Contacts of the strand formed by residues 92 - 99 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A TRP* 4.9 7.4 - + + -
71A LEU* 4.1 7.9 - - + -
73A PHE* 3.5 40.8 - + - -
75A VAL* 5.0 1.8 - - + -
91A THR* 1.3 78.6 - - - +
93A ASN* 1.3 71.8 + - - +
117A THR* 3.7 1.2 - - - +
118A ILE* 2.7 74.3 + - + +
155A PHE* 4.1 25.8 - + + -
156A GLN 3.4 14.8 - - - +
157A ASP* 4.6 5.4 - - - -
158A ILE* 5.0 3.8 - - - -
162A VAL* 3.7 30.7 - - + -
164A LEU* 4.4 10.8 - - + -
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Residues in contact with ASN 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A THR* 5.6 0.3 + - - -
92A PHE* 1.3 83.3 - - - +
94A LEU* 1.3 59.2 + - - +
95A TYR* 3.5 22.3 + - + -
114A LYS* 3.2 31.9 + - - +
116A ASP 3.8 2.0 - - - -
117A THR* 3.7 9.9 + - - +
154A ALA 3.8 0.2 - - - +
155A PHE* 3.4 9.9 - - - +
156A GLN* 2.6 57.5 + - + +
158A ILE* 4.0 19.2 - - - +
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Residues in contact with LEU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ILE* 4.3 14.4 - - + -
71A LEU* 4.5 7.0 - - + -
92A PHE 4.3 0.2 + - - -
93A ASN* 1.3 73.4 - - - +
95A TYR* 1.3 72.0 + - - +
114A LYS* 3.7 0.7 - - - +
115A ILE* 2.7 62.9 + - + +
116A ASP 3.0 17.0 + - - +
118A ILE* 3.9 16.1 - - + +
141A ARG* 4.1 22.2 - - + -
153A LEU* 4.4 15.0 - - + -
154A ALA 3.7 4.3 - - - +
155A PHE* 3.8 30.3 - - + +
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Residues in contact with TYR 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A TRP* 3.7 34.8 - + + -
93A ASN* 3.5 30.9 + - + -
94A LEU* 1.3 85.1 - - - +
96A TYR* 1.3 60.4 + - - +
109A LYS 5.2 1.8 - - - -
112A PHE* 3.8 32.1 - - + -
113A THR 3.2 22.7 - - - -
114A LYS* 3.5 34.5 - - + +
115A ILE* 4.1 4.3 - - - +
153A LEU* 3.4 4.0 - - - +
154A ALA 2.8 35.1 + - - +
156A GLN* 3.8 11.2 + - + -
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Residues in contact with TYR 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ILE* 6.2 1.3 - - + -
95A TYR* 1.3 76.1 - - - +
97A ALA* 1.3 68.9 + - - +
98A GLU* 4.0 17.8 + - + -
111A LEU 4.5 0.2 - - - +
112A PHE* 3.4 7.9 - - - -
113A THR* 2.8 64.7 + - + +
114A LYS 5.2 0.2 - - - -
115A ILE* 3.6 27.6 - - + -
143A VAL* 3.4 28.2 - - + +
144A GLY 6.1 0.2 - - - -
146A LEU* 3.8 23.6 - - + +
151A PHE* 5.2 4.3 - + + -
152A TYR 3.2 15.5 - - - +
153A LEU* 4.0 9.4 - - + -
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Residues in contact with ALA 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A TYR* 1.3 82.1 - - - +
98A GLU* 1.3 66.4 + - - +
103A TYR* 5.7 5.4 - - + -
111A LEU* 3.6 23.3 - - + +
112A PHE* 3.7 25.3 - - + -
151A PHE* 3.3 2.4 - - - +
152A TYR* 2.8 36.6 + - + +
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Residues in contact with GLU 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ARG* 4.9 0.2 - - - -
96A TYR* 4.0 16.3 + - + -
97A ALA* 1.3 81.1 - - - +
99A SER* 1.3 67.2 + - - +
103A TYR* 5.0 2.8 + - - -
145A PRO 4.3 5.0 - - - +
146A LEU* 3.3 34.3 - - + +
147A THR* 2.7 32.5 + - - -
148A ARG* 3.1 27.2 + - + +
150A GLY 3.4 9.1 - - - +
151A PHE* 4.4 3.1 - - + -
152A TYR* 5.7 0.2 - - - -
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Residues in contact with SER 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A TRP* 3.5 9.7 + - - -
97A ALA 4.2 0.2 + - - -
98A GLU* 1.3 77.6 - - - +
100A ASP* 1.3 59.9 + - - +
101A LEU* 2.4 35.9 + - - -
103A TYR* 3.7 28.8 - - - -
148A ARG* 3.7 11.2 - - - +
150A GLY 2.9 33.9 + - - +
151A PHE* 4.5 0.4 - - - +
152A TYR* 4.3 2.7 - - - -
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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