Contacts of the helix formed by residues 26 - 42 (chain B) in PDB entry 2F4N
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 26 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A ILE* 4.8 3.4 - - - -
65A TYR* 6.3 0.8 - - - -
66A VAL* 4.0 25.1 - - - +
69A THR* 3.8 18.8 - - - +
70A ALA* 3.4 10.6 - - - +
25B GLU* 1.3 75.4 - - - +
27B TYR* 1.3 64.6 + - - +
28B VAL 3.4 2.5 - - - -
29B GLY 3.2 5.0 + - - -
30B ALA* 3.0 19.9 + - - +
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Residues in contact with TYR 27 (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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65A TYR* 6.0 1.0 - + - -
69A THR* 4.0 11.4 - - + -
179A ASP* 4.9 7.7 + - - -
180A ARG* 6.4 0.2 - - - -
181A PHE* 6.6 0.2 - + - -
235A ASN* 6.2 0.2 - - - +
236A SER* 4.0 8.8 + - - -
237A GLU* 3.3 34.5 + - - -
21B PHE* 3.6 43.3 - + + -
25B GLU* 3.5 38.1 - - + +
26B GLY* 1.3 77.4 - - - +
28B VAL* 1.3 64.0 + - - +
30B ALA* 2.9 18.8 + - + +
31B MSE 3.0 15.5 + - + +
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Residues in contact with VAL 28 (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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50A ASP 5.4 0.4 - - - +
51A ILE 5.2 7.6 - - - +
17B LEU* 5.3 1.1 - - + -
19B THR* 3.8 8.7 - - + +
21B PHE* 3.9 9.6 - - + -
22B GLY 3.7 20.6 + - - +
23B THR* 5.6 5.8 - - + -
25B GLU 5.2 1.8 + - - +
26B GLY 3.4 0.8 - - - -
27B TYR* 1.3 77.0 - - - +
29B GLY* 1.3 65.1 + - - +
31B MSE 3.2 10.3 + - - +
32B LYS* 3.0 42.6 + - + +
53B HIS* 3.4 52.0 - - + +
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Residues in contact with GLY 29 (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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50A ASP 4.8 0.2 - - - -
51A ILE* 4.5 22.1 + - - -
70A ALA* 3.7 14.4 - - - -
74A PHE* 3.1 14.4 - - - -
26B GLY* 3.2 8.3 + - - -
27B TYR 3.2 1.0 - - - -
28B VAL* 1.3 80.9 - - - +
30B ALA* 1.3 61.0 + - - +
32B LYS* 3.3 10.5 + - - +
33B GLY 3.0 17.5 + - - -
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Residues in contact with ALA 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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69A THR* 3.6 23.3 - - + +
70A ALA* 3.6 12.5 - - - +
73A TYR* 3.7 21.4 - - + +
26B GLY 3.0 7.3 + - - +
27B TYR* 2.9 13.6 + - - +
29B GLY* 1.3 76.5 - - - +
31B MSE 1.3 58.0 + - - +
33B GLY* 2.9 3.8 + - - -
34B ARG* 2.8 28.2 + - - +
142B ASP* 5.2 6.1 - - - +
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Residues in contact with MSE 31 (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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17B LEU* 4.5 15.3 - - + -
19B THR* 4.5 8.5 - - - -
21B PHE* 3.6 35.4 - - + -
27B TYR 3.0 10.4 + - - +
28B VAL* 3.3 11.7 - - - +
30B ALA* 1.3 77.0 - - - +
32B LYS* 1.3 63.5 + - - +
34B ARG* 3.3 6.3 + - - +
35B ILE* 3.1 36.8 + - + +
80B VAL* 5.4 1.3 - - - -
82B VAL* 4.3 18.4 - - + -
141B ARG* 4.3 20.9 - - + +
142B ASP* 4.1 19.7 + - - +
145B ALA* 3.8 22.2 - - + +
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Residues in contact with LYS 32 (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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49A ILE* 3.4 32.3 - - + +
50A ASP* 3.4 26.5 + - - +
74A PHE* 4.5 1.1 - - + -
17B LEU* 4.0 15.7 - - + +
28B VAL* 3.0 30.8 + - + +
29B GLY* 3.6 8.3 - - - +
31B MSE 1.3 75.6 - - - +
33B GLY* 1.3 58.2 + - - +
35B ILE* 3.8 7.2 - - - +
36B LEU* 2.8 37.1 + - + +
48B ILE* 4.2 21.7 - - + +
50B ASP* 2.8 39.1 + - - -
53B HIS* 5.6 0.2 - - - -
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Residues in contact with GLY 33 (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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73A TYR 3.1 16.4 - - - +
74A PHE* 3.5 36.8 - - - -
29B GLY 3.0 7.3 + - - -
30B ALA 2.9 9.0 + - - -
32B LYS* 1.3 73.6 - - - +
34B ARG* 1.3 64.1 + - - -
36B LEU* 3.2 2.7 + - - +
37B ASN* 2.8 19.8 + - - +
