Contacts of the helix formed by residues 22 - 34 (chain B) in PDB entry 3NJ8
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 22 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B ASP* 3.3 11.6 + - - -
21B HIS* 1.3 84.4 - - - +
23B TYR* 1.3 65.9 + - - +
24B GLY* 3.1 3.3 + - - -
25B TRP* 3.5 15.9 + - - +
26B ALA* 3.7 4.7 + - - +
227B LEU* 4.4 0.9 - - - -
229B SER* 3.7 6.6 - - - -
263B SER* 4.6 2.9 - - - -
316B NAD 3.2 30.5 - - - -
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Residues in contact with TYR 23 (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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22B GLY* 1.3 70.1 - - - -
24B GLY* 1.3 69.7 + - - +
26B ALA* 3.1 6.4 + - - +
27B ILE* 3.1 22.8 + - - +
127B SER* 3.9 1.8 - - - +
177B LEU* 3.7 20.6 - - + -
224B ALA* 4.2 7.4 - - + -
225B GLY 2.4 27.0 + - - -
226B PRO 4.1 0.5 - - - -
227B LEU* 3.1 29.2 - - + +
261B LEU* 4.1 8.4 - - + +
262B HIS 4.6 3.1 - - - -
263B SER* 3.6 13.2 - - - -
266B VAL* 3.2 43.0 - - + +
316B NAD 2.8 69.2 + + - +
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Residues in contact with GLY 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B VAL* 4.1 2.9 - - - +
16B GLY 4.2 4.3 - - - -
17B VAL* 3.5 22.6 - - - +
22B GLY* 3.1 2.4 - - - -
23B TYR* 1.3 78.2 - - - +
25B TRP* 1.3 65.2 - - - +
27B ILE* 3.2 6.4 + - - +
28B ALA* 3.2 17.5 + - - +
127B SER* 3.2 27.9 + - - -
316B NAD 4.6 2.0 + - - -
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Residues in contact with TRP 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B VAL* 3.8 19.0 - - + +
19B ASP* 3.4 25.9 + - - +
20B SER* 3.7 21.8 - - - -
22B GLY 3.5 12.3 + - - +
23B TYR 3.3 0.2 - - - -
24B GLY* 1.3 72.9 - - - +
26B ALA* 1.3 67.9 + - - +
28B ALA* 2.9 9.6 + - + +
29B LYS* 2.8 41.6 + - + +
50B PHE* 4.0 21.8 - + - -
54B LEU* 4.5 5.6 - - + -
59B LEU* 4.7 7.6 - - + -
62B ASP* 3.7 37.8 + - + +
63B ARG* 3.7 35.7 - - + -
71B ILE* 5.9 1.3 - - + -
73B PHE* 4.0 28.3 - + - -
263B SER* 5.8 2.7 - - - -
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Residues in contact with ALA 26 (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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22B GLY 3.7 1.6 + - - +
23B TYR* 3.1 11.6 + - - +
25B TRP* 1.3 82.9 - - - +
27B ILE* 1.3 63.6 + - - +
29B LYS* 3.0 17.9 + - - +
30B HIS* 3.0 18.5 + - - +
263B SER* 3.5 46.0 - - - +
264B ASP* 4.1 10.5 - - - +
267B GLY* 4.2 6.5 - - - +
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Residues in contact with ILE 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B VAL* 4.8 1.1 - - + -
23B TYR 3.1 17.8 + - - +
24B GLY 3.5 4.7 - - - +
26B ALA* 1.3 74.3 - - - +
28B ALA* 1.3 65.9 + - - +
29B LYS 3.0 0.5 + - - -
30B HIS* 3.1 3.8 + - - +
31B LEU* 2.9 36.3 + - + +
125B VAL* 3.4 49.4 - - + -
127B SER* 4.3 1.8 - - - +
175B VAL* 5.4 2.0 - - + -
177B LEU* 3.9 27.4 - - + -
266B VAL* 4.5 7.9 - - + -
267B GLY* 4.1 12.1 - - - -
270B ALA* 3.6 29.8 - - + -
274B LEU* 4.3 0.7 - - + -
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Residues in contact with ALA 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B VAL* 4.0 14.8 - - + +
