Contacts of the helix formed by residues 93 - 101 (chain A) in PDB entry 1II7
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 SER 93 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A GLU* 2.6 38.9 + - - -
86A ASP 4.0 7.6 - - - -
88A THR* 3.5 23.6 - - - -
91A GLY 3.5 1.8 + - - -
92A PRO* 1.3 76.3 - - - +
94A VAL* 1.3 65.3 + - - +
95A LEU* 3.4 10.4 + - - +
96A ASN* 3.0 23.2 + - - +
97A LEU* 3.1 9.7 + - - +
58B PRO* 3.5 7.2 - - - +
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Residues in contact with VAL 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A PHE* 3.6 39.3 - - + -
54A SER 4.6 2.9 + - - +
56A PRO* 3.9 12.3 - - + -
61A LEU* 3.4 33.4 - - + -
86A ASP* 4.3 20.6 + - + +
93A SER* 1.3 71.0 - - - +
95A LEU* 1.3 64.6 + - + +
97A LEU* 3.3 6.5 + - + +
98A LEU* 2.9 30.3 + - + +
58B PRO* 3.5 22.8 - - + +
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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
----------------------------------------------------------
50A LEU* 3.8 30.7 - - + -
51A PHE* 4.3 8.1 - - + -
80A ALA* 4.2 16.8 - - + +
81A ILE* 3.4 39.0 - - - +
82A GLU* 3.5 19.7 - - + +
86A ASP* 4.0 17.3 - - - +
93A SER* 3.2 6.8 + - - +
94A VAL* 1.3 76.3 - - + +
96A ASN* 1.3 60.5 + - - +
98A LEU* 3.1 6.3 + - + -
99A GLU* 2.8 29.8 + - - +
104A VAL* 3.6 10.0 - - + +
106A VAL* 3.8 15.9 - - + -
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Residues in contact with ASN 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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82A GLU* 4.1 9.7 + - - +
91A GLY 4.5 1.4 - - - +
92A PRO* 3.5 16.9 - - + +
93A SER* 3.0 32.0 + - - +
95A LEU* 1.3 78.5 - - - +
97A LEU* 1.3 62.2 + - - +
99A GLU* 3.1 21.5 + - - +
100A ASP* 3.0 27.2 + - - +
106A VAL* 4.2 13.9 - - - +
110A ARG* 5.3 5.5 - - - +
62B LYS* 5.2 6.7 - - - +
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Residues in contact with LEU 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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61A LEU* 4.4 12.6 - - + -
92A PRO* 5.7 0.6 - - + +
93A SER 3.1 9.3 + - - +
94A VAL* 3.5 14.1 - - + +
96A ASN* 1.3 79.3 - - - +
98A LEU* 1.3 63.9 + - + +
100A ASP* 3.0 21.7 + - - +
101A PHE* 3.1 47.3 + - + -
58B PRO* 3.9 16.6 - - + +
61B LEU* 4.1 27.6 - - + -
62B LYS* 3.8 39.3 - - + +
65B ILE* 4.4 3.4 - - + -
97B LEU* 6.3 0.9 - - + -
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Residues in contact with LEU 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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50A LEU* 4.1 7.0 - - + -
51A PHE* 3.5 37.0 - - + -
61A LEU* 5.4 3.8 - - + +
64A ALA* 5.2 0.4 - - + -
65A ILE* 3.9 30.1 - - + +
68A LEU* 3.7 22.2 - - + -
94A VAL* 2.9 23.1 + - + +
95A LEU* 3.1 9.2 + - + +
97A LEU* 1.3 76.2 - - + +
99A GLU* 1.3 58.7 + - - +
101A PHE* 2.9 28.7 + - + +
103A LEU* 3.1 31.5 + - + +
104A VAL* 3.9 12.8 - - + -
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Residues in contact with GLU 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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95A LEU 2.8 13.1 + - - +
96A ASN* 3.1 19.6 + - - +
97A LEU 3.1 0.2 - - - -
98A LEU* 1.3 73.0 - - - +
100A ASP* 1.3 60.3 + - - +
101A PHE 3.0 1.6 - - - -
102A GLY* 2.8 20.7 + - - +
104A VAL* 3.5 23.2 - - + +
105A TYR* 4.0 3.6 - - + -
106A VAL* 3.4 19.5 + - + +
110A ARG* 2.8 42.4 + - - -
114A VAL* 5.5 0.2 - - - +
119A LEU* 3.3 19.1 - - - +
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Residues in contact with ASP 100 (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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96A ASN 3.0 17.7 + - - +
97A LEU* 3.0 11.9 + - - +
99A GLU* 1.3 76.6 - - - +
101A PHE* 1.3 72.2 + - + +
102A GLY 3.3 1.0 + - - -
62B LYS* 3.0 47.0 + - - +
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Residues in contact with PHE 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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65A ILE* 3.8 33.0 - - + -
72A LYS* 3.4 15.2 + - - -
97A LEU* 3.4 39.7 - - + -
98A LEU* 2.9 21.3 + - + +
100A ASP* 1.3 85.9 - - + +
102A GLY* 1.3 60.4 + - - +
103A LEU* 3.4 14.8 + - + +
65B ILE* 3.5 36.1 - - + -
97B LEU* 6.3 0.2 - - + -
101B PHE* 3.8 17.5 - + - -
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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