0 45.3 + - - -
123E ASP* 5.0 5.8 + - - -
157E SER* 3.4 18.6 - - - -
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Residues in contact with SER 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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86D HIS* 1.3 75.6 - - - +
88D ILE* 1.3 65.1 + - - +
89D THR* 3.7 6.4 + - - +
111D VAL* 3.4 6.5 - - - +
112D ARG* 2.9 44.6 + - - +
112E ARG* 5.1 6.3 - - - -
120E TYR* 3.9 18.0 + - - -
122E GLU* 3.5 18.4 - - - -
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Residues in contact with ILE 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* 5.4 1.1 - - + -
87D SER* 1.3 75.5 - - - +
89D THR* 1.3 62.6 + - - +
90D GLN* 3.6 28.7 - - - +
91D GLN* 4.2 4.9 - - + +
109D ALA* 4.9 5.6 - - + -
110D PHE 3.5 6.1 - - - +
111D VAL* 4.6 6.5 - - + +
147D VAL* 3.8 26.5 - - + -
110E PHE* 3.8 24.7 - - + -
122E GLU* 3.0 30.9 + - + +
123E ASP* 3.7 37.9 - - - +
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Residues in contact with THR 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 SER* 3.7 6.2 + - - +
88D ILE* 1.3 74.6 - - - +
90D GLN* 1.3 64.1 + - - +
110D PHE* 2.8 22.0 + - - +
112D ARG* 4.0 26.2 - - + -
122D GLU* 2.7 30.4 + - - +
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Residues in contact with GLN 90 (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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88D ILE* 3.2 9.6 - - - +
89D THR* 1.3 88.1 + - - +
91D GLN* 1.3 65.6 - - - +
92D ASN* 3.7 32.7 - - - +
109D ALA* 3.4 1.4 - - - -
110D PHE* 2.8 47.9 + - + -
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Residues in contact with GLN 91 (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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88D ILE* 4.2 4.4 - - + +
90D GLN* 1.3 82.4 - - - +
92D ASN* 1.3 67.4 + - - +
93D VAL 4.3 0.2 + - - -
107D VAL* 3.5 17.5 - - + +
108D CYS 3.2 12.3 - - - +
109D ALA* 4.0 1.7 - - + +
143D ARG* 2.9 69.2 + - - +
146D ALA* 3.7 5.5 - - - +
147D VAL* 3.6 13.9 - - - +
110E PHE* 3.2 36.9 - - + -
124E VAL* 3.9 1.2 - - - +
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Residues in contact with ASN 92 (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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143C ARG* 4.9 4.1 + - - +
90D GLN* 3.7 22.2 - - - +
91D GLN* 1.3 78.2 + - - +
93D VAL* 1.3 76.5 - - - +
94D ASP* 3.5 13.2 + - - +
107D VAL* 3.6 2.5 - - - -
108D CYS* 2.9 48.2 + - - -
110D PHE* 5.6 0.4 - - + -
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Residues in contact with VAL 93 (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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92D ASN* 1.3 80.2 + - - +
94D ASP* 1.3 64.2 + - - +
95D PHE 3.9 13.0 - - - +
96D VAL* 3.9 24.5 - - + -
107D VAL* 3.7 25.4 - - + -
139D LEU* 4.4 7.9 - - + -
143D ARG* 3.6 37.9 - - - +
94E ASP* 5.7 0.2 - - - -
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Residues in contact with ASP 94 (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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93C VAL* 5.8 0.4 - - - -
139C LEU* 3.5 14.7 - - + +
143C ARG* 2.5 34.9 + - - -
92D ASN* 3.5 17.7 + - - +
93D VAL* 1.3 73.5 - - - +
95D PHE* 1.3 71.8 + - + +
106D GLY 2.8 16.3 + - - +
108D CYS* 4.7 0.2 - - - -
126D TYR* 2.5 33.7 + - - +
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Residues in contact with PHE 95 (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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135C LYS* 3.6 42.2 - - + +
136C ALA* 3.4 35.7 - - + -
139C LEU* 4.0 12.1 - - + -
93D VAL* 3.4 3.7 - - - +
94D ASP* 1.3 90.7 - - + +
96D VAL* 1.3 68.1 + - - +
97D ASP* 3.7 18.6 - - - +
104D TYR* 3.3 35.0 - - + -
105D VAL* 3.4 5.4 - - - +
106D GLY* 3.3 35.2 + - - -
126D TYR* 4.1 0.9 - - - -
130D GLU* 5.8 0.4 - - - -
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Residues in contact with VAL 96 (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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93D VAL* 3.9 18.4 - - + -
95D PHE* 1.3 79.3 - - - +
97D ASP* 1.3 64.3 + - - +
98D LEU 4.3 0.7 + - - -
103D PHE* 4.3 20.9 - - + -
104D TYR 3.5 3.4 - - - -
105D VAL* 4.3 9.9 - - + -
135D LYS* 4.3 23.8 - - + -
139D LEU* 4.0 22.9 - - + -
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Residues in contact with ASP 97 (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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135C LYS* 2.8 39.9 + - - +
95D PHE* 3.7 10.6 - - - +
96D VAL* 1.3 81.1 + - - +
98D LEU* 1.3 60.0 + - - +
99D ASN* 4.0 19.4 - - - +
103D PHE* 3.2 8.4 - - - -
104D TYR* 2.7 52.7 + - + +
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Residues in contact with LEU 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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96D VAL 4.3 0.8 + - - -
97D ASP* 1.3 71.5 - - - +
99D ASN* 1.3 66.7 + - - +
100D ASN 3.9 19.5 - - - +
101D GLY* 4.1 13.0 - - - -
102D LYS 3.3 12.6 - - - +
103D PHE* 3.7 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