Contacts of the helix formed by residues 100 - 108 (chain D) in PDB entry 1N33
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 ARG 100 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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403A C 4.4 0.4 + - - -
68D TYR* 5.1 4.6 + - - -
70D ILE* 3.4 36.4 - - - +
74D GLN* 3.9 20.6 + - - +
78D LEU* 4.7 12.4 - - + +
96D LEU 3.4 7.8 + - - +
97D LEU* 3.4 23.6 - - - +
98D GLU 3.0 1.8 - - - -
99D SER* 1.3 75.5 - - - +
101D LEU* 1.3 55.6 + - - +
102D ASP* 3.1 32.7 + - - +
103D ASN* 2.6 35.2 + - + +
104D VAL 3.1 2.6 + - - -
118D ARG* 4.0 14.5 - - - +
136D PRO* 3.8 0.8 - - - +
137D SER* 3.3 43.9 + - - +
138D TYR 3.6 7.4 - - - -
139D ARG* 4.9 1.3 - - + +
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Residues in contact with LEU 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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99D SER 2.7 7.3 + - - -
100D ARG* 1.3 68.7 - - - +
102D ASP* 1.3 59.8 + - - +
104D VAL* 2.6 28.3 + - + -
105D VAL* 2.8 18.2 + - + +
121D VAL* 4.1 14.8 - - + -
126D ILE* 4.5 10.1 - - + -
128D VAL* 4.4 12.8 - - + -
133D VAL* 3.7 30.7 - - + +
135D LEU 4.1 7.2 - - - +
136D PRO 3.5 3.7 + - - +
138D TYR* 2.9 21.3 + - + +
140D VAL* 3.6 24.9 - - + -
146D ILE* 4.1 29.2 - - + -
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Residues in contact with ASP 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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68D TYR* 5.2 8.0 - - - +
100D ARG* 3.1 42.3 + - - +
101D LEU* 1.3 80.1 - - - +
103D ASN* 1.3 84.3 + - - +
105D VAL* 2.9 28.3 - - - +
106D TYR* 3.9 0.9 - - - +
114D ARG* 4.8 10.3 - - - +
117D ALA* 3.5 10.7 - - - +
118D ARG* 4.1 22.5 + - + +
121D VAL* 4.6 4.7 - - + -
136D PRO* 3.4 29.3 + - + +
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Residues in contact with ASN 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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68D TYR* 4.4 5.7 - - + -
97D LEU 4.3 3.4 - - - +
98D GLU* 2.8 47.8 + - - +
100D ARG* 2.6 26.0 + - + +
102D ASP* 1.3 81.4 + - - +
104D VAL* 1.3 49.3 + - - +
106D TYR* 2.6 32.0 + - - +
107D ARG* 2.7 26.5 + - - +
114D ARG* 2.8 43.2 + - - +
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Residues in contact with VAL 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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98D GLU 3.4 21.5 - - - +
99D SER 4.3 1.3 - - - -
100D ARG 3.6 7.0 - - - +
101D LEU* 2.6 20.9 + - + +
103D ASN* 1.3 72.5 - - - +
105D VAL* 1.3 53.5 + - - +
107D ARG* 3.4 9.8 - - + +
108D LEU* 2.7 48.1 + - + +
140D VAL* 4.0 12.8 - - + -
146D ILE* 4.6 20.4 - - + -
173D TRP* 6.1 0.7 - - - +
174D LEU* 4.6 17.5 - - + -
184D LYS 6.0 0.2 - - - -
185D PHE* 4.4 16.2 - - + +
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Residues in contact with VAL 105 (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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101D LEU* 2.8 21.8 + - + +
102D ASP* 2.9 30.3 - - - +
104D VAL* 1.3 74.1 - - - +
106D TYR* 1.3 57.3 + - - +
108D LEU* 3.8 6.2 - - - +
109D GLY 3.5 0.9 + - - -
110D PHE* 3.0 46.6 + - + +
111D ALA 3.9 1.0 + - - -
117D ALA* 3.2 28.3 - - + +
120D LEU* 5.0 4.9 - - + -
121D VAL* 4.4 2.2 - - + -
126D ILE* 3.7 37.2 - - + -
146D ILE* 5.1 4.0 - - + -
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Residues in contact with TYR 106 (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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20D TYR* 5.3 9.9 + - - +
23D GLY* 5.6 1.8 - - - -
27D TYR* 5.7 0.7 + - - -
102D ASP 3.9 2.2 - - - +
103D ASN* 2.6 18.2 + - - +
105D VAL* 1.3 72.7 - - - +
107D ARG* 1.3 85.8 + - - +
108D LEU 3.0 1.3 - - - -
109D GLY* 2.5 27.8 + - - +
111D ALA 4.3 5.4 - - - -
112D VAL 3.8 9.9 - - - -
113D SER* 3.3 37.0 - - - +
114D ARG* 3.5 38.1 + - + -
117D ALA* 3.8 18.6 - - + -
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Residues in contact with ARG 107 (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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98D GLU* 2.7 24.5 + - + -
103D ASN* 2.7 24.0 + - - +
104D VAL* 3.4 9.9 - - + +
106D TYR* 1.3 94.8 - - - +
108D LEU* 1.3 57.6 + - - +
109D GLY 3.3 2.3 + - - -
114D ARG* 2.8 31.9 - - - +
165D MET* 4.9 2.3 - - - +
170D VAL* 3.6 17.9 - - - +
171D GLY* 6.1 2.0 - - - +
173D TRP* 2.9 31.6 - - + +
174D LEU* 3.3 19.7 - - + -
194D LEU* 3.1 25.7 - - - +
196D LEU* 4.6 11.5 - - - +
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Residues in contact with LEU 108 (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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104D VAL* 2.7 27.0 + - + +
105D VAL* 4.2 0.9 - - - +
106D TYR 3.0 0.2 - - - -
107D ARG* 1.3 73.0 - - - +
109D GLY* 1.3 63.3 + - - +
110D PHE* 2.9 41.1 + - + -
146D ILE* 4.3 10.8 - - + +
162D LEU* 4.5 2.3 - - - +
165D MET* 3.8 13.4 - - - +
170D VAL* 4.4 9.0 - - + -
174D LEU* 3.2 41.3 - - + -
175D SER 4.2 7.9 - - - +
176D LEU* 4.3 12.1 - - + +
183D GLY* 3.8 26.0 - - - -
184D LYS 3.9 9.2 - - - +
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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