Contacts of the strand formed by residues 90 - 99 (chain D) in PDB entry 1H48
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 THR 90 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81D TRP* 3.8 10.1 - - - -
85D GLN* 4.5 11.0 - - - +
88D GLY 4.7 5.2 - - - +
89D TYR* 1.3 80.9 - - - +
91D LEU* 1.3 62.9 + - - +
154D LEU* 3.6 6.6 - - - +
155D ILE* 2.8 51.6 + - - +
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Residues in contact with LEU 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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48D LEU* 3.5 31.6 - - + -
81D TRP* 3.6 20.6 - - + -
90D THR* 1.3 77.1 + - - +
92D GLY* 1.3 68.8 + - - +
93D ASN* 4.1 2.5 - - - +
94D VAL* 3.7 17.9 - - + -
120D LEU* 4.0 17.0 - - + +
122D CYS* 3.7 37.9 - - + -
126D ASP* 4.5 16.3 - - + +
153D LEU 4.3 2.5 - - - +
154D LEU* 3.8 9.0 - - + -
155D ILE* 4.2 9.1 - - - +
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Residues in contact with GLY 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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1D MET* 6.0 0.4 - - - -
90D THR 3.7 2.0 + - - -
91D LEU* 1.3 76.4 - - - +
93D ASN* 1.3 64.8 + - - +
126D ASP* 3.6 19.9 - - - +
153D LEU* 2.7 26.1 + - - -
155D ILE* 4.1 17.8 - - - +
1F MET 5.1 5.8 - - - -
2F ARG* 4.8 2.3 + - - +
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Residues in contact with ASN 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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91D LEU* 4.1 2.6 - - - +
92D GLY* 1.3 77.8 - - - +
94D VAL* 1.3 76.5 + - - +
126D ASP* 3.3 15.3 - - - +
152D ALA* 3.6 0.7 - - - -
153D LEU* 3.0 31.6 + - - +
1F MET 4.1 0.2 - - - +
2F ARG* 3.4 32.3 - - + +
3F ILE* 2.8 52.7 + - - +
50F GLY 4.6 2.0 + - - -
51F ALA* 4.0 11.9 + - - +
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Residues in contact with VAL 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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44D LEU* 3.8 30.7 - - + -
48D LEU* 4.0 2.7 - - + -
91D LEU* 3.7 25.8 - - + -
93D ASN* 1.3 86.0 + - - +
95D ASP* 1.3 63.4 + - - +
96D VAL* 4.9 4.0 - - + -
116D ILE* 4.4 6.5 - - + -
120D LEU* 4.4 3.4 - - + -
126D ASP 2.9 15.6 + - - +
127D VAL* 4.0 26.2 - - + -
128D ASN* 3.0 23.9 + - - +
151D VAL* 3.4 8.3 - - - +
152D ALA* 3.9 11.9 - - + -
2F ARG* 5.6 0.2 + - - -
3F ILE* 5.3 0.2 - - - -
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Residues in contact with ASP 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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94D VAL* 1.3 76.2 - - - +
96D VAL* 1.3 67.0 + - - +
128D ASN* 2.9 28.7 + - - -
130D LYS* 2.8 27.3 + - - -
150D ALA* 3.2 2.6 - - - -
151D VAL* 2.8 47.2 + - + +
3F ILE 4.1 11.4 - - - +
4F GLY* 3.6 0.2 - - - -
5F HIS* 2.9 24.3 + - - +
50F GLY* 3.4 21.4 - - - +
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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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40D ALA* 4.3 14.6 - - + +
44D LEU* 4.3 24.7 - - + -
94D VAL* 4.9 3.8 - - + -
95D ASP* 1.3 81.1 + - - +
97D THR* 1.3 63.0 + - - +
98D ILE* 4.6 0.4 - - + -
116D ILE* 4.9 5.4 - - + -
128D ASN 3.0 13.8 + - - +
129D VAL* 3.5 23.7 - - + -
130D LYS* 2.8 36.1 + - - +
148D CYS* 3.4 26.2 - - - -
149D GLU 3.4 6.1 - - - +
150D ALA* 4.2 11.2 - - + -
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Residues in contact with THR 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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95D ASP 5.3 0.2 - - - -
96D VAL* 1.3 72.1 - - - +
98D ILE* 1.3 61.7 + - - +
99D ILE* 3.8 9.8 + - + +
130D LYS* 2.9 37.7 + - + +
132D THR* 4.1 25.6 - - + -
148D CYS* 3.1 8.2 - - - -
149D GLU* 2.9 35.1 + - - +
5F HIS* 3.3 20.2 + - - +
7F PHE* 4.3 17.3 - - + +
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Residues in contact with ILE 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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20D ILE* 3.7 28.9 - - + -
40D ALA* 4.4 4.5 - - + -
97D THR* 1.3 74.7 - - - +
99D ILE* 1.3 62.7 + - - +
100D ALA* 4.0 8.2 + - + -
105D MET* 3.8 39.9 - - + -
109D ILE* 5.0 1.6 - - + -
112D MET* 3.8 23.1 - - + -
129D VAL* 3.9 15.0 - - + -
130D LYS 2.8 14.5 + - - +
131D ALA* 3.3 3.8 - - + +
132D THR* 2.9 27.9 + - - +
146D ILE* 4.3 9.9 - - + -
147D ALA 4.0 2.5 - - - +
148D CYS* 4.0 14.8 - - + -
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Residues in contact with ILE 99 (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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7D PHE* 5.3 2.7 - - + -
97D THR* 4.2 8.3 - - + +
98D ILE* 1.3 76.7 - - - +
100D ALA* 1.3 63.8 + - - +
132D THR* 3.4 22.0 - - + +
133D THR 4.9 0.2 - - - -
134D THR* 3.5 31.6 - - + -
140D THR* 3.8 13.3 - - + +
146D ILE* 3.5 3.0 - - - +
147D ALA* 2.7 55.4 + - + +
149D GLU* 4.2 27.4 - - + +
904E GPP 6.5 1.1 - - + -
7F PHE* 3.8 27.6 - - + -
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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