Contacts of the helix formed by residues 91 - 100 (chain A) in PDB entry 3D9M
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 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A GLU* 3.0 35.8 + - - +
87A ARG 5.9 0.2 + - - -
88A PHE 3.6 4.5 + - - -
89A SER 3.3 0.2 - - - -
90A ASN* 1.3 88.4 - - - +
92A ILE* 1.3 64.6 + - - +
93A ILE* 3.2 2.9 - - - -
94A SER* 3.0 16.7 + - - -
95A THR* 3.0 21.8 + - - +
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Residues in contact with ILE 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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66A ILE* 6.1 2.7 - - + -
88A PHE* 3.3 18.3 + - + +
89A SER* 3.3 15.3 + - - +
90A ASN 3.5 0.6 + - - -
91A ASN* 1.3 77.6 - - - +
93A ILE* 1.3 74.3 + - + +
95A THR* 3.5 8.0 - - + -
96A PHE* 3.0 44.3 + - + +
117A TRP* 4.1 2.2 - - + -
123A PHE* 3.8 42.6 - - + -
127A ILE* 3.7 23.8 - - + -
131A LEU* 3.8 22.2 - - + -
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Residues in contact with ILE 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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90A ASN 5.4 0.4 + - - +
91A ASN 3.2 1.0 - - - -
92A ILE* 1.3 84.4 - - + +
94A SER* 1.3 58.1 + - - +
96A PHE* 3.3 2.3 + - - +
97A GLN* 2.9 27.7 + - + +
127A ILE* 4.9 4.9 - - + +
130A PRO* 3.9 31.9 - - + -
131A LEU* 3.9 18.8 - - + -
134A MET* 4.0 17.3 - - + +
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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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91A ASN* 3.0 18.6 + - - +
93A ILE* 1.3 76.1 - - - +
95A THR* 1.3 66.9 + - - +
97A GLN* 3.2 15.1 + - - +
98A ASN* 3.1 30.6 + - - +
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Residues in contact with THR 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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48A GLU* 3.8 27.0 + - + +
51A ILE* 3.9 31.6 - - + -
66A ILE* 4.0 15.7 - - + -
88A PHE* 5.1 1.4 + - + -
91A ASN* 3.0 16.8 + - - +
92A ILE* 3.5 13.9 - - + -
94A SER* 1.3 75.8 - - - +
96A PHE* 1.3 60.0 + - + +
98A ASN* 3.2 13.8 + - - +
99A LEU* 2.8 35.2 + - + +
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Residues in contact with PHE 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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63A LEU* 3.7 16.8 - - + -
66A ILE* 5.4 2.5 - - + -
92A ILE* 3.0 42.5 + - + +
93A ILE 3.8 2.2 - - - +
95A THR* 1.3 79.0 - - + +
97A GLN* 1.3 58.6 + - - +
99A LEU* 3.6 19.0 - - + +
100A TYR* 2.9 63.7 + + + -
110A ILE* 3.6 25.1 - - + -
114A LEU* 3.7 17.9 - - + -
117A TRP* 3.6 30.7 - + - -
131A LEU* 3.7 20.4 - - + -
134A MET* 4.0 2.2 - - + -
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Residues in contact with GLN 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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93A ILE* 2.9 16.0 + - + +
94A SER* 3.4 16.8 + - - +
96A PHE* 1.3 76.4 - - - +
98A ASN* 1.3 63.1 + - - +
100A TYR* 3.6 7.8 + - - +
101A ARG* 3.4 44.7 + - - +
134A MET* 3.6 16.2 - - + +
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Residues in contact with ASN 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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48A GLU 4.9 2.2 + - - -
51A ILE* 3.9 17.6 - - + +
52A GLN* 3.6 37.4 - - - +
59A LYS* 3.6 16.3 - - - +
94A SER* 3.1 19.9 + - - +
95A THR* 3.2 10.9 + - - +
97A GLN* 1.3 76.7 - - - +
99A LEU* 1.3 63.2 + - - +
101A ARG* 3.1 40.5 + - - +
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Residues in contact with LEU 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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51A ILE* 3.6 26.2 - - + -
59A LYS* 3.1 38.6 - - - +
60A VAL* 5.2 0.2 - - - -
63A LEU* 4.0 23.8 - - + -
66A ILE* 5.1 0.2 - - + -
95A THR* 2.8 24.9 + - + +
96A PHE* 3.2 50.2 + - + +
98A ASN* 1.3 69.1 - - - +
100A TYR* 1.3 56.9 + - - +
101A ARG 3.0 10.7 + - - -
102A CYS* 3.1 24.9 + - - +
110A ILE* 3.6 13.4 - - + +
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Residues in contact with TYR 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 PHE* 2.9 40.5 + + + +
97A GLN* 4.2 5.2 - - - +
98A ASN 3.3 0.8 - - - -
99A LEU* 1.3 72.0 - - - +
101A ARG* 1.3 58.9 + - - +
102A CYS* 3.1 18.1 + - - +
107A LYS* 4.5 11.2 - - + -
110A ILE* 3.6 34.1 - - + +
114A LEU* 3.3 17.2 - - - +
131A LEU 2.9 18.4 + - - -
134A MET* 3.6 33.2 - - + -
135A ALA* 3.2 27.4 - - + +
138A LEU* 3.6 36.3 - - + +
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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