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Residues in contact with ARG 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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73A TYR* 2.9 56.5 + - + +
30B ALA 2.8 14.7 + - - +
31B MSE 3.3 8.9 + - - +
33B GLY* 1.3 68.5 - - - +
35B ILE* 1.3 66.7 + - - +
37B ASN* 2.6 52.6 + - - +
38B ILE* 3.0 21.1 + - + +
142B ASP* 4.8 15.0 - - - +
145B ALA* 4.2 13.7 - - + -
146B VAL* 3.8 30.7 - - + -
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Residues in contact with ILE 35 (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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15B ILE* 4.0 25.6 - - + -
17B LEU* 3.9 34.5 - - + -
31B MSE 3.1 17.9 + - + +
32B LYS* 3.8 3.8 - - - +
34B ARG* 1.3 81.0 - - - +
36B LEU* 1.3 64.5 + - - +
38B ILE* 3.3 3.5 + - - +
39B LEU* 3.0 38.8 + - + +
48B ILE* 3.9 20.6 - - + -
80B VAL* 5.1 0.2 - - + -
145B ALA* 3.5 33.7 - - + +
149B ALA* 4.3 11.9 - - + -
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Residues in contact with LEU 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ILE* 3.7 32.1 - - + +
47A LYS* 4.2 23.1 - - + -
49A ILE* 3.8 21.5 - - + -
74A PHE* 3.8 24.2 - - + -
75A PRO* 4.5 4.9 - - + +
32B LYS* 2.8 20.7 + - + +
33B GLY* 3.5 4.7 - - - +
35B ILE* 1.3 75.1 - - - +
37B ASN* 1.3 62.0 + - - +
39B LEU* 3.8 11.7 - - + +
40B LYS* 3.2 23.9 + - - +
48B ILE* 3.4 26.0 - - + -
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Residues in contact with ASN 37 (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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73A TYR 3.9 3.8 - - - +
74A PHE 4.9 0.9 - - - +
75A PRO* 3.2 36.1 - - + +
33B GLY 2.8 8.8 + - - +
34B ARG* 2.6 43.9 + - - +
36B LEU* 1.3 68.7 - - - +
38B ILE* 1.3 66.3 - - + +
40B LYS* 3.1 5.1 + - - +
41B LYS* 3.0 23.8 + - - +
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Residues in contact with ILE 38 (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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34B ARG* 3.0 21.7 + - + +
35B ILE* 3.7 6.7 - - - +
37B ASN* 1.3 78.4 - - + +
39B LEU* 1.3 64.3 + - - +
41B LYS* 3.0 17.1 + - - -
42B TYR* 3.2 28.6 + - + -
146B VAL* 3.5 50.5 - - + -
149B ALA* 3.6 16.8 - - + -
150B GLU* 4.8 1.6 - - - +
153B ILE* 3.4 24.0 - - + -
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Residues in contact with LEU 39 (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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47A LYS* 6.3 0.2 - - - -
35B ILE* 3.0 28.0 + - + +
36B LEU* 3.8 14.1 - - + +
38B ILE* 1.3 76.1 - - - +
40B LYS* 1.3 58.5 + - - +
42B TYR 3.4 1.9 + - - -
43B ASN 3.1 6.9 + - - -
44B LYS* 2.8 53.0 + - + +
46B ALA* 3.8 28.9 - - + +
48B ILE* 5.3 3.1 - - + -
149B ALA* 3.5 40.4 - - + +
152B LEU* 4.0 11.9 - - + -
153B ILE* 4.2 10.5 - - + -
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Residues in contact with LYS 40 (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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9A ASP* 5.6 9.3 + - + +
13A ASP* 5.0 10.8 - - - +
14A ILE* 5.9 1.6 - - + -
75A PRO* 4.9 12.6 - - + -
36B LEU 3.2 16.5 + - - +
37B ASN* 3.1 7.4 + - - +
39B LEU* 1.3 77.0 - - - +
41B LYS* 1.3 61.2 + - - +
42B TYR 3.2 0.2 - - - -
43B ASN* 3.3 13.0 + - - +
44B LYS 5.4 0.2 - - - -
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Residues in contact with LYS 41 (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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37B ASN* 3.0 14.8 + - - +
38B ILE* 3.0 14.8 + - - +
40B LYS* 1.3 77.9 - - - +
42B TYR* 1.3 81.6 + - + +
43B ASN 3.4 0.9 - - - -
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Residues in contact with TYR 42 (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 ILE* 3.2 22.2 + - + +
39B LEU 4.3 1.3 - - - +
40B LYS 3.2 0.2 - - - -
41B LYS* 1.3 111.9 + - + +
43B ASN* 1.3 71.9 + - - +
44B LYS* 3.2 3.1 + - - +
153B ILE* 3.5 47.6 - - + +
154B ASN* 5.4 4.9 - - - -
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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