Contacts of the helix formed by residues 88 - 95 (chain A) in PDB entry 3RGZ
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 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A GLY* 1.3 71.2 - - - -
89A SER* 1.3 54.0 + - - +
91A VAL* 2.9 10.1 + - + +
92A SER* 2.7 52.8 + - - -
96A LEU* 3.8 27.6 - - + -
111A ILE* 3.7 9.5 - - + +
112A ASN 3.1 15.7 + - - +
113A GLY* 5.0 1.0 - - - -
114A SER 3.7 14.8 - - - +
115A VAL* 3.6 36.6 - - + -
116A SER* 4.3 4.3 - - - -
118A PHE* 4.0 17.7 - + - -
129A LEU* 3.8 38.4 - - + -
134A LEU* 4.0 14.8 - - + -
144A LEU* 4.5 5.2 - - + -
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Residues in contact with SER 89 (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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87A GLY* 4.4 5.9 - - - -
88A PHE* 1.3 81.7 - - - +
90A ALA* 1.3 55.4 + - - +
92A SER* 3.3 9.3 + - - -
93A SER* 2.4 41.2 + - - -
114A SER 4.8 3.6 + - - -
116A SER* 5.7 4.7 - - - -
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Residues in contact with ALA 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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42A PHE* 3.8 6.3 - - + -
45A VAL* 4.3 20.6 - - + -
86A VAL* 4.3 17.9 - - + -
87A GLY 3.0 12.9 + - - +
89A SER* 1.3 79.6 + - - +
91A VAL* 1.3 63.3 + - - +
93A SER* 3.9 4.4 - - - -
94A SER* 3.2 28.2 + - - -
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Residues in contact with VAL 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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42A PHE* 4.0 21.5 - - + -
86A VAL* 4.4 1.6 - - + -
87A GLY 3.4 11.0 + - - +
88A PHE* 2.9 18.9 + - + +
90A ALA* 1.3 76.3 - - - +
92A SER* 1.3 60.4 + - - +
95A LEU* 2.9 29.9 + - + +
96A LEU* 3.2 12.2 + - + -
104A LEU* 4.0 15.7 - - + -
106A LEU* 3.6 34.1 - - + -
111A ILE* 4.1 23.6 - - + -
129A LEU* 5.3 1.6 - - + -
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Residues in contact with SER 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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88A PHE* 2.7 41.6 + - - -
89A SER* 3.3 14.4 + - - -
91A VAL* 1.3 74.5 - - - +
93A SER* 1.3 65.7 + - - +
94A SER 3.6 0.2 + - - -
96A LEU* 3.9 20.1 - - - +
97A SER* 3.9 10.9 + - - -
116A SER 5.4 0.2 + - - -
118A PHE* 3.6 36.8 - - - +
119A LYS 4.3 1.0 - - - +
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Residues in contact with SER 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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38A GLN* 4.1 2.4 - - - +
89A SER* 2.4 27.6 + - - -
90A ALA* 3.9 6.4 - - - -
92A SER* 1.3 78.9 + - - +
94A SER* 1.3 61.8 + - - +
97A SER* 3.1 16.3 + - - -
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Residues in contact with SER 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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38A GLN* 3.1 41.2 - - - +
41A SER* 3.2 19.7 + - - -
42A PHE* 3.6 29.5 + - - +
45A VAL* 5.9 0.5 - - - +
90A ALA 3.2 14.5 + - - -
93A SER* 1.3 81.9 - - - +
95A LEU* 1.3 64.9 + - - +
97A SER* 4.1 0.7 - - - -
98A LEU* 4.1 2.4 - - - +
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Residues in contact with LEU 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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38A GLN 4.9 0.9 - - - +
39A LEU* 4.2 24.5 - - + -
42A PHE* 3.8 56.8 - - + -
55A TRP* 4.9 3.1 - - + -
77A ILE* 4.2 10.3 - - + -
79A LEU* 4.3 12.3 - - + -
91A VAL* 2.9 19.8 + - + +
94A SER* 1.3 74.1 - - - +
96A LEU* 1.3 60.2 + - - +
97A SER 3.1 4.9 - - - -
98A LEU* 3.1 28.4 + - - +
101A LEU* 3.4 11.2 - - - +
104A LEU* 4.1 31.6 - - + -
106A LEU* 4.7 3.6 - - + -
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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