Contacts of the helix formed by residues 28 - 48 (chain B) in PDB entry 5L26
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 ASN 28 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ALA 3.3 6.4 + - - +
27B ILE* 1.3 70.6 - - - +
29B ILE* 1.3 64.2 + - - +
30B ARG* 3.0 24.7 + - - +
31B THR* 3.2 27.2 + - - +
32B VAL* 3.2 26.2 + - - +
136B LEU 5.1 0.6 + - - -
137B GLY* 5.8 2.2 + - - -
218B LYS* 5.0 4.1 + - + +
222B PRO* 4.6 4.5 - - + +
223B GLU 6.3 0.7 - - - +
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Residues in contact with ILE 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ILE* 3.2 13.0 + - + +
28B ASN* 1.3 70.2 + - - +
30B ARG* 1.3 61.5 + - - +
32B VAL* 3.8 9.2 - - + -
33B ALA* 2.8 47.0 + - + +
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Residues in contact with ARG 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ASN* 3.0 12.0 + - - +
29B ILE* 1.3 78.9 - - - +
31B THR* 1.3 58.2 + - - +
33B ALA* 4.7 1.7 - - - +
34B GLY* 3.1 24.4 + - - +
134B LYS 3.6 19.8 + - - -
135B MET* 3.7 19.4 + - - +
136B LEU 4.2 1.4 + - - +
137B GLY* 3.9 25.9 - - - +
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Residues in contact with THR 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ASN* 3.2 33.3 + - - +
29B ILE 3.1 0.6 - - - -
30B ARG* 1.3 79.9 - - - +
32B VAL* 1.3 54.5 + - - +
34B GLY* 3.3 0.7 + - - -
35B ALA* 2.8 37.3 + - + +
136B LEU* 2.7 36.0 + - + +
137B GLY 4.9 1.9 - - - -
138B THR* 4.0 13.6 - - + +
214B LEU* 5.3 2.5 - - + +
215B LEU* 6.3 0.2 - - - -
218B LYS* 3.8 30.5 - - + -
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Residues in contact with VAL 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ILE* 4.2 9.6 - - + -
28B ASN 3.2 19.7 + - - +
29B ILE* 3.5 12.8 - - + +
31B THR* 1.3 73.3 - - - +
33B ALA* 1.3 65.6 + - + +
35B ALA* 4.3 1.6 - - - -
36B PHE* 3.0 25.8 + - - +
215B LEU* 3.2 30.1 - - + +
218B LYS* 4.0 21.5 - - + +
219B LEU* 3.7 33.0 - - + -
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Residues in contact with ALA 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ILE* 2.8 29.9 + - + +
30B ARG* 4.7 1.8 - - - +
32B VAL* 1.3 78.6 - - + +
34B GLY* 1.3 58.0 + - - +
36B PHE* 4.0 7.7 - - - +
37B LEU* 3.1 31.0 + - - +
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Residues in contact with GLY 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ARG 3.1 21.3 + - - -
31B THR 3.7 0.4 - - - -
33B ALA* 1.3 77.7 - - - +
35B ALA* 1.3 58.1 + - - +
37B LEU* 3.3 7.8 + - - +
38B ILE* 3.0 33.4 + - - +
135B MET 5.4 1.6 - - - -
136B LEU* 3.4 12.6 - - - -
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Residues in contact with ALA 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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31B THR* 2.8 18.6 + - + +
32B VAL* 3.8 4.9 - - - +
34B GLY* 1.3 74.5 - - - +
36B PHE* 1.3 64.1 + - - +
38B ILE* 3.2 5.5 + - - +
39B GLN* 3.1 25.1 + - - +
136B LEU* 3.4 20.1 - - + +
211B PRO* 3.7 25.5 - - - +
214B LEU 5.0 0.9 - - - -
215B LEU* 3.9 18.4 - - + +
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Residues in contact with PHE 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 5.7 3.6 - - + -
10B MET* 3.5 32.1 - - + -
14B ILE* 4.2 17.5 - - + -
32B VAL 3.0 17.9 + - - +
33B ALA* 4.1 7.0 - - - +
35B ALA* 1.3 76.6 - - - +
37B LEU* 1.3 65.7 + - + +
39B GLN* 3.6 4.1 + - - +
40B VAL* 3.3 34.8 + - + +
215B LEU* 4.1 15.8 - - + +
407B MET* 3.7 39.3 - - + -
411B ILE* 5.3 3.1 - - + -
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Residues in contact with LEU 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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33B ALA 3.1 20.9 + - - +
34B GLY* 3.5 8.3 - - - +
35B ALA 3.2 0.2 - - - -
36B PHE* 1.3 82.9 - - + +
38B ILE* 1.3 62.2 - - + +
40B VAL* 3.2 11.2 - - + +
41B ALA* 3.1 34.3 + - + +
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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
----------------------------------------------------------
34B GLY 3.0 14.6 + - - +
35B ALA 3.2 4.9 + - - +
37B LEU* 1.3 82.2 - - + +
39B GLN* 1.3 61.0 + - - +
41B ALA* 3.0 7.2 + - + +
42B LEU* 2.9 41.7 + - + +
131B PHE* 3.8 34.1 - - + -
132B LEU* 4.5 7.6 - - + -
135B MET* 4.2 11.4 - - + -
136B LEU* 3.7 32.5 - - + -
211B PRO* 4.1 18.8 - - + -
