Contacts of the helix formed by residues 98 - 106 (chain A) in PDB entry 1A9Q
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 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A TYR* 3.5 44.0 - + + -
10A TYR* 3.5 44.9 - + - -
13A THR* 3.4 24.5 - - + -
55A ASN* 3.6 20.4 - - + -
56A PHE* 3.8 21.5 - + - -
57A PRO* 3.7 17.7 - - + -
94A TRP 3.7 6.5 + - - -
95A LYS 3.3 13.3 + - - +
97A THR* 1.3 76.0 - - - +
99A PRO* 1.4 70.6 - - + +
100A VAL 3.3 0.5 + - - -
101A ARG 3.3 8.5 + - - -
102A VAL* 3.4 28.0 + - + +
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Residues in contact with PRO 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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56A PHE* 3.8 31.0 - - + -
81A MET* 3.6 37.9 - - + -
85A PHE* 3.9 7.9 - - + -
95A LYS 4.0 2.9 - - - +
96A VAL 3.5 12.3 - - - +
97A THR* 3.4 4.9 - - - -
98A PHE* 1.4 98.8 - - + +
100A VAL* 1.3 62.7 + - + +
102A VAL* 3.1 7.8 + - + +
103A PHE* 2.9 33.8 + - + -
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Residues in contact with VAL 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ILE* 4.3 14.4 - - + -
97A THR* 3.1 13.2 + - - +
99A PRO* 1.3 76.7 - - + +
101A ARG* 1.3 62.2 + - - +
103A PHE* 3.4 12.8 + - + +
104A ARG* 3.2 19.4 + - - +
111A LEU* 4.5 4.9 - - + -
224A GLU* 4.1 34.8 - - + +
227A VAL* 4.1 8.5 - - + +
228A ALA* 3.6 41.1 - - + +
231A CYS* 4.8 1.9 - - - -
233A LEU* 4.0 11.2 - - + +
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Residues in contact with ARG 101 (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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3A ASN* 3.9 15.8 - - - +
10A TYR* 3.3 52.7 + - + -
97A THR* 3.8 3.0 + - - +
98A PHE 3.3 1.8 + - - +
99A PRO 3.2 0.4 - - - -
100A VAL* 1.3 75.1 - - - +
102A VAL* 1.3 65.5 + - - +
104A ARG* 3.3 9.1 + - - +
105A LEU* 3.2 25.1 + - - +
146A PRO 5.2 4.8 + - - -
147A LEU* 3.6 18.1 - - - +
152A GLU* 5.1 7.9 - - - +
155A PHE* 3.5 40.3 - - + +
227A VAL* 3.8 27.2 + - + +
230A HIS* 3.4 30.1 + - - -
231A CYS* 4.9 5.8 - - - +
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Residues in contact with VAL 102 (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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10A TYR* 4.2 12.8 - - + +
13A THR* 4.0 6.7 - - + -
14A ALA* 4.0 26.0 - - - +
17A LEU* 4.0 20.6 - - + -
56A PHE* 5.1 4.7 - - + -
98A PHE* 3.4 47.8 - - + +
99A PRO* 3.1 9.5 + - + +
101A ARG* 1.3 74.2 - - - +
103A PHE* 1.3 71.0 + - + +
105A LEU* 3.1 16.4 + - - +
106A LEU* 3.1 15.7 + - + +
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Residues in contact with PHE 103 (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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28A ALA* 3.6 25.1 - - + -
29A VAL 5.5 0.4 - - - -
30A ILE* 4.5 5.6 - - + -
56A PHE* 5.5 2.0 - + - -
68A LEU* 3.9 23.8 - - + -
79A VAL* 4.0 23.8 - - + -
81A MET* 3.7 39.5 - - + -
99A PRO* 2.9 27.2 + - + -
100A VAL* 3.4 13.0 - - - +
102A VAL* 1.3 80.8 - - + +
104A ARG* 1.3 61.8 + - - +
106A LEU* 3.1 20.5 + - + +
108A VAL* 3.0 38.4 + - + +
111A LEU* 4.2 13.0 - - + -
233A LEU* 5.0 3.6 - - + -
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Residues in contact with ARG 104 (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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100A VAL 3.2 9.7 + - - +
101A ARG* 3.4 10.8 - - - +
102A VAL 3.2 0.2 - - - -
103A PHE* 1.3 79.7 - - - +
105A LEU* 1.3 60.7 + - + +
107A GLY* 3.1 19.8 + - - -
108A VAL 3.3 20.5 + - - -
109A GLU* 4.2 14.3 - - - +
155A PHE* 5.1 7.6 - - + -
231A CYS* 2.9 45.9 + - + -
232A GLY* 3.8 18.7 + - - -
233A LEU* 3.6 20.7 - - + +
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Residues in contact with LEU 105 (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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7A TYR* 3.6 28.7 - - + +
10A TYR* 3.7 17.5 - - + -
11A GLN* 3.7 39.0 - - + +
14A ALA* 3.9 15.1 - - + +
18A LEU* 4.9 6.6 - - - +
101A ARG 3.2 10.0 + - - +
102A VAL* 3.1 9.8 + - - +
104A ARG* 1.3 80.2 - - + +
106A LEU* 1.3 60.1 + - - +
107A GLY 3.3 0.4 - - - -
155A PHE* 4.3 15.0 - - + -
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Residues in contact with LEU 106 (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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14A ALA* 3.5 33.4 - - + +
17A LEU* 4.0 24.7 - - + -
18A LEU* 3.5 30.8 - - + +
24A ARG* 5.1 7.3 - - - +
25A PRO* 4.6 16.5 - - + +
70A PHE* 4.4 20.4 - - + -
79A VAL* 5.2 0.2 - - + -
102A VAL* 3.1 16.8 + - + +
103A PHE* 3.1 28.8 + - + +
105A LEU* 1.3 78.8 - - - +
107A GLY* 1.3 58.5 + - - +
108A VAL* 3.5 6.1 - - + -
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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