Contacts of the helix formed by residues 94 - 104 (chain D) in PDB entry 6B0Z
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 94 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77D THR* 3.3 22.2 + - - +
93D LYS* 1.3 75.0 - - - +
95D PRO* 1.3 69.0 - - - +
96D ASN* 3.3 8.5 + - - -
97D GLY* 2.9 19.5 + - - -
98D THR* 3.2 10.6 + - - -
503D FLC 2.3 40.0 + - - +
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Residues in contact with PRO 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D LEU* 4.5 11.2 - - + -
49D ARG* 3.2 38.4 - - - +
54D ASP* 5.3 2.2 - - - +
57D THR* 4.0 21.1 - - + +
72D LYS* 4.6 4.3 - - - -
75D THR* 3.7 21.5 - - - +
76D ILE 4.1 1.6 - - - +
77D THR* 3.8 13.0 - - - +
93D LYS 3.0 8.4 - - - +
94D SER* 1.3 83.0 - - - +
96D ASN* 1.3 62.1 + - - +
98D THR* 3.1 7.4 + - - +
99D ILE* 3.0 29.8 + - - +
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Residues in contact with ASN 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D LYS* 3.2 17.6 - - - +
75D THR* 3.8 9.5 + - - -
77D THR* 4.4 1.4 + - - -
94D SER* 3.0 4.9 + - - -
95D PRO* 1.3 79.2 - - - +
97D GLY* 1.3 56.7 + - - +
99D ILE* 4.0 8.1 - - - +
100D ARG* 2.8 49.2 + - - +
304D GLU* 5.4 0.3 - - - +
306D GLU* 3.0 27.3 - - - +
501D NDP 3.3 28.0 + - - -
503D FLC 3.2 25.1 + - - +
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Residues in contact with GLY 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D SER* 2.9 16.5 + - - -
96D ASN* 1.3 79.0 - - - +
98D THR* 1.3 61.4 + - - +
100D ARG* 3.7 17.1 - - - +
101D ASN* 3.0 25.1 + - - +
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Residues in contact with THR 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D ASP* 4.5 9.1 + - - +
57D THR* 3.8 23.1 - - + +
58D LYS* 4.8 6.3 - - + +
93D LYS* 4.8 6.4 + - - +
94D SER 3.2 9.8 + - - -
95D PRO* 3.1 11.0 + - - +
97D GLY* 1.3 75.9 - - - +
99D ILE* 1.3 63.3 + - - +
101D ASN* 3.3 6.1 + - - +
102D ILE* 3.0 47.0 + - + +
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Residues in contact with ILE 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D MET* 4.4 11.7 - - - -
44D LEU* 4.6 2.5 - - + -
57D THR* 3.9 24.2 - - + +
61D ALA* 4.0 13.2 - - + +
64D ILE* 4.2 9.6 - - + -
72D LYS* 4.1 19.7 - - + -
95D PRO 3.0 22.8 + - - +
96D ASN* 4.0 4.9 - - - +
98D THR* 1.3 74.7 - - - +
100D ARG* 1.3 63.5 + - - +
102D ILE 3.1 0.5 + - - -
103D LEU* 2.9 57.4 + - + +
295D LEU* 4.8 1.6 - - + -
304D GLU* 3.9 26.0 - - - +
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Residues in contact with ARG 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D ASN* 2.8 41.2 + - - +
97D GLY* 3.7 23.1 - - - +
99D ILE* 1.3 72.6 - - - +
101D ASN* 1.3 58.2 + - - +
104D GLY* 2.9 28.2 + - - -
105D GLY 5.3 4.7 - - - +
107D VAL* 3.9 24.3 - - - +
109D ARG* 6.0 2.0 - - - +
134D ALA* 5.6 14.4 - - - +
295D LEU* 3.9 26.9 - - + +
306D GLU* 5.3 5.5 + - - -
503D FLC 4.5 11.3 + - - -
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Residues in contact with ASN 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D GLY 3.0 18.6 + - - +
98D THR* 3.6 4.5 - - - +
100D ARG* 1.3 77.7 - - - +
102D ILE* 1.3 81.7 + - - +
103D LEU 3.4 0.5 + - - -
104D GLY* 3.6 6.2 + - - -
140D ARG* 5.9 2.4 - - - +
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Residues in contact with ILE 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D LYS* 4.0 19.7 - - + +
61D ALA* 3.8 26.9 - - + -
62D GLU* 3.5 27.1 - - - +
65D LYS* 4.3 14.7 + - + +
98D THR* 3.0 36.6 + - + +
99D ILE 3.1 2.4 + - - +
101D ASN* 1.3 89.2 - - - +
103D LEU* 1.3 62.6 + - + +
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Residues in contact with LEU 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D ALA* 3.5 41.7 - - + +
64D ILE* 3.5 28.9 - - + -
65D LYS* 4.3 14.8 - - + -
99D ILE* 2.9 33.7 + - + +
101D ASN 4.2 0.2 - - - -
102D ILE* 1.3 83.2 - - + +
104D GLY* 1.3 67.6 + - - +
295D LEU* 4.2 13.2 - - + -
297D CYS* 3.7 22.7 - - - +
298D PRO* 5.3 1.9 - - - +
302D THR* 4.8 0.7 - - + -
304D GLU* 4.4 7.0 - - + +
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Residues in contact with GLY 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D ARG* 2.9 20.9 + - - -
101D ASN 3.6 6.2 + - - -
103D LEU* 1.3 82.8 - - - +
105D GLY* 1.3 62.2 + - - -
295D LEU* 3.6 17.2 - - - +
297D CYS* 3.5 12.3 - - - -
298D PRO* 4.9 0.4 - - - -
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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