17B VAL* 5.6 0.2 - - + -
24B GLY 3.2 7.7 + - - +
25B TRP* 2.9 15.8 + - + +
27B ILE* 1.3 76.8 - - - +
29B LYS* 1.3 59.5 - - - +
31B LEU* 3.8 2.8 - - - +
32B ALA* 3.1 24.9 + - - +
38B VAL* 3.9 26.3 - - + +
40B LEU* 4.0 15.3 - - + -
71B ILE* 4.8 0.2 - - - +
73B PHE* 4.2 12.8 - - + -
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Residues in contact with LYS 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B TRP* 2.8 30.9 + - + +
26B ALA* 3.0 11.6 + - - +
28B ALA* 1.3 77.4 - - - +
30B HIS* 1.3 68.4 + - + +
32B ALA* 3.6 3.3 + - - +
33B SER* 3.2 22.2 + - - -
61B GLU 4.8 2.4 + - - -
62B ASP* 2.7 39.0 + - - +
63B ARG 4.7 0.9 - - - -
64B LYS 3.9 19.7 + - - +
65B LEU* 4.5 2.8 - - + +
71B ILE* 3.9 20.9 - - + +
73B PHE* 6.4 0.2 - - - -
264B ASP* 5.0 13.9 + - - +
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Residues in contact with HIS 30 (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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277A LEU* 4.1 14.2 - - + +
279A ARG* 5.2 5.7 + - - -
26B ALA 3.0 16.1 + - - +
27B ILE 3.9 4.9 - - - +
29B LYS* 1.3 80.6 - - + +
31B LEU* 1.3 65.5 + - - +
33B SER* 2.6 24.2 + - - -
34B ALA* 3.3 11.4 + - - +
264B ASP* 3.5 40.8 + - + +
267B GLY* 3.9 15.6 - - - +
268B GLY* 3.5 28.1 + - - -
271B LEU* 4.1 18.7 - - + +
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Residues in contact with LEU 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 3.9 21.0 - - + +
12B ALA* 4.4 7.4 - - + -
14B VAL* 4.3 12.8 - - + -
27B ILE* 2.9 39.1 + - + +
28B ALA 3.8 4.0 - - - +
30B HIS* 1.3 74.5 - - - +
32B ALA* 1.3 65.7 + - - +
34B ALA* 3.1 12.8 + - - +
35B GLY 3.6 0.2 + - - -
36B ALA* 3.4 21.0 + - + +
38B VAL* 4.2 11.0 - - + -
123B ILE* 4.2 19.7 - - + -
125B VAL* 4.0 8.5 - - + -
271B LEU* 3.9 15.0 - - + +
274B LEU* 3.9 24.9 - - + -
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Residues in contact with ALA 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ALA 3.1 13.7 + - - +
31B LEU* 1.3 77.7 - - - +
33B SER* 1.3 56.2 + - - +
34B ALA 3.0 0.2 - - - -
35B GLY* 2.9 22.0 + - - -
36B ALA 3.9 6.3 + - - +
38B VAL* 3.7 17.8 - - + +
65B LEU* 4.7 4.7 - - + +
71B ILE* 3.0 42.0 - - + -
72B GLU 5.4 2.0 - - - +
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Residues in contact with SER 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PRO* 4.7 11.6 - - - +
29B LYS 3.2 12.0 + - - -
30B HIS* 2.6 30.8 + - - +
32B ALA* 1.3 78.5 - - - +
34B ALA* 1.3 57.8 + - - +
35B GLY 3.3 0.6 + - - -
65B LEU* 3.6 23.3 - - - -
66B PRO* 4.8 10.3 - - - -
271B LEU* 5.2 1.9 - - - +
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Residues in contact with ALA 34 (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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4A PRO* 4.6 7.9 - - + -
5B ILE 3.2 20.0 - - - +
6B ASP* 3.4 11.4 - - - +
7B LEU* 3.0 43.2 + - + -
8B ARG* 4.0 0.7 + - - +
30B HIS 3.3 9.4 + - - +
31B LEU 3.1 3.8 + - - +
32B ALA 3.0 0.8 - - - -
33B SER* 1.3 77.5 - - - +
35B GLY* 1.3 58.1 + - - +
36B ALA 3.6 0.9 - - - -
271B LEU* 4.0 12.1 - - + -
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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