Contacts of the helix formed by residues 116 - 120 (chain A) in PDB entry 1PHP
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 ASN 116 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A SER 3.5 8.3 - - - -
59A HIS* 3.4 1.9 - - - -
60A LEU* 3.0 42.2 + - - +
63A PRO* 4.1 2.7 - - - +
71A LEU* 2.9 30.7 + - - +
73A LEU* 3.7 8.8 - - + +
115A GLU* 1.3 79.0 + - - +
117A VAL* 1.3 65.6 + - - +
118A ARG* 3.0 18.5 + - - +
119A PHE* 3.3 44.2 + - + +
120A TYR* 4.2 4.3 - - - -
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Residues in contact with VAL 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ARG* 4.2 2.7 - - - +
57A ALA* 4.1 23.6 - - + -
58A SER 3.0 30.6 + - - +
59A HIS* 4.1 9.2 - - + +
94A ALA* 4.6 3.6 - - + -
114A LEU* 5.5 0.9 - - + -
115A GLU 3.1 10.1 + - - +
116A ASN* 1.3 72.3 + - - +
118A ARG* 1.3 61.4 + - - +
119A PHE 3.2 4.5 + - - -
120A TYR* 3.4 19.2 + - - +
123A GLU* 3.4 43.4 - - + +
130A LEU* 5.1 0.5 - - - +
134A PHE* 3.9 25.4 - - + -
155A SER* 3.9 9.9 - - - +
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Residues in contact with ARG 118 (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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19A ARG* 4.8 5.1 - - - +
59A HIS* 3.2 52.4 + - + +
61A GLY 3.6 14.2 + - - -
62A ARG* 4.9 9.4 - - - +
63A PRO* 3.4 26.1 - - + +
65A GLY* 2.9 29.5 + - - -
116A ASN* 3.0 7.5 + - - +
117A VAL* 1.3 76.8 - - + +
119A PHE* 1.3 52.3 + - - +
120A TYR 3.1 7.6 - - - +
123A GLU* 4.0 15.8 - - + +
124A GLU* 3.8 31.4 + - - +
148A ALA* 5.4 4.8 - - - +
153A HIS* 3.7 27.0 + - - -
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Residues in contact with PHE 119 (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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63A PRO* 3.7 13.9 - - + -
65A GLY 3.3 15.4 - - - +
66A LYS* 3.3 27.8 + - - +
67A VAL* 3.8 25.4 + - + +
68A VAL 3.3 33.4 - - - -
71A LEU* 3.7 18.4 - - + -
72A ARG* 3.9 14.1 - - + -
92A ASN 5.3 0.9 - - - -
115A GLU* 3.6 35.9 - - + -
116A ASN* 3.5 29.6 - - + +
117A VAL 3.2 0.6 - - - -
118A ARG* 1.3 75.5 - - - +
120A TYR* 1.3 69.5 + + + +
121A PRO* 3.9 1.6 - - - +
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Residues in contact with TYR 120 (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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65A GLY* 3.9 3.4 - - - -
93A GLU* 3.4 18.0 - - - +
94A ALA* 2.9 45.8 + - + -
95A VAL* 3.8 20.6 + - + +
115A GLU* 5.3 1.3 - - + -
116A ASN 4.2 7.4 - - - -
117A VAL* 3.4 19.9 - - - +
118A ARG 3.1 4.7 - - - +
119A PHE* 1.3 91.2 - + + +
121A PRO* 1.3 72.4 - - + +
122A GLY 4.3 1.1 - - - +
123A GLU* 3.1 17.0 + - - +
124A GLU* 4.5 2.8 + - - +
130A LEU* 3.9 31.4 - - + -
134A PHE* 5.5 1.6 - + - -
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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