Contacts of the helix formed by residues 89 - 94 (chain A) in PDB entry 3HN3
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 ASP 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A PHE* 4.8 10.7 - - - -
84A ASN 5.4 0.7 - - - +
87A SER* 3.1 17.7 + - - +
88A GLN* 1.3 74.4 - - - +
90A TRP* 1.3 65.4 + - - +
91A ARG* 2.9 25.0 + - - +
92A LEU* 3.1 26.9 + - + +
93A ARG* 3.5 9.2 + - - +
553E PRO* 4.2 3.8 - - - +
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Residues in contact with TRP 90 (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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88A GLN 3.2 16.3 + - - -
89A ASP* 1.3 74.1 + - - +
91A ARG* 1.3 69.6 + - + +
92A LEU 3.4 0.3 + - - -
93A ARG* 3.5 9.2 + - - +
94A HIS* 3.9 18.2 + - - +
375D TRP* 6.0 1.0 - - - +
514E LEU* 4.0 18.6 - - + -
552E ASP* 4.4 10.0 + - - -
553E PRO* 3.8 24.7 - - + +
554E PRO* 3.4 37.9 - - + -
564E SER* 4.3 11.7 - - - -
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Residues in contact with ARG 91 (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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51A PHE* 4.0 21.3 - - + -
89A ASP* 2.9 11.7 + - - +
90A TRP* 1.3 81.7 - - + +
92A LEU* 1.3 64.3 + - - +
93A ARG 3.5 0.2 - - - -
94A HIS* 3.8 2.5 + - - +
95A PHE* 3.1 23.6 + - - +
515E GLU* 6.3 1.4 - - - +
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Residues in contact with LEU 92 (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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47A PHE* 4.1 21.1 - - + -
49A ALA* 3.9 27.6 - - + -
51A PHE* 4.4 6.7 - - + -
75A VAL* 6.0 2.2 - - + -
77A MET* 4.7 4.9 - - + -
83A PHE* 3.4 44.0 - - + +
84A ASN* 5.3 1.1 - - - +
87A SER* 3.7 21.8 - - - +
89A ASP* 3.1 24.0 + - + +
91A ARG* 1.3 77.9 - - - +
93A ARG* 1.3 65.2 + - - +
95A PHE* 3.2 20.4 + - + +
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Residues in contact with ARG 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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84A ASN* 2.9 53.4 + - + +
85A ASP* 3.0 23.0 + - - +
89A ASP 3.5 7.4 + - - +
90A TRP* 3.5 9.2 + - - +
91A ARG 3.5 0.6 - - - -
92A LEU* 1.3 77.7 - - - +
94A HIS* 1.3 100.0 + - + +
95A PHE 4.9 0.2 - - - +
209A PHE* 3.6 29.5 - - + -
593A MET* 3.4 41.6 - - - +
594A THR 4.6 1.8 + - - -
595A GLU* 5.4 1.0 + - - +
596A GLN* 5.0 3.4 - - - +
551E GLN* 4.1 9.1 - - - +
553E PRO* 5.4 15.3 - - + -
555E LEU* 3.8 26.1 - - - +
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Residues in contact with HIS 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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90A TRP 3.9 13.8 + - - +
91A ARG* 3.8 5.3 + - - +
92A LEU 3.2 0.4 - - - -
93A ARG* 1.3 116.5 + - + +
95A PHE* 1.3 66.2 + - - +
96A VAL* 3.6 12.0 + - - +
209A PHE* 4.0 17.9 - + - -
595A GLU* 4.3 11.5 + - - -
596A GLN* 3.9 21.9 + - - -
513E HIS* 6.5 1.6 - - + -
553E PRO* 6.5 1.3 - - + -
554E PRO 5.9 0.4 - - - -
555E LEU* 4.5 4.9 - - + -
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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