Contacts of the helix formed by residues 91 - 100 (chain A) in PDB entry 5DO7
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 GLY 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A ILE* 4.6 10.6 - - - +
69A LEU* 3.9 4.8 - - - +
89A GLY 3.4 1.6 + - - -
90A SER* 1.3 84.8 + - - +
92A LYS* 1.3 65.5 + - - +
93A THR 3.3 2.2 - - - -
94A THR* 3.0 17.3 + - - -
95A LEU* 3.0 18.5 + - - +
266A LEU* 4.0 6.3 - - - -
269A GLY* 4.0 15.5 - - - -
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Residues in contact with LYS 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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84A ILE* 3.8 24.2 - - + +
85A LEU 4.0 2.2 - - - -
86A GLY* 2.6 55.0 + - - +
87A SER 3.7 6.7 + - - -
88A SER* 5.5 0.8 - - - +
90A SER* 3.2 11.4 - - - -
91A GLY* 1.3 74.0 - - - +
93A THR* 1.3 87.4 + - + +
95A LEU* 2.8 17.3 + - - +
96A LEU* 3.0 10.4 + - - +
218A GLU* 4.7 10.6 + - - -
248A THR* 3.9 28.4 - - + +
249A ILE 4.7 13.2 - - - +
250A HIS* 4.9 10.9 - - - +
266A LEU* 3.6 16.8 - - + +
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Residues in contact with THR 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 SER* 3.9 15.3 + - - -
92A LYS* 1.3 95.8 - - + +
94A THR* 1.3 73.6 + - - +
96A LEU* 2.8 15.7 + - - +
97A ASP* 2.8 22.4 + - - -
134A GLN* 4.9 5.6 - - - +
217A ASP* 3.7 27.1 - - - +
218A GLU* 4.4 15.0 - - - +
248A THR* 4.4 8.5 - - - +
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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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45A TYR* 4.5 16.4 - - + -
68A ILE* 3.8 38.4 - - + +
69A LEU* 5.3 2.5 - - + -
90A SER* 5.0 1.2 + - - -
91A GLY* 3.0 19.9 + - - -
93A THR* 1.3 83.0 + - - +
95A LEU* 1.3 57.4 + - - +
97A ASP* 3.5 8.4 + - - +
98A ALA* 2.8 29.8 + - + +
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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
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40A ILE* 5.3 8.1 - - + -
43A ALA* 6.1 3.4 - - + -
69A LEU* 3.4 34.9 - - + +
72A VAL* 4.4 22.7 - - + -
84A ILE* 5.1 12.8 - - + -
91A GLY 3.0 7.4 + - - +
92A LYS 2.8 10.7 + - - +
94A THR* 1.3 75.1 - - - +
96A LEU* 1.3 73.4 + - + +
98A ALA* 2.8 6.0 + - + +
99A MET* 2.8 57.7 + - + +
246A VAL* 6.3 0.4 - - + -
266A LEU* 4.3 16.8 - - + -
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Residues in contact with LEU 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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84A ILE* 5.2 1.8 - - + -
92A LYS 3.0 6.9 + - - +
93A THR 2.8 11.1 + - - +
95A LEU* 1.3 85.2 - - + +
97A ASP* 1.3 69.0 + - - +
99A MET* 3.4 10.5 + - - +
100A SER* 3.4 11.6 + - - -
131A TYR* 4.2 9.6 - - + -
215A LEU* 3.8 36.9 - - + +
216A PHE 3.6 27.4 - - - +
217A ASP* 4.0 11.7 - - + +
246A VAL* 4.2 16.4 - - + +
247A LEU 4.9 0.4 - - - -
248A THR* 3.5 32.3 - - + +
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Residues in contact with ASP 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 THR* 2.8 20.2 + - - +
94A THR* 3.6 10.3 - - - +
96A LEU* 1.3 75.9 - - - +
98A ALA* 1.3 66.1 + - - +
100A SER* 2.6 26.0 + - - -
101A GLY 3.5 1.7 + - - -
102A ARG* 2.8 47.7 + - + -
131A TYR* 1.9 37.9 + - - -
134A GLN* 4.9 2.3 + - - -
217A ASP* 3.7 11.4 - - - +
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Residues in contact with ALA 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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45A TYR* 4.8 26.0 - - + -
69A LEU* 5.3 4.0 - - + -
94A THR* 2.8 20.1 + - + +
95A LEU* 2.8 15.4 + - - +
97A ASP* 1.3 70.4 - - - +
99A MET* 1.3 54.7 + - + +
101A GLY* 2.8 29.1 + - - -
102A ARG* 5.0 2.9 - - - +
103A LEU 4.7 8.7 - - - +
122A ARG* 5.4 1.9 + - - -
125A PHE* 5.1 4.0 - - - -
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Residues in contact with MET 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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38A LEU* 5.0 5.6 - - + -
40A ILE* 3.9 28.3 - - + -
95A LEU* 2.8 43.8 + - + +
96A LEU* 3.6 12.8 - - - +
98A ALA* 1.3 72.4 - - + +
100A SER* 1.3 56.9 + - - +
101A GLY 3.2 0.3 + - - -
113A VAL* 4.3 19.7 - - + -
125A PHE* 2.8 38.8 - - + -
129A PHE* 3.6 34.0 - - + -
215A LEU* 4.7 11.7 - - + -
246A VAL* 6.4 1.6 - - - -
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Residues in contact with SER 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 LEU 3.4 3.5 + - - -
97A ASP* 2.6 26.4 + - - -
99A MET* 1.3 73.7 - - - +
101A GLY* 1.3 57.9 + - - +
102A ARG* 3.3 8.1 + - - +
125A PHE* 4.4 3.8 - - - -
126A GLN* 3.4 25.7 + - - +
129A PHE* 4.7 9.1 - - - +
131A TYR* 3.8 36.8 - - - -
215A LEU* 3.9 21.5 - - - +
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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