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Residues in contact with GLN 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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35B ALA 3.1 14.0 + - - +
36B PHE* 4.1 4.4 - - - +
38B ILE* 1.3 78.1 - - - +
40B VAL* 1.3 57.7 + - - +
42B LEU* 3.7 5.6 + - - +
43B GLY* 3.1 21.7 + - - -
208B MET* 3.8 31.5 - - + +
211B PRO* 4.1 11.8 - - + -
212B GLY* 3.4 21.9 - - - +
215B LEU* 4.1 11.1 - - - +
404B SER 3.5 6.1 - - - +
407B MET* 3.5 23.4 - - - +
408B SER* 2.6 35.7 + - - +
411B ILE* 3.8 11.7 - - + +
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Residues in contact with VAL 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B MET* 4.8 10.3 - - + -
36B PHE* 3.3 27.3 + - + +
37B LEU* 3.2 18.6 - - + +
39B GLN* 1.3 76.6 - - - +
41B ALA* 1.3 62.9 + - - +
42B LEU 3.4 0.2 - - - -
43B GLY 3.6 1.1 - - - +
44B ALA* 2.9 27.2 + - - +
411B ILE* 3.7 23.1 - - + +
414B LEU* 6.0 1.1 - - + -
415B PHE* 4.1 20.4 - - + -
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Residues in contact with ALA 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 LEU* 3.1 25.9 + - + +
38B ILE* 3.0 10.2 + - + +
40B VAL* 1.3 76.2 - - - +
42B LEU* 1.3 61.1 + - + +
44B ALA* 3.3 6.2 + - - +
45B LEU* 2.9 29.4 + - - +
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Residues in contact with LEU 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* 2.9 32.4 + - + +
39B GLN* 4.0 4.3 - - - +
41B ALA* 1.3 75.9 - - + +
43B GLY* 1.3 56.4 + - - +
45B LEU* 3.5 21.1 - - + +
46B VAL* 3.0 41.9 + - + +
207B PHE* 4.0 37.0 - - + +
208B MET* 4.3 12.6 - - + +
211B PRO* 5.0 3.4 - - + -
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Residues in contact with GLY 43 (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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39B GLN 3.1 14.4 + - - -
40B VAL 3.4 3.8 + - - -
41B ALA 3.2 0.6 - - - -
42B LEU* 1.3 77.1 - - - +
44B ALA* 1.3 55.7 + - - +
47B LEU* 3.1 36.2 + - - +
208B MET* 3.6 21.0 - - - +
411B ILE* 3.9 12.1 - - - -
415B PHE* 3.4 7.8 - - - -
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Residues in contact with ALA 44 (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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40B VAL 2.9 16.5 + - - +
41B ALA* 3.8 5.6 - - - +
43B GLY* 1.3 73.0 - - - +
45B LEU* 1.3 64.6 + - - +
48B TYR* 3.1 32.1 + - + +
49B VAL* 3.3 10.2 + - + +
415B PHE* 3.2 25.0 - - + -
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Residues in contact with LEU 45 (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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41B ALA 2.9 17.8 + - - +
42B LEU* 3.2 23.8 + - + +
44B ALA* 1.3 77.8 - - - +
46B VAL* 1.3 65.9 + - + +
47B LEU 3.7 0.2 + - - -
49B VAL* 3.2 25.1 - - + +
51B GLN* 6.3 0.9 - - + -
52B GLY* 3.1 31.6 - - - -
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Residues in contact with VAL 46 (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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42B LEU* 3.0 25.6 + - + +
43B GLY 3.9 1.3 - - - +
45B LEU* 1.3 88.1 - - + +
47B LEU* 1.3 73.7 + - + +
52B GLY 4.1 8.5 - - - +
53B ARG* 3.4 19.3 - - - +
56B LEU* 3.5 37.4 - - + +
204B ALA* 3.7 28.9 - - + -
208B MET* 3.9 5.4 - - + -
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Residues in contact with LEU 47 (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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43B GLY* 3.1 18.5 + - - +
46B VAL* 1.3 94.5 - - + +
48B TYR* 1.3 58.7 + - - +
53B ARG* 3.6 16.1 - - - +
56B LEU* 4.7 7.9 - - + -
201B TYR* 4.2 28.3 - - + -
208B MET* 4.4 8.5 - - + -
361B PHE* 4.1 13.0 - - + -
411B ILE 5.0 0.2 - - - -
412B ALA* 3.7 40.2 - - + +
415B PHE* 3.8 27.6 - - + +
416B THR* 5.0 7.1 - - + +
419B SER 4.1 6.4 - - - +
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Residues in contact with TYR 48 (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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44B ALA* 3.1 24.1 + - + +
46B VAL 3.8 0.4 - - - -
47B LEU* 1.3 78.4 - - - +
49B VAL* 1.3 85.3 + - + +
50B PRO* 3.5 1.9 - - + +
53B ARG* 3.2 22.5 + - - -
415B PHE* 4.2 20.6 - + + -
418B LEU* 3.6 33.0 - - + -
419B SER* 5.0 11.2 - - - -
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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
------------------------------------------------------------
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