Contacts of the strand formed by residues 92 - 99 (chain F) in PDB entry 3HPN
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 PHE 92 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25F TRP* 5.0 7.0 - + + -
71F LEU* 4.1 7.6 - - + -
73F PHE* 3.6 39.3 - + - -
75F VAL* 5.1 2.2 - - + -
91F THR* 1.3 78.6 - - - +
93F ASN* 1.3 72.2 + - - +
117F THR* 3.8 0.9 - - - +
118F ILE* 2.6 75.8 + - + +
155F PHE* 4.1 26.0 - + + -
156F GLN 3.5 14.6 - - - +
157F ASP* 4.7 5.6 - - - +
158F ILE* 5.0 4.0 - - - -
162F VAL* 3.8 28.7 - - + -
164F LEU* 4.3 11.4 - - + -
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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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91F THR* 5.6 0.3 + - - -
92F PHE* 1.3 86.6 - - - +
94F LEU* 1.3 60.1 + - - +
95F TYR* 3.6 21.9 + - + -
114F LYS* 3.3 30.8 + - - +
116F ASP 3.8 1.8 - - - -
117F THR* 3.8 9.4 + - - +
155F PHE* 3.4 6.9 - - - +
156F GLN* 2.6 58.5 + - + +
158F ILE* 4.1 18.9 - - - +
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Residues in contact with LEU 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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69F ILE* 4.3 17.7 - - + -
71F LEU* 4.4 6.7 - - + -
92F PHE 4.3 0.2 + - - -
93F ASN* 1.3 74.1 - - - +
95F TYR* 1.3 67.8 + - - +
114F LYS* 3.7 1.2 - - - +
115F ILE* 2.8 52.6 + - + +
116F ASP 3.1 17.1 + - - +
118F ILE* 3.9 15.0 - - + -
141F ARG* 4.1 30.7 - - + -
153F LEU* 4.4 12.1 - - + -
154F ALA 3.7 4.0 - - - +
155F PHE* 3.6 32.3 - - + -
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Residues in contact with TYR 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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53F TRP* 3.7 33.9 - + + -
93F ASN* 3.6 30.4 + - + -
94F LEU* 1.3 81.2 - - - +
96F TYR* 1.3 59.7 + - - +
109F LYS 5.3 1.1 - - - -
112F PHE* 3.8 31.0 - - + -
113F THR 3.3 9.2 - - - -
114F LYS* 3.3 44.1 - - + +
115F ILE* 4.1 4.2 - - - +
153F LEU* 3.4 8.0 - - - +
154F ALA* 2.8 35.4 + - + +
156F GLN* 3.8 13.3 + - + -
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Residues in contact with TYR 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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67F ILE* 6.3 1.3 - - + -
95F TYR* 1.3 75.3 - - - +
97F ALA* 1.3 69.2 + - - +
98F GLU* 3.9 20.1 + - + -
112F PHE* 3.2 8.6 - - - -
113F THR* 2.8 68.0 + - + +
114F LYS 5.1 0.2 - - - -
115F ILE* 3.6 23.3 - - + -
143F VAL* 3.5 25.3 - - + +
144F GLY 6.1 0.3 - - - -
146F LEU* 3.9 26.8 - - + +
151F PHE* 5.2 4.0 - + + -
152F TYR 3.1 16.8 - - - +
153F LEU* 4.0 9.0 - - + -
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Residues in contact with ALA 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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96F TYR* 1.3 82.2 - - - +
98F GLU* 1.3 67.3 + - - +
103F TYR* 5.9 4.3 - - + -
111F LEU* 3.5 24.7 - - + +
112F PHE* 3.7 26.9 - - + -
151F PHE* 3.3 2.3 - - - +
152F TYR* 2.8 36.8 + - + +
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Residues in contact with GLU 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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61F ARG* 4.8 0.3 - - - -
96F TYR* 3.9 18.4 + - + -
97F ALA* 1.3 79.2 - - - +
99F SER* 1.3 65.6 + - - +
103F TYR* 5.0 2.6 + - - -
145F PRO 4.2 4.9 - - - +
146F LEU* 3.2 34.6 - - + +
147F THR* 2.7 31.9 + - - -
148F ARG* 3.2 24.7 + - + +
150F GLY 3.5 9.7 - - - +
151F PHE* 4.4 3.1 - - + -
152F TYR* 5.7 0.4 - - - -
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Residues in contact with SER 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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58F TRP* 3.6 8.1 + - - -
97F ALA 4.2 0.2 + - - -
98F GLU* 1.3 77.3 - - - +
100F ASP* 1.3 60.2 + - - +
101F LEU* 2.5 34.6 + - - -
103F TYR* 3.7 29.5 - - - -
148F ARG* 3.8 11.0 - - - +
150F GLY* 2.9 34.4 + - - +
151F PHE* 4.5 0.4 - - - +
152F TYR* 4.1 2.9 - - - -
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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