Contacts of the helix formed by residues 91 - 98 (chain A) in PDB entry 3Q28
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 TYR 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A LEU* 1.3 70.8 - - - +
92A PRO* 1.3 75.9 - - + +
93A PHE* 3.8 30.5 - + + -
94A THR* 2.7 29.9 + - + -
95A TRP* 3.5 3.9 + - - -
303A VAL 3.7 20.2 - - - -
304A ALA* 3.1 26.9 + - - -
306A LYS* 3.8 38.2 + - + +
309A GLU* 3.7 25.7 - - + +
310A GLU* 4.8 5.9 - - - +
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Residues in contact with PRO 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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90A LEU 3.5 5.4 - - - +
91A TYR* 1.3 89.1 - - + +
93A PHE* 1.3 63.5 + - + +
95A TRP* 3.1 23.5 + - + +
96A ASP* 3.2 17.8 + - - +
99A ARG* 5.2 0.2 + - - -
306A LYS* 4.5 11.7 - - - +
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Residues in contact with PHE 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 TYR* 3.2 32.2 + + + -
92A PRO* 1.3 80.3 - - + +
94A THR* 1.3 68.5 + - + +
96A ASP* 3.3 16.3 + - + +
97A ALA* 3.3 18.4 + - - +
111A VAL* 3.7 37.5 - - + -
260A VAL* 6.2 0.4 - - + -
262A VAL* 5.1 4.9 - - + -
322A MET* 6.1 4.5 - - + -
330A ILE* 4.0 28.8 - - + +
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Residues in contact with THR 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 LEU* 4.0 3.6 - - - +
91A TYR* 2.7 26.7 + - + +
93A PHE* 1.3 103.6 - - + +
95A TRP* 1.3 64.6 + - - +
97A ALA* 3.2 19.0 + - - +
98A VAL* 3.6 4.2 + - - +
108A PRO* 3.5 35.3 - - - +
111A VAL* 4.1 11.7 - - + -
262A VAL* 4.4 6.7 - - + +
304A ALA* 3.7 23.7 - - + +
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Residues in contact with TRP 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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80A ILE* 3.9 21.1 - - + -
82A PRO* 3.9 15.5 - - + -
86A PHE* 4.0 17.3 - + - -
87A GLN* 2.9 55.8 + - + +
90A LEU* 3.5 27.3 - - + +
91A TYR 3.5 13.4 + - - -
92A PRO* 3.1 12.6 + - + +
94A THR* 1.3 79.7 + - - +
96A ASP* 1.3 65.4 + - - +
98A VAL* 3.2 21.4 + - + +
99A ARG* 3.3 29.7 + - - +
104A LEU* 3.8 22.7 - - + +
106A ALA 4.0 0.2 - - - -
107A TYR* 4.1 4.5 - + - -
108A PRO* 3.4 30.3 - - + -
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Residues in contact with ASP 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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92A PRO* 3.2 17.6 + - - +
93A PHE* 3.5 17.4 - - + +
94A THR 3.3 0.2 - - - -
95A TRP* 1.3 77.1 - - - +
97A ALA* 1.3 62.2 + - - +
99A ARG* 2.4 53.0 + - - +
333A ASN* 4.8 1.0 + - - -
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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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65A HIS* 3.3 34.3 - - + +
93A PHE 3.3 7.6 + - - +
94A THR 3.2 11.5 + - - +
95A TRP 3.2 0.8 - - - -
96A ASP* 1.3 79.1 - - - +
98A VAL* 1.3 59.1 + - - +
99A ARG 3.4 0.2 - - - -
262A VAL* 3.6 30.1 - - + -
330A ILE* 4.5 9.6 - - + -
333A ASN* 3.3 17.7 + - - +
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Residues in contact with VAL 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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65A HIS* 4.3 5.8 - - + -
68A PHE* 5.2 0.4 - - + -
94A THR 3.8 11.4 - - - +
95A TRP* 3.2 21.1 + - + +
97A ALA* 1.3 81.0 - - + +
99A ARG* 1.3 59.3 + - - +
104A LEU* 3.6 4.0 - - + -
105A ILE* 3.0 37.1 + - + +
106A ALA* 3.2 34.8 - - + +
108A PRO* 3.8 14.4 - - + -
262A VAL* 5.1 0.2 - - + -
264A SER* 3.3 35.0 - - - +
333A ASN* 4.6 0.2 - - - -
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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