Contacts of the strand formed by residues 90 - 99 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81F TRP* 3.9 7.9 - - - -
85F GLN* 4.6 10.8 - - - +
88F GLY 4.5 5.6 - - - +
89F TYR* 1.3 79.4 - - - +
91F LEU* 1.3 62.4 + - - +
154F LEU* 3.5 6.8 - - - +
155F ILE* 2.8 54.0 + - - +
156F LYS 4.5 4.4 + - - +
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Residues in contact with LEU 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F LEU* 3.9 17.3 - - + -
81F TRP* 3.6 19.9 - - + -
90F THR* 1.3 78.0 + - - +
92F GLY* 1.3 70.9 + - - +
93F ASN 4.2 0.9 - - - +
94F VAL* 3.6 26.5 - - + -
120F LEU* 4.0 18.6 - - + +
122F CYS* 3.5 41.1 - - + -
126F ASP* 4.3 17.6 - - + +
127F VAL* 5.1 0.2 - - + -
153F LEU 4.1 8.3 - - - +
154F LEU* 4.2 3.8 - - + -
155F ILE* 3.7 10.6 - - - +
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Residues in contact with GLY 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E MET 5.4 3.1 - - - -
2E ARG* 4.5 2.3 + - - -
1F MET* 5.3 3.4 - - - -
90F THR 3.7 1.4 + - - -
91F LEU* 1.3 74.6 - - - +
93F ASN* 1.3 65.4 + - - +
126F ASP* 3.5 24.1 - - - +
153F LEU* 2.9 21.8 + - - -
155F ILE* 3.8 18.7 - - - +
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Residues in contact with ASN 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E MET 4.1 0.2 - - - +
2E ARG* 3.2 35.5 - - + +
3E ILE* 2.8 51.8 + - - +
50E GLY 4.7 2.0 + - - -
51E ALA* 4.1 11.5 + - - +
91F LEU* 4.1 3.8 - - - +
92F GLY* 1.3 78.0 - - - +
94F VAL* 1.3 73.8 + - - +
126F ASP 3.3 13.2 - - - +
152F ALA* 3.5 1.0 - - - -
153F LEU* 3.0 32.6 + - - +
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Residues in contact with VAL 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E ARG* 5.6 0.5 + - - -
3E ILE* 5.5 0.2 - - - -
44F LEU* 3.7 32.5 - - + -
48F LEU* 3.9 4.7 - - + -
91F LEU* 3.6 22.2 - - + -
93F ASN* 1.3 86.8 + - - +
95F ASP* 1.3 61.9 + - - +
96F VAL* 4.8 4.3 - - + -
116F ILE* 4.4 6.7 - - + -
120F LEU* 4.4 4.3 - - + -
126F ASP 3.0 12.3 + - - +
127F VAL* 4.1 28.9 - - + -
128F ASN* 3.0 23.3 + - - +
151F VAL 3.4 5.8 - - - +
152F ALA* 3.8 13.0 - - + -
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Residues in contact with ASP 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E ILE 4.1 10.8 - - - +
5E HIS* 2.8 23.8 + - - +
50E GLY* 3.6 15.6 - - - +
94F VAL* 1.3 76.0 - - - +
96F VAL* 1.3 64.5 + - - +
128F ASN* 2.9 33.1 + - - +
130F LYS* 2.6 27.4 + - - -
150F ALA* 3.2 4.0 - - - -
151F VAL* 3.0 47.2 + - + +
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Residues in contact with VAL 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F ALA* 4.4 14.8 - - + +
44F LEU* 4.3 24.5 - - + -
94F VAL* 4.8 4.3 - - + -
95F ASP* 1.3 80.7 + - - +
97F THR* 1.3 68.5 + - - +
98F ILE* 4.5 1.1 - - + -
116F ILE* 5.1 5.2 - - + -
128F ASN 2.8 15.6 + - - +
129F VAL* 3.6 21.4 - - + -
130F LYS* 2.9 32.2 + - - +
148F CYS* 3.4 26.5 - - - -
149F GLU 3.5 4.5 - - - +
150F ALA* 4.1 11.7 - - + -
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Residues in contact with THR 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E HIS* 3.3 22.7 + - - +
7E PHE* 4.4 20.0 - - + +
46E ASP* 5.9 0.4 - - - +
95F ASP 5.2 0.2 + - - -
96F VAL* 1.3 72.6 - - - +
98F ILE* 1.3 66.5 + - - +
99F ILE* 3.8 14.8 + - + +
130F LYS* 2.8 38.8 + - + -
132F THR* 4.5 8.7 - - + +
148F CYS* 3.3 7.9 - - - -
149F GLU* 2.8 35.9 + - - -
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Residues in contact with ILE 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F ILE* 3.8 26.9 - - + -
40F ALA* 4.4 4.0 - - + -
96F VAL* 4.5 2.5 - - + -
97F THR* 1.3 74.4 - - - +
99F ILE* 1.3 64.4 + - - +
100F ALA* 4.0 5.1 + - + -
105F MET* 4.0 39.0 - - + -
109F ILE* 5.0 0.7 - - + -
112F MET* 4.0 12.6 - - + -
129F VAL* 3.7 26.7 - - + -
130F LYS 2.9 13.8 + - - +
131F ALA* 3.3 4.5 - - + +
132F THR* 2.9 26.7 + - - +
146F ILE* 4.1 16.2 - - + -
147F ALA 3.8 3.1 - - - -
148F CYS* 4.0 14.8 - - + -
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Residues in contact with ILE 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E PHE* 3.7 32.8 - - + -
904E GPP 4.2 21.8 - - + -
7F PHE* 5.3 0.2 - - + -
97F THR* 4.1 9.4 - - + +
98F ILE* 1.3 78.3 - - - +
100F ALA* 1.3 63.8 + - - +
132F THR* 3.4 12.6 - - + +
134F THR* 3.6 31.6 - - + +
140F THR* 3.8 14.3 - - + +
146F ILE* 3.4 3.8 - - - +
147F ALA* 2.8 52.1 + - + +
149F GLU* 4.3 17.5 - - + -
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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