Contacts of the strand formed by residues 84 - 98 (chain U) 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 U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26U PHE* 3.8 5.1 - - - -
72U ILE* 4.2 11.9 - - + -
75U ALA* 3.4 33.7 - - + -
76U ASN* 2.8 26.5 + - - +
79U PHE* 3.9 11.2 - + + -
80U GLY 3.5 14.8 - - - -
81U TYR 4.2 6.4 - - - +
82U ASN 3.6 0.7 - - - -
83U GLY* 1.3 77.9 + - - +
85U ALA* 1.3 79.1 + - - +
86U HIS* 3.7 16.4 - + - -
113U VAL* 4.1 11.2 - - + -
114U GLN 3.1 10.8 - - - +
115U LEU* 3.9 13.9 - - + -
151U LEU* 3.9 26.5 - - + -
155U LEU* 4.2 7.2 - - + -
119V SER* 4.8 2.6 - - - -
121V HIS* 3.4 39.9 + + - -
157V SER* 3.9 19.5 - - - -
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Residues in contact with ALA 85 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26U PHE* 3.7 11.4 - - + -
84U TRP* 1.3 80.8 - - - +
86U HIS* 1.3 59.2 + - - +
113U VAL* 3.0 7.8 - - - +
114U GLN 2.7 31.5 + - - +
120V TYR* 2.8 57.9 - - + +
121V HIS* 3.9 3.6 - - - -
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Residues in contact with HIS 86 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84U TRP* 3.7 5.3 - - + -
85U ALA* 1.3 79.5 - - - +
87U SER* 1.3 62.8 + - - +
88U ILE* 5.4 0.2 - - + -
111U VAL* 4.0 15.5 - - + -
112U ARG 3.0 12.8 - - - +
113U VAL* 4.0 4.7 - - + -
147U VAL* 5.2 6.4 - - + +
151U LEU* 3.7 41.7 - - + +
120V TYR* 3.2 10.9 + - - -
121V HIS* 2.8 46.5 - + + -
122V GLU 3.0 46.6 + - - -
123V ASP* 5.0 6.0 + - + -
157V SER* 3.6 17.3 - - - -
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Residues in contact with SER 87 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86U HIS* 1.3 74.7 - - - +
88U ILE* 1.3 65.8 + - - +
89U THR* 3.6 5.9 + - - +
111U VAL* 3.4 6.9 - - - +
112U ARG* 2.9 47.0 + - - +
112V ARG* 5.1 6.7 - - - -
120V TYR* 3.9 19.2 + - - -
122V GLU* 3.5 18.2 - - - -
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Residues in contact with ILE 88 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86U HIS* 5.4 0.7 - - + -
87U SER* 1.3 74.6 - - - +
89U THR* 1.3 62.1 + - - +
90U GLN* 3.7 27.8 - - - +
91U GLN* 4.2 4.3 - - + +
109U ALA* 5.0 4.0 - - + -
110U PHE 3.4 8.3 - - - +
111U VAL* 4.6 5.8 - - + +
147U VAL* 3.8 29.6 - - + -
110V PHE* 3.7 33.2 - - + -
122V GLU* 3.0 29.8 + - + +
123V ASP* 3.8 26.9 - - - +
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Residues in contact with THR 89 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87U SER* 3.6 6.2 + - - +
88U ILE* 1.3 73.1 - - - +
90U GLN* 1.3 64.0 + - - +
110U PHE* 2.8 23.6 + - - +
112U ARG* 4.0 28.0 - - + -
122U GLU* 2.6 30.9 + - - +
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Residues in contact with GLN 90 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88U ILE* 3.1 10.4 - - - +
89U THR* 1.3 88.6 + - - +
91U GLN* 1.3 65.6 + - - +
92U ASN* 3.7 32.5 - - - +
109U ALA* 3.4 1.4 - - - -
110U PHE* 2.8 50.5 + - + -
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Residues in contact with GLN 91 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88U ILE* 4.2 4.4 - - + +
90U GLN* 1.3 83.2 + - - +
92U ASN* 1.3 64.3 + - - +
93U VAL 4.3 0.6 + - - -
107U VAL* 3.6 18.4 - - + +
108U CYS 3.3 13.9 - - - +
109U ALA* 4.0 2.1 - - + +
143U ARG* 2.9 69.3 + - - +
146U ALA* 3.8 5.1 - - - +
147U VAL* 3.5 15.8 - - - +
110V PHE* 3.2 35.8 - - + -
124V VAL* 3.8 0.9 - - - +
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Residues in contact with ASN 92 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143T ARG* 4.9 4.2 + - - +
90U GLN* 3.7 22.5 - - - +
91U GLN* 1.3 77.0 + - - +
93U VAL* 1.3 76.9 + - - +
94U ASP* 3.4 13.8 + - - +
107U VAL* 3.6 2.8 - - - +
108U CYS* 2.8 50.5 + - - -
110U PHE* 5.6 0.4 - - + -
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Residues in contact with VAL 93 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91U GLN 4.3 0.6 + - - -
92U ASN* 1.3 81.4 + - - +
94U ASP* 1.3 64.3 + - - +
95U PHE* 3.8 13.4 - - - +
96U VAL* 3.9 24.9 - - + -
106U GLY 3.9 5.6 - - - +
107U VAL* 3.8 19.1 - - + -
139U LEU* 4.4 7.6 - - + -
143U ARG* 3.5 38.6 - - - +
94V ASP* 5.3 0.4 - - - +
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Residues in contact with ASP 94 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93T VAL* 5.3 1.2 - - - +
139T LEU* 3.4 14.5 - - + +
143T ARG* 2.6 33.9 + - - -
92U ASN* 3.4 16.3 + - - +
93U VAL* 1.3 73.5 - - - +
95U PHE* 1.3 71.8 + - + +
106U GLY 2.8 18.1 + - - +
126U TYR* 2.6 32.3 + - - +
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Residues in contact with PHE 95 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135T LYS* 3.6 40.4 - - + +
136T ALA* 3.3 43.1 - - + -
139T LEU* 3.9 12.3 - - + -
93U VAL* 3.4 4.7 - - - +
94U ASP* 1.3 90.7 - - + +
96U VAL* 1.3 70.5 + - - +
97U ASP* 3.6 17.7 - - - +
104U TYR* 3.2 35.2 - - + -
105U VAL* 3.4 4.7 - - - +
106U GLY* 3.3 33.3 + - - +
126U TYR* 4.0 0.4 - - - -
130U GLU* 5.7 0.2 - - - -
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Residues in contact with VAL 96 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93U VAL* 3.9 17.3 - - + -
95U PHE* 1.3 80.5 - - - +
97U ASP* 1.3 65.5 + - - +
98U LEU 4.2 0.3 + - - -
103U PHE* 4.2 19.7 - - + -
104U TYR 3.6 2.9 - - - -
105U VAL* 4.1 13.5 - - + -
135U LYS* 4.3 23.6 - - + -
139U LEU* 3.9 22.4 - - + -
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Residues in contact with ASP 97 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135T LYS* 2.8 41.7 + - - +
95U PHE* 3.6 7.9 - - - +
96U VAL* 1.3 81.5 + - - +
98U LEU* 1.3 59.2 + - - +
99U ASN* 3.9 19.5 - - - +
102U LYS 3.7 0.3 - - - +
103U PHE* 3.1 8.6 - - - -
104U TYR* 2.6 53.2 + - + +
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Residues in contact with LEU 98 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96U VAL 4.2 1.2 + - - -
97U ASP* 1.3 72.0 - - - +
99U ASN* 1.3 65.0 + - - +
100U ASN 3.8 20.0 - - - +
101U GLY* 4.0 12.1 - - - -
102U LYS 3.3 14.1 - - - +
103U PHE* 3.8 33.4 - - + -
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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