Contacts of the strand formed by residues 150 - 157 (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 GLY 150 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58F TRP* 3.4 20.1 - - - -
59F VAL 3.2 13.0 - - - -
61F ARG* 4.0 3.1 - - - -
98F GLU* 3.5 3.6 - - - +
99F SER 2.9 26.1 + - - +
148F ARG* 3.2 7.4 - - - +
149F LYS* 1.3 79.7 - - - +
151F PHE* 1.3 67.1 + - - +
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Residues in contact with PHE 151 (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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4F LEU* 4.0 15.3 - - + -
5F LEU* 6.4 0.2 - - + -
58F TRP* 3.4 5.9 - - - +
59F VAL* 2.8 72.4 + - + +
60F TYR 4.0 4.0 - - - -
61F ARG* 4.5 9.4 - - + -
67F ILE* 3.6 27.1 - - + -
96F TYR* 5.2 3.1 - + + -
97F ALA 3.3 13.5 - - - +
98F GLU* 4.2 12.6 - - + +
99F SER 4.5 0.7 - - - +
146F LEU* 3.8 23.8 - - + -
150F GLY* 1.3 78.3 - - - +
152F TYR* 1.3 68.6 + - - +
153F LEU* 3.8 23.8 - - + -
169F VAL* 4.0 14.6 - - + -
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Residues in contact with TYR 152 (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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55F ARG* 3.5 34.5 - - + -
56F THR* 3.4 20.4 - - - -
57F ASN 3.7 5.2 - - - -
58F TRP* 3.4 35.4 - + - -
96F TYR* 3.1 9.5 - - - +
97F ALA* 2.8 36.2 + - + +
99F SER* 4.1 6.1 - - - -
102F ASP* 2.6 28.3 + - - -
103F TYR* 2.8 40.7 + + - +
104F GLY 3.9 1.2 + - - -
112F PHE* 3.8 23.3 - + + -
151F PHE* 1.3 76.9 - - - +
153F LEU* 1.3 66.3 + - - +
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Residues in contact with LEU 153 (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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5F LEU* 5.4 0.7 - - + -
55F ARG* 3.4 4.0 - - - +
56F THR* 3.0 46.7 + - + +
59F VAL* 6.4 0.2 - - + -
67F ILE* 4.4 3.1 - - + -
69F ILE* 3.8 39.7 - - + -
94F LEU* 4.4 7.6 - - + -
95F TYR 3.4 7.9 - - - +
96F TYR* 4.0 11.2 - - + -
112F PHE* 4.4 1.1 - - - -
151F PHE* 3.8 22.2 - - + -
152F TYR* 1.3 82.2 - - - +
154F ALA* 1.3 61.5 + - - +
155F PHE* 4.8 4.5 - - + -
167F VAL* 4.7 9.0 - - + -
169F VAL* 3.6 29.8 - - + -
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Residues in contact with ALA 154 (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* 3.9 21.8 - - + -
54F LEU 3.1 11.0 - - - +
55F ARG* 4.3 7.6 - - + -
94F LEU* 3.7 4.7 - - - +
95F TYR* 2.8 37.5 + - + +
107F PHE* 4.4 1.1 - - + -
112F PHE* 3.7 27.1 - - + -
153F LEU* 1.3 76.7 - - - +
155F PHE* 1.3 69.0 + - - +
156F GLN 4.2 0.2 - - - -
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Residues in contact with PHE 155 (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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16F TRP* 3.6 23.3 - + - -
25F TRP* 3.1 27.1 + - + -
53F TRP* 3.3 4.7 - - - -
54F LEU* 2.7 58.5 + - + +
56F THR* 4.3 9.6 - - + -
71F LEU* 3.7 19.5 - - + -
92F PHE* 4.1 17.0 - + + -
93F ASN 3.4 5.4 - - - +
94F LEU* 3.6 26.7 - - + -
153F LEU* 4.9 5.4 - - + -
154F ALA* 1.3 80.9 - - - +
156F GLN* 1.3 58.8 + - - +
157F ASP 3.9 0.2 - - - -
164F LEU* 3.9 14.8 - - + -
167F VAL* 4.0 27.1 - - + -
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Residues in contact with GLN 156 (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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25F TRP* 4.5 2.0 - - - -
51F ASP* 2.7 31.7 + - - +
52F ASN 3.2 4.3 - - - +
53F TRP* 3.7 34.9 - - + +
92F PHE* 3.5 6.6 - - - +
93F ASN* 2.6 69.0 + - + +
95F TYR* 3.8 10.2 + - + -
154F ALA 4.2 0.6 - - - -
155F PHE* 1.3 70.5 - - - +
157F ASP* 1.3 68.9 + - - +
158F ILE* 3.8 14.2 + - - +
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Residues in contact with ASP 157 (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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25F TRP* 3.7 17.9 - - + +
42F VAL* 3.4 35.0 - - + +
44F ASN* 5.1 0.7 - - - +
50F GLN* 4.2 1.4 - - - +
51F ASP* 3.5 6.9 + - - -
52F ASN* 2.6 59.4 + - + +
91F THR 5.1 0.2 - - - +
92F PHE* 4.7 4.0 - - + -
156F GLN* 1.3 74.3 - - - +
158F ILE* 1.3 59.4 + - - +
159F GLY* 3.0 10.4 + - - -
160F ALA* 3.0 34.6 + - - +
162F VAL* 4.7 2.0 - - + +
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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