Contacts of the helix formed by residues 118 - 124 (chain B) in PDB entry 3NIE
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 LEU 118 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117B ASP* 1.3 72.9 - - - +
119B LYS* 1.3 58.1 + - - +
121B LEU* 3.3 26.3 - - + +
122B PHE* 3.0 46.4 + - + -
136B ILE* 4.0 27.4 - - + -
140B LEU* 5.3 3.8 - - + -
159B PRO* 3.4 15.8 + - + +
162B CYS* 3.1 31.6 + - + +
164B LEU* 4.1 15.7 - - + -
170B VAL* 5.5 3.8 - - + -
246B ILE* 3.5 31.0 - - + -
250B LEU* 4.4 5.4 - - + -
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Residues in contact with LYS 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ARG 5.6 3.4 + - - -
117B ASP* 3.1 10.8 + - - +
118B LEU* 1.3 75.9 - - - +
120B LYS* 1.3 66.5 + - + +
122B PHE* 3.5 5.9 + - - +
123B LYS* 3.5 51.7 + - - +
159B PRO* 3.4 16.0 + - + +
160B ALA* 3.7 31.2 - - + +
430B ANP 5.5 1.3 - - - +
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Residues in contact with LYS 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ILE* 3.1 29.2 - - - -
37B GLY* 4.9 0.9 - - - -
115B ASP 5.6 0.2 - - - +
116B SER* 3.6 23.8 - - - +
117B ASP* 2.9 33.3 + - - +
119B LYS* 1.3 72.8 - - + +
121B LEU* 1.3 70.0 + - - +
123B LYS* 2.9 20.9 + - - +
124B THR* 3.0 18.5 + - + +
430B ANP 3.5 9.6 - - - +
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Residues in contact with LEU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A TYR* 4.2 13.7 - - + +
17A GLN* 4.5 12.1 - - - +
116B SER* 4.3 2.4 + - - +
117B ASP 2.8 15.1 + - - +
118B LEU* 3.1 24.2 + - + +
120B LYS* 1.3 76.9 - - - +
122B PHE* 1.3 70.9 + - + +
124B THR* 3.0 33.6 + - + +
126B ILE* 5.1 4.9 - - + -
128B LEU* 3.9 28.9 - - + -
136B ILE* 4.1 6.3 - - + -
164B LEU* 3.7 23.3 - - + -
250B LEU* 4.6 0.9 - - + -
253B MET* 3.8 21.2 - - + +
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Residues in contact with PHE 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ARG* 3.7 4.9 + - - -
118B LEU* 3.0 32.3 + - + +
119B LYS* 4.0 6.1 - - - +
120B LYS 3.1 0.8 - - - -
121B LEU* 1.3 81.2 - - + +
123B LYS* 1.3 61.0 + - + +
124B THR 3.4 0.2 - - - -
159B PRO* 3.9 21.3 - - + -
246B ILE* 4.2 4.7 - - + -
249B GLU* 3.2 58.1 - - + +
250B LEU* 3.9 30.3 - - + -
253B MET* 3.7 24.0 - - + -
264B ARG* 3.3 33.2 + - + +
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Residues in contact with LYS 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LEU* 5.7 0.3 - - - +
38A ARG* 3.2 35.8 + - - +
43A TYR* 2.6 30.1 + - - -
119B LYS* 3.5 49.6 + - - +
120B LYS* 2.9 13.1 + - - +
122B PHE* 1.3 77.2 - - + +
124B THR* 1.3 56.8 - - - +
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Residues in contact with THR 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A GLN* 5.4 6.0 + - + +
20A ILE* 4.1 20.2 - - + -
35A LEU* 5.3 4.5 - - + -
43A TYR* 3.8 1.8 + - - -
116B SER* 6.0 0.2 - - - +
120B LYS* 3.0 23.6 - - + +
121B LEU* 3.0 20.2 + - + +
123B LYS* 1.3 79.2 - - - +
125B PRO* 1.3 67.2 - - - +
126B ILE* 3.0 23.1 + - - +
264B ARG* 2.7 32.2 + - - -
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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