Contacts of the helix formed by residues 14 - 27 (chain C) in PDB entry 3NJ4
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 14 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ALA* 5.7 0.2 - - + -
11C ASP* 3.0 44.5 + - + +
13C GLY* 1.3 77.2 - - - +
15C ALA* 1.3 63.5 + - - +
16C ALA 3.2 1.9 + - - -
17C TRP* 3.3 18.8 + - + +
18C GLY 2.9 19.1 + - - -
86C ASP* 3.4 34.8 - - + +
87C HIS* 3.5 25.5 - - + +
90C ALA* 3.6 3.4 - - + -
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Residues in contact with ALA 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C ILE* 2.9 18.4 + - + +
14C LEU* 1.3 76.7 - - - +
16C ALA* 1.3 57.1 + - - +
18C GLY* 3.6 0.3 - - - -
19C ARG* 2.8 32.1 + - - +
87C HIS 4.2 0.2 - - - -
90C ALA* 3.1 30.2 - - - +
91C ALA* 3.5 12.0 - - - +
94C LYS* 3.9 22.0 - - + +
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Residues in contact with ALA 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C GLY 3.9 9.9 + - - +
14C LEU 3.2 0.8 - - - -
15C ALA* 1.3 80.3 - - - +
17C TRP* 1.3 64.1 + - - +
19C ARG* 3.2 12.6 + - - +
20C LYS* 3.3 19.7 + - - +
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Residues in contact with TRP 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A ILE* 3.2 33.8 + - + +
322A LYS* 3.7 32.1 - - + +
13C GLY 5.0 0.2 + - - -
14C LEU* 3.3 21.9 + - + +
16C ALA* 1.3 78.8 - - - +
18C GLY* 1.3 61.6 + - - +
20C LYS* 3.5 9.2 + - + +
21C ALA* 3.4 17.8 + - - +
87C HIS* 3.5 44.4 - + + -
351C MET* 6.2 1.6 - - + -
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Residues in contact with GLY 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C LEU 2.9 9.7 + - - -
15C ALA 3.6 0.9 - - - -
17C TRP* 1.3 77.7 - - - +
19C ARG* 1.3 65.7 + - - +
21C ALA* 3.1 5.7 + - - +
22C LEU* 3.0 23.4 + - - +
58C VAL* 5.2 1.2 - - - +
87C HIS* 3.1 38.6 - - - -
88C ALA* 4.5 1.5 - - - -
91C ALA* 4.0 6.1 - - - -
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Residues in contact with ARG 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ALA 2.8 19.4 + - - +
16C ALA* 3.6 6.7 - - - +
18C GLY* 1.3 72.7 - - - +
20C LYS* 1.3 63.6 + - + +
22C LEU* 3.1 25.7 + - - +
23C ASP* 3.1 38.7 + - - +
26C GLU* 4.3 5.7 + - - -
65C GLU* 2.8 43.8 + - - -
91C ALA* 3.8 25.5 + - + +
92C ILE* 5.0 0.4 - - - +
95C ALA* 4.0 8.7 - - - +
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Residues in contact with LYS 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A VAL* 3.5 23.9 - - + +
320A ASN 2.6 30.9 + - - +
321A ILE* 4.0 30.7 + - + +
327A ARG* 5.2 0.2 + - - -
16C ALA* 3.3 15.1 + - - +
17C TRP* 3.5 13.2 - - - +
18C GLY 3.1 0.6 - - - -
19C ARG* 1.3 78.1 - - + +
21C ALA* 1.3 61.6 + - - +
23C ASP* 3.1 20.9 + - - +
24C ILE* 3.3 19.2 + - - +
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Residues in contact with ALA 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A ILE* 4.8 4.6 - - + +
17C TRP* 3.4 12.6 + - - +
18C GLY 3.1 9.0 + - - +
20C LYS* 1.3 79.0 - - - +
22C LEU* 1.3 56.7 + - - +
24C ILE* 3.4 10.7 + - - +
25C ALA* 2.9 31.4 + - - +
58C VAL* 3.7 24.4 - - + +
87C HIS* 4.3 10.8 - - + +
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Residues in contact with LEU 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C GLY 3.0 12.5 + - - +
19C ARG* 3.1 41.5 + - - +
21C ALA* 1.3 75.9 - - - +
23C ASP* 1.3 60.5 + - - +
25C ALA* 4.0 0.7 - - - +
26C GLU* 3.0 43.8 + - - +
58C VAL* 3.2 35.7 - - + +
61C ALA* 3.5 21.1 - - + -
62C VAL* 3.4 16.4 - - + +
65C GLU* 4.5 4.0 - - - +
88C ALA* 5.2 2.2 - - - +
91C ALA* 3.8 22.0 - - + -
92C ILE* 4.6 2.7 - - + -
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Residues in contact with ASP 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A ARG* 4.1 16.7 + - - +
335A ARG* 5.1 3.8 + - - +
19C ARG* 3.3 32.1 + - - +
20C LYS* 3.1 14.0 + - - +
22C LEU* 1.3 75.3 - - - +
24C ILE* 1.3 66.9 - - - +
26C GLU* 3.6 16.7 - - - +
27C ASN* 3.4 17.5 + - - +
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Residues in contact with ILE 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A THR* 5.3 9.4 - - - +
293A ASP* 4.1 6.4 - - - +
321A ILE* 3.8 38.6 - - + -
325A VAL* 5.8 2.5 - - + -
327A ARG* 3.7 30.7 - - + +
337A ILE* 4.1 26.2 - - + -
20C LYS 3.3 14.3 + - - +
21C ALA* 3.8 7.6 - - - +
22C LEU 3.3 0.2 - - - -
23C ASP* 1.3 75.7 - - - +
25C ALA* 1.3 66.8 + - - +
27C ASN* 3.0 18.5 + - - +
28C GLU* 3.7 10.9 + - + +
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Residues in contact with ALA 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ALA 2.9 17.9 + - - +
22C LEU 4.0 3.1 - - - +
24C ILE* 1.3 77.4 - - - +
26C GLU* 1.3 64.1 + - - +
28C GLU* 2.7 19.7 + - - +
29C MET* 3.2 31.3 + - + +
58C VAL* 3.8 17.9 - - + -
59C GLU* 4.6 1.6 - - - +
62C VAL* 4.4 1.1 - - + -
355C SER* 4.0 17.0 - - - -
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Residues in contact with GLU 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ARG* 4.3 2.9 + - - -
22C LEU* 3.0 36.6 + - - +
23C ASP* 3.6 17.6 - - - +
25C ALA* 1.3 75.6 - - - +
27C ASN* 1.3 56.9 + - - +
28C GLU 2.8 7.1 + - - -
29C MET* 2.9 17.3 + - - +
33C MET* 3.3 54.9 - - + +
36C ARG* 4.0 9.4 + - - -
62C VAL* 4.1 15.9 - - + +
65C GLU* 4.2 12.8 - - - +
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Residues in contact with ASN 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ASP* 2.6 29.1 + - - +
293A ASP* 3.3 29.7 - - - +
327A ARG* 4.3 2.7 - - - +
335A ARG* 3.4 12.0 + - - +
23C ASP 3.4 7.9 + - - +
24C ILE 3.0 6.1 + - - +
26C GLU* 1.3 75.2 - - - +
28C GLU* 1.3 62.1 + - - +
30C PRO* 5.5 0.7 - - - -
401C LYS* 2.8 35.7 + - - +
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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
------------------------------------------------------